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lauriebelch / SOCfinder

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not enough value #6

Open oclaisse opened 1 month ago

oclaisse commented 1 month ago

Hello Laurence, I am working with Claire Lehenaff on prophages, bacterial diversity and interactions in beverages fermentation context. We would try to investigate social genes in one of our specific species OEnococcus oeni. So I made install your program on the miage server in INRAE Paris by Veronique Martin veronique.martin@inrae.fr and we have this issue.

File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_mine.py", line 100, in seqid, source, featuretype, start, end, score, strand, frame, attributes = fields ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: not enough values to unpack (expected 9, got 1)

I have see that there is one similar and we try to deprecate python version to 3.9.0 as we see at the end of this one, and after we have this other issue:

File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_mine.py", line 13, in import gffutils ModuleNotFoundError: No module named 'gffutils'

Veronique solve it and now again we have the same one:

Traceback (most recent call last): File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_mine.py", line 100, in seqid, source, featuretype, start, end, score, strand, frame, attributes = fields ValueError: not enough values to unpack (expected 9, got 1)

Can you help us to sovle and you can also send answer please to Véronique

Sincerely

oclaisse commented 1 month ago

ps: it works with your example ./SOC_mine.py -g test2/P_salmonis.faa -f test2/P_salmonis.fna -gff test2/P_salmonis.gff -O P_salmonis -n

lauriebelch commented 1 month ago

Hi oclaisse,

This looks like a problem with a .gff file. Are you able to send a .gff that you are using, and I can take a look?

Thanks, Laurie

oclaisse commented 1 month ago

Hi Laurence, yes, it is a gff3 file form bakta

Sincerely

Olivier

Hi oclaisse,

This looks like a problem with a .gff file. Are you able to send a .gff that you are using, and I can take a look?

Thanks, Laurie

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gff-version 3

feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo

organism IOEB_9805

Annotated with Bakta

Software: v1.9.1

Database: v5.0, full

DOI: 10.1099/mgen.0.000685

URL: github.com/oschwengers/bakta

sequence-region 1183500001 1 5575

1183500001 Bakta region 1 5575 . + . ID=1183500001;Name=1183500001 1183500001 Infernal rRNA 144 260 3.4e-11 - . ID=AEKKBH_00005;Name=5S ribosomal RNA;locus_tag=AEKKBH_00005;gene=rrf;product=5S ribosomal RNA;Dbxref=GO:0005840,GO:0003735,RFAM:RF00001,KEGG:K01985,SO:0000652 1183500001 Infernal rRNA 334 3222 1.3e-05 - . ID=AEKKBH_00010;Name=23S ribosomal RNA;locus_tag=AEKKBH_00010;gene=rrl;product=23S ribosomal RNA;Dbxref=GO:0005840,GO:0003735,RFAM:RF02541,KEGG:K01980,SO:0001001 1183500001 tRNAscan-SE tRNA 3437 3509 . - . ID=AEKKBH_00015;Name=tRNA-Ala(tgc);locus_tag=AEKKBH_00015;product=tRNA-Ala(tgc);Dbxref=SO:0000254;gene=trnA;anti_codon=tgc;amino_acid=Ala 1183500001 Infernal rRNA 3609 5172 1.3e-47 - . ID=AEKKBH_00020;Name=16S ribosomal RNA;locus_tag=AEKKBH_00020;gene=rrs;product=16S ribosomal RNA;Dbxref=GO:0005840,GO:0003735,RFAM:RF00177,KEGG:K01977,SO:0001000

sequence-region 1183500002 1 89372

1183500002 Bakta region 1 89372 . + . ID=1183500002;Name=1183500002 1183500002 Prodigal CDS 8 1294 . + 0 ID=AEKKBH_00025;Name=D-serine ammonia-lyase;locus_tag=AEKKBH_00025;product=D-serine ammonia-lyase;Dbxref=COG:COG3048,COG:E,EC:4.3.1.18,GO:0008721,GO:0016836,GO:0030170,GO:0046416,KEGG:K01753,SO:0001217,UniRef:UniRef50_Q04G28,UniRef:UniRef90_Q04G28;gene=dsdA 1183500002 Prodigal CDS 1272 2132 . - 0 ID=AEKKBH_00030;Name=NAD(P)H-hydrate repair enzyme Nnr%2C NAD(P)H-hydrate dehydratase domain;locus_tag=AEKKBH_00030;product=NAD(P)H-hydrate repair enzyme Nnr%2C NAD(P)H-hydrate dehydratase domain;Dbxref=COG:COG0063,COG:F,RefSeq:WP_002816394.1,SO:0001217,UniParc:UPI0000E88D63,UniRef:UniRef100_A0NHK0,UniRef:UniRef50_Q04G27,UniRef:UniRef90_Q04G27;gene=nnr2 1183500002 Prodigal CDS 2260 2985 . + 0 ID=AEKKBH_00035;Name=F0F1 ATP synthase subunit A;locus_tag=AEKKBH_00035;product=F0F1 ATP synthase subunit A;Dbxref=COG:C,COG:COG0356,RefSeq:WP_002818520.1,SO:0001217,UniParc:UPI0001C670B8,UniRef:UniRef100_A0A483BAY5,UniRef:UniRef50_D5T3F6,UniRef:UniRef90_Q04G26;gene=atpB 1183500002 Prodigal CDS 3025 3237 . + 0 ID=AEKKBH_00040;Name=F0F1 ATP synthase subunit C;locus_tag=AEKKBH_00040;product=F0F1 ATP synthase subunit C;Dbxref=COG:C,COG:COG0636,GO:0005886,GO:0008289,GO:0045263,GO:0046933,RefSeq:WP_002816393.1,SO:0001217,UniParc:UPI0000391EAA,UniRef:UniRef100_Q04G25,UniRef:UniRef50_Q88UT8,UniRef:UniRef90_Q04G25;gene=atpE 1183500002 Prodigal CDS 3262 3792 . + 0 ID=AEKKBH_00045;Name=F0F1 ATP synthase subunit B;locus_tag=AEKKBH_00045;product=F0F1 ATP synthase subunit B;Dbxref=COG:C,COG:COG0711,GO:0005886,GO:0045263,GO:0046933,KEGG:K02109,RefSeq:WP_002818522.1,SO:0001217,UniParc:UPI0001C670B9,UniRef:UniRef100_A0NHJ8,UniRef:UniRef50_Q04G24,UniRef:UniRef90_Q04G24;gene=atpF 1183500002 Prodigal CDS 3792 4343 . + 0 ID=AEKKBH_00050;Name=ATP synthase F1 subunit delta;locus_tag=AEKKBH_00050;product=ATP synthase F1 subunit delta;Dbxref=COG:C,COG:COG0712,GO:0005886,GO:0045261,GO:0046933,RefSeq:WP_002816390.1,SO:0001217,UniParc:UPI00003C9923,UniRef:UniRef100_Q04G23,UniRef:UniRef50_Q04G23,UniRef:UniRef90_Q04G23;gene=atpH 1183500002 Prodigal CDS 4347 5909 . + 0 ID=AEKKBH_00055;Name=F0F1 ATP synthase subunit alpha;locus_tag=AEKKBH_00055;product=F0F1 ATP synthase subunit alpha;Dbxref=COG:C,COG:COG0056,EC:7.1.2.2,GO:0005524,GO:0005886,GO:0045261,GO:0046933,GO:0046961,RefSeq:WP_032820479.1,SO:0001217,UniParc:UPI0005106DE0,UniRef:UniRef100_UPI0005106DE0,UniRef:UniRef50_P56757,UniRef:UniRef90_Q04G22;gene=atpA 1183500002 Prodigal CDS 5909 6820 . + 0 ID=AEKKBH_00060;Name=ATP synthase F1 subunit gamma;locus_tag=AEKKBH_00060;product=ATP synthase F1 subunit gamma;Dbxref=COG:C,COG:COG0224,GO:0005524,GO:0005886,GO:0042777,GO:0045261,GO:0046933,RefSeq:WP_032805875.1,SO:0001217,UniParc:UPI0004A18C70,UniRef:UniRef100_A0A483BKQ3,UniRef:UniRef50_A3CM13,UniRef:UniRef90_Q04G21;gene=atpG 1183500002 Prodigal CDS 6835 8349 . + 0 ID=AEKKBH_00065;Name=F0F1 ATP synthase subunit beta;locus_tag=AEKKBH_00065;product=F0F1 ATP synthase subunit beta;Dbxref=COG:C,COG:COG0055,SO:0001217,UniParc:UPI00000B7AB7,UniRef:UniRef100_Q8KM28,UniRef:UniRef50_Q1AVH9,UniRef:UniRef90_Q8KM28;gene=atpD 1183500002 Prodigal CDS 8363 8791 . + 0 ID=AEKKBH_00070;Name=F0F1 ATP synthase subunit epsilon;locus_tag=AEKKBH_00070;product=F0F1 ATP synthase subunit epsilon;Dbxref=COG:C,COG:COG0355,RefSeq:WP_002816714.1,SO:0001217,UniParc:UPI0000E88F70,UniRef:UniRef100_A0A483BD84,UniRef:UniRef50_K0DBW5,UniRef:UniRef90_A0A483BD84;gene=atpC 1183500002 Prodigal CDS 8847 9068 . + 0 ID=AEKKBH_00075;Name=DUF1146 domain-containing protein;locus_tag=AEKKBH_00075;product=DUF1146 domain-containing protein;Dbxref=RefSeq:WP_002816715.1,SO:0001217,UniParc:UPI0000E88F6A,UniRef:UniRef100_A0A483BA53,UniRef:UniRef50_G9WGK5,UniRef:UniRef90_A0A483BA53 1183500002 Prodigal CDS 9107 10231 . + 0 ID=AEKKBH_00080;Name=Cell shape-determining ATPase MreB%2C actin-like superfamily;locus_tag=AEKKBH_00080;product=Cell shape-determining ATPase MreB%2C actin-like superfamily;Dbxref=COG:COG1077,COG:DZ,RefSeq:WP_002816716.1,SO:0001217,UniParc:UPI0000E88F6D,UniRef:UniRef100_A0NID7,UniRef:UniRef50_F9DR92,UniRef:UniRef90_A0NID7;gene=mreB 1183500002 Prodigal CDS 10236 10448 . + 0 ID=AEKKBH_00085;Name=DUF2969 domain-containing protein;locus_tag=AEKKBH_00085;product=DUF2969 domain-containing protein;Dbxref=RefSeq:WP_002816718.1,SO:0001217,UniParc:UPI0000391BCE,UniRef:UniRef100_A0A6H3GSF1,UniRef:UniRef50_G9WGK3,UniRef:UniRef90_A0A483B9X7 1183500002 Prodigal CDS 10459 11682 . + 0 ID=AEKKBH_00090;Name=Peptodoglycan polymerase FtsW/RodA/SpoVE;locus_tag=AEKKBH_00090;product=Peptodoglycan polymerase FtsW/RodA/SpoVE;Dbxref=COG:COG0772,COG:D,RefSeq:WP_032820480.1,SO:0001217,UniParc:UPI00050E53A4,UniRef:UniRef100_UPI00050E53A4,UniRef:UniRef50_A0A151G9P2,UniRef:UniRef90_A0A483CKN6;gene=ftsW 1183500002 Prodigal CDS 11679 12656 . + 0 ID=AEKKBH_00095;Name=DUF2785 domain-containing protein;locus_tag=AEKKBH_00095;product=DUF2785 domain-containing protein;Dbxref=RefSeq:WP_002816721.1,SO:0001217,UniParc:UPI0000391BCB,UniRef:UniRef100_A0A6H3GQ45,UniRef:UniRef50_G9WGK1,UniRef:UniRef90_D3L8E1 1183500002 Prodigal CDS 12728 13861 . + 0 ID=AEKKBH_00100;Name=D-alanine--D-alanine ligase;locus_tag=AEKKBH_00100;product=D-alanine--D-alanine ligase;Dbxref=COG:COG1181,COG:MR,EC:6.3.2.4,GO:0005524,GO:0005737,GO:0008360,GO:0008716,GO:0009252,GO:0046872,GO:0071555,RefSeq:WP_002816722.1,SO:0001217,UniParc:UPI0000E88F6C,UniRef:UniRef100_A0A6H3GVD6,UniRef:UniRef50_Q03ZI1,UniRef:UniRef90_Q04G13;gene=ddl 1183500002 Prodigal CDS 13868 16603 . + 0 ID=AEKKBH_00105;Name=DNA polymerase I;locus_tag=AEKKBH_00105;product=DNA polymerase I;Dbxref=COG:COG0749,COG:L,EC:2.7.7.7,KEGG:K02335,RefSeq:WP_080290027.1,SO:0001217,UniParc:UPI00050F1DD7,UniRef:UniRef100_UPI00050F1DD7,UniRef:UniRef50_A0NIE2,UniRef:UniRef90_A0NIE2;gene=polA 1183500002 Prodigal CDS 16590 17123 . + 0 ID=AEKKBH_00110;Name=Isopentenyldiphosphate isomerase;locus_tag=AEKKBH_00110;product=Isopentenyldiphosphate isomerase;Dbxref=COG:COG1443,COG:I,RefSeq:WP_002822798.1,SO:0001217,UniParc:UPI000277BADA,UniRef:UniRef100_A0NIE3,UniRef:UniRef50_A0NIE3,UniRef:UniRef90_A0NIE3;gene=idi 1183500002 Prodigal CDS 17116 17940 . + 0 ID=AEKKBH_00115;Name=bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;locus_tag=AEKKBH_00115;product=bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;Dbxref=COG:COG0266,COG:L,EC:3.2.2.23,EC:4.2.99.18,KEGG:K10563,RefSeq:WP_002822799.1,SO:0001217,UniParc:UPI000277BADB,UniRef:UniRef100_A0A6H3GSK5,UniRef:UniRef50_A0A8E2NUW3,UniRef:UniRef90_Q04G10;gene=mutM 1183500002 Prodigal CDS 17928 18542 . + 0 ID=AEKKBH_00120;Name=dephospho-CoA kinase;locus_tag=AEKKBH_00120;product=dephospho-CoA kinase;Dbxref=COG:COG0237,COG:H,EC:2.7.1.24,KEGG:K00859,RefSeq:WP_075646973.1,SO:0001217,UniParc:UPI0003118808,UniRef:UniRef100_A0NIE4,UniRef:UniRef50_G9WGJ6,UniRef:UniRef90_A0NIE4;gene=coaE 1183500002 Prodigal CDS 18539 19789 . + 0 ID=AEKKBH_00125;Name=Replication initiation and membrane attachment protein DnaB;locus_tag=AEKKBH_00125;product=Replication initiation and membrane attachment protein DnaB;Dbxref=COG:COG3611,COG:L,KEGG:K03346,RefSeq:WP_002822800.1,SO:0001217,UniParc:UPI000277BADC,UniRef:UniRef100_A0A483BA81,UniRef:UniRef50_G9WGJ5,UniRef:UniRef90_Q04G08;gene=dnaB 1183500002 Prodigal CDS 19786 20589 . + 0 ID=AEKKBH_00130;Name=DNA replication protein DnaC;locus_tag=AEKKBH_00130;product=DNA replication protein DnaC;Dbxref=COG:COG1484,COG:L,RefSeq:WP_002816727.1,SO:0001217,UniParc:UPI0000E88F81,UniRef:UniRef100_A0NIE6,UniRef:UniRef50_A0NIE6,UniRef:UniRef90_A0NIE6;gene=dnaC 1183500002 Prodigal CDS 20594 21019 . - 0 ID=AEKKBH_00135;Name=putative hydrocarbon binding protein%2C contains 4VR domain;locus_tag=AEKKBH_00135;product=putative hydrocarbon binding protein%2C contains 4VR domain;Dbxref=COG:COG1719,COG:R,RefSeq:WP_002816729.1,SO:0001217,UniParc:UPI0000391BC3,UniRef:UniRef100_A0A6H3GSF6,UniRef:UniRef50_G9WGJ3,UniRef:UniRef90_A0A483B9Y5 1183500002 Prodigal CDS 21083 21928 . + 0 ID=AEKKBH_00140;Name=glutamate racemase;locus_tag=AEKKBH_00140;product=glutamate racemase;Dbxref=COG:COG0796,COG:M,EC:5.1.1.3,GO:0008360,GO:0008881,GO:0009252,GO:0071555,RefSeq:WP_002822801.1,SO:0001217,UniParc:UPI000277BADD,UniRef:UniRef100_A0A6H3GJ49,UniRef:UniRef50_Q04G05,UniRef:UniRef90_Q04G05;gene=murI 1183500002 Prodigal CDS 21925 22458 . + 0 ID=AEKKBH_00145;Name=putative phosphodiesterase%2C calcineurin family;locus_tag=AEKKBH_00145;product=putative phosphodiesterase%2C calcineurin family;Dbxref=COG:COG0622,COG:R,RefSeq:WP_002816731.1,SO:0001217,UniParc:UPI0000E88F7F,UniRef:UniRef100_A0NIE9,UniRef:UniRef50_Q04G04,UniRef:UniRef90_Q04G04;gene=yfcE 1183500002 Prodigal CDS 22500 22922 . + 0 ID=AEKKBH_00150;Name=Uncharacterized conserved protein YoxC%2C contains an MCP-like domain;locus_tag=AEKKBH_00150;product=Uncharacterized conserved protein YoxC%2C contains an MCP-like domain;Dbxref=COG:COG4768,COG:S,RefSeq:WP_002816732.1,SO:0001217,UniParc:UPI0000E88F77,UniRef:UniRef100_A0A483BA59,UniRef:UniRef50_G9WGJ0,UniRef:UniRef90_Q04G03 1183500002 Prodigal CDS 22928 23413 . + 0 ID=AEKKBH_00155;Name=YtxH domain-containing protein;locus_tag=AEKKBH_00155;product=YtxH domain-containing protein;Dbxref=RefSeq:WP_002822804.1,SO:0001217,UniParc:UPI000277BADF,UniRef:UniRef100_A0NIF1,UniRef:UniRef50_Q04G02,UniRef:UniRef90_Q04G02;gene=ytxH 1183500002 Prodigal CDS 23527 24513 . + 0 ID=AEKKBH_00160;Name=DNA-binding transcriptional regulator%2C LacI/PurR family;locus_tag=AEKKBH_00160;product=DNA-binding transcriptional regulator%2C LacI/PurR family;Dbxref=COG:COG1609,COG:K,RefSeq:WP_032805871.1,SO:0001217,UniParc:UPI0004A0F3FD,UniRef:UniRef100_UPI0004A0F3FD,UniRef:UniRef50_A0A410NAA3,UniRef:UniRef90_A0A483BG69;gene=purR 1183500002 tRNAscan-SE tRNA 24574 24647 . + . ID=AEKKBH_00165;Name=tRNA-Lys(ttt);locus_tag=AEKKBH_00165;product=tRNA-Lys(ttt);Dbxref=SO:0000265;gene=trnK;anti_codon=ttt;amino_acid=Lys 1183500002 Prodigal CDS 25297 25536 . + 0 ID=AEKKBH_00170;Name=Ferritin;locus_tag=AEKKBH_00170;product=Ferritin;Dbxref=RefSeq:WP_002820289.1,SO:0001217,UniParc:UPI0000391BB8,UniRef:UniRef100_A0A483BDC3,UniRef:UniRef50_A0A483BDC3,UniRef:UniRef90_A0A483BDC3 1183500002 Prodigal CDS 25575 25931 . - 0 ID=AEKKBH_00175;Name=Phage protein;locus_tag=AEKKBH_00175;product=Phage protein;Dbxref=RefSeq:WP_002816735.1,SO:0001217,UniParc:UPI0000E88F7E,UniRef:UniRef100_A0NIF3,UniRef:UniRef50_Q04FZ4,UniRef:UniRef90_Q04FZ4 1183500002 Prodigal CDS 26104 26883 . - 0 ID=AEKKBH_00180;Name=(S)-acetoin forming diacetyl reductase;locus_tag=AEKKBH_00180;product=(S)-acetoin forming diacetyl reductase;Dbxref=COG:COG1028,COG:I,RefSeq:WP_032820483.1,SO:0001217,UniParc:UPI00050E07E0,UniRef:UniRef100_UPI00050E07E0,UniRef:UniRef50_A0A410NA76,UniRef:UniRef90_A0NIF4;gene=fabG 1183500002 Prodigal CDS 26991 27431 . - 0 ID=AEKKBH_00185;Name=DNA-binding transcriptional regulator%2C IscR family;locus_tag=AEKKBH_00185;product=DNA-binding transcriptional regulator%2C IscR family;Dbxref=COG:COG1959,COG:K,RefSeq:WP_002816738.1,SO:0001217,UniParc:UPI0000E88F7B,UniRef:UniRef100_A0NIF5,UniRef:UniRef50_A1BND2,UniRef:UniRef90_Q04FZ2;gene=iscR 1183500002 Prodigal CDS 27511 28485 . - 0 ID=AEKKBH_00190;Name=Transcriptional regulator YtlR;locus_tag=AEKKBH_00190;product=Transcriptional regulator YtlR;Dbxref=RefSeq:WP_002816739.1,SO:0001217,UniParc:UPI0000E88F73,UniRef:UniRef100_A0NIF6,UniRef:UniRef50_A0A410NA71,UniRef:UniRef90_A0NIF6;gene=ytlR 1183500002 Prodigal CDS 28857 29486 . + 0 ID=AEKKBH_00195;Name=Peptidoglycan-binding protein LysM;locus_tag=AEKKBH_00195;product=Peptidoglycan-binding protein LysM;Dbxref=RefSeq:WP_002822809.1,SO:0001217,UniParc:UPI000277BAE1,UniRef:UniRef100_A0A6H3GJ64,UniRef:UniRef50_D3L8G9,UniRef:UniRef90_D3L8G9;gene=lysM 1183500002 Prodigal CDS 29545 30852 . + 0 ID=AEKKBH_00200;Name=c-di-AMP phosphodiesterase AtaC or nucleotide pyrophosphatase%2C AlkP superfamily;locus_tag=AEKKBH_00200;product=c-di-AMP phosphodiesterase AtaC or nucleotide pyrophosphatase%2C AlkP superfamily;Dbxref=COG:COG1524,COG:T,RefSeq:WP_002822810.1,SO:0001217,UniParc:UPI000277BAE2,UniRef:UniRef100_A0A6H3GQ64,UniRef:UniRef50_A0A483BVF1,UniRef:UniRef90_A0A483BVF1;gene=ataC 1183500002 tRNAscan-SE tRNA 31101 31172 . + . ID=AEKKBH_00205;Name=tRNA-Glu(ttc);locus_tag=AEKKBH_00205;product=tRNA-Glu(ttc);Dbxref=SO:0000259;gene=trnE;anti_codon=ttc;amino_acid=Glu 1183500002 Bakta CDS 31318 31398 . - 0 ID=AEKKBH_00210;Name=30S ribosomal protein S15;locus_tag=AEKKBH_00210;product=30S ribosomal protein S15;Dbxref=SO:0001217,UniParc:UPI0000E55419,UniRef:UniRef100_Q04FY9,UniRef:UniRef50_Q04FY9,UniRef:UniRef90_Q04FY9 1183500002 Prodigal CDS 32477 33196 . + 0 ID=AEKKBH_00215;Name=2-succinyl-6-hydroxy-2%2C4-cyclohexadiene-1-carboxylate synthase MenH and related esterases%2C alpha/beta hydrolase fold;locus_tag=AEKKBH_00215;product=2-succinyl-6-hydroxy-2%2C4-cyclohexadiene-1-carboxylate synthase MenH and related esterases%2C alpha/beta hydrolase fold;Dbxref=COG:COG0596,COG:HR,RefSeq:WP_032820486.1,SO:0001217,UniParc:UPI000517D436,UniRef:UniRef100_UPI000517D436,UniRef:UniRef50_A0A483BR01,UniRef:UniRef90_A0A483BR01;gene=menH 1183500002 Prodigal CDS 33504 34463 . - 0 ID=AEKKBH_00220;Name=Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase;locus_tag=AEKKBH_00220;product=Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase;Dbxref=COG:CHR,COG:COG1052,RefSeq:WP_002818544.1,SO:0001217,UniParc:UPI0000391BAF,UniRef:UniRef100_Q04FY7,UniRef:UniRef50_A0A091C238,UniRef:UniRef90_A0A483BVY1;gene=ldhA 1183500002 Prodigal CDS 34647 35006 . - 0 ID=AEKKBH_00225;Name=DNA-binding transcriptional regulator%2C MerR family;locus_tag=AEKKBH_00225;product=DNA-binding transcriptional regulator%2C MerR family;Dbxref=COG:COG0789,COG:K,RefSeq:WP_002816744.1,SO:0001217,UniParc:UPI00003C9952,UniRef:UniRef100_A0A483BGV9,UniRef:UniRef50_G9WEY5,UniRef:UniRef90_A0A483BGV9;gene=soxR 1183500002 Prodigal CDS 35090 35944 . + 0 ID=AEKKBH_00230;Name=NADP-dependent 3-hydroxy acid dehydrogenase YdfG;locus_tag=AEKKBH_00230;product=NADP-dependent 3-hydroxy acid dehydrogenase YdfG;Dbxref=COG:C,COG:COG4221,RefSeq:WP_002822813.1,SO:0001217,UniParc:UPI000277BAE4,UniRef:UniRef100_A0A483BAA1,UniRef:UniRef50_A0A483BAA1,UniRef:UniRef90_A0A483BAA1;gene=ydfG 1183500002 Prodigal CDS 36194 36781 . - 0 ID=AEKKBH_00235;Name=Transcriptional regulator;locus_tag=AEKKBH_00235;product=Transcriptional regulator;Dbxref=RefSeq:WP_002822814.1,SO:0001217,UniParc:UPI000277BAE5,UniRef:UniRef100_A0A6H3GP94,UniRef:UniRef50_C0XIA1,UniRef:UniRef90_A0NIG2 1183500002 Prodigal CDS 36885 38180 . + 0 ID=AEKKBH_00240;Name=MFS transporter;locus_tag=AEKKBH_00240;product=MFS transporter;Dbxref=RefSeq:WP_002820282.1,SO:0001217,UniParc:UPI0000391BAB,UniRef:UniRef100_Q04FY3,UniRef:UniRef50_D3L8H7,UniRef:UniRef90_D3L8H7 1183500002 Prodigal CDS 38710 39990 . + 0 ID=AEKKBH_00245;Name=H+/Cl- antiporter ClcA;locus_tag=AEKKBH_00245;product=H+/Cl- antiporter ClcA;Dbxref=COG:COG0038,COG:P,RefSeq:WP_002816749.1,SO:0001217,UniParc:UPI0000391BAA,UniRef:UniRef100_A0NIG3,UniRef:UniRef50_J9YHY8,UniRef:UniRef90_Q04FY2;gene=clcA 1183500002 Prodigal CDS 40137 40571 . + 0 ID=AEKKBH_00250;Name=Integral membrane protein;locus_tag=AEKKBH_00250;product=Integral membrane protein;Dbxref=RefSeq:WP_002818548.1,SO:0001217,UniParc:UPI0000E5541B,UniRef:UniRef100_A0NIG4,UniRef:UniRef50_A0A3T0TNQ2,UniRef:UniRef90_A0NIG4 1183500002 Prodigal CDS 40658 40867 . - 0 ID=AEKKBH_00255;Name=KTSC domain-containing protein;locus_tag=AEKKBH_00255;product=KTSC domain-containing protein;Dbxref=RefSeq:WP_002818550.1,SO:0001217,UniParc:UPI0000391BA9,UniRef:UniRef100_A0A483BA82,UniRef:UniRef50_A0A483BA82,UniRef:UniRef90_A0A483BA82 1183500002 Prodigal CDS 41203 41472 . - 0 ID=AEKKBH_00260;Name=Conserved domain protein;locus_tag=AEKKBH_00260;product=Conserved domain protein;Dbxref=RefSeq:WP_002816753.1,SO:0001217,UniParc:UPI00003C994F,UniRef:UniRef100_A0NIG6,UniRef:UniRef50_A0NIG6,UniRef:UniRef90_A0NIG6 1183500002 Prodigal CDS 41548 41964 . + 0 ID=AEKKBH_00265;Name=Prophage protein;locus_tag=AEKKBH_00265;product=Prophage protein;Dbxref=RefSeq:WP_257614045.1,SO:0001217,UniParc:UPI000AEF4120,UniRef:UniRef100_Q04FX8,UniRef:UniRef50_Q04FX8,UniRef:UniRef90_Q04FX8 1183500002 Prodigal CDS 42073 42249 . + 0 ID=AEKKBH_00270;Name=Phage tail protein;locus_tag=AEKKBH_00270;product=Phage tail protein;Dbxref=RefSeq:WP_002818554.1,SO:0001217,UniParc:UPI00003C994E,UniRef:UniRef100_Q04FX7,UniRef:UniRef50_Q04FX7,UniRef:UniRef90_Q04FX7 1183500002 Prodigal CDS 42273 42407 . + 0 ID=AEKKBH_00275;Name=GPW-gp25 domain-containing protein;locus_tag=AEKKBH_00275;product=GPW-gp25 domain-containing protein;Dbxref=RefSeq:WP_002818555.1,SO:0001217,UniParc:UPI0000E5541D,UniRef:UniRef100_A0A483BDD4,UniRef:UniRef50_A0A3T0TNU9,UniRef:UniRef90_A0A6N4A728 1183500002 Prodigal CDS 44173 44355 . + 0 ID=AEKKBH_00280;Name=putative integral membrane protein;locus_tag=AEKKBH_00280;product=putative integral membrane protein;Dbxref=RefSeq:WP_002818556.1,SO:0001217,UniParc:UPI0000E5541E,UniRef:UniRef100_Q04FX5,UniRef:UniRef50_Q04FX5,UniRef:UniRef90_Q04FX5 1183500002 Prodigal CDS 44467 44994 . + 0 ID=AEKKBH_00285;Name=putative integral membrane protein;locus_tag=AEKKBH_00285;product=putative integral membrane protein;Dbxref=RefSeq:WP_011677541.1,SO:0001217,UniParc:UPI00003C994D,UniRef:UniRef100_Q04FX4,UniRef:UniRef50_Q04FX4,UniRef:UniRef90_Q04FX4 1183500002 Prodigal CDS 45747 46199 . - 0 ID=AEKKBH_00290;Name=DUF4430 domain-containing protein;locus_tag=AEKKBH_00290;product=DUF4430 domain-containing protein;Dbxref=RefSeq:WP_002818561.1,SO:0001217,UniParc:UPI0000391BA5,UniRef:UniRef100_Q04FX3,UniRef:UniRef50_Q04FX3,UniRef:UniRef90_Q04FX3 1183500002 Prodigal CDS 46569 46742 . - 0 ID=AEKKBH_00295;Name=Small%2C acid-soluble spore protein%2C SspJ family;locus_tag=AEKKBH_00295;product=Small%2C acid-soluble spore protein%2C SspJ family;Dbxref=RefSeq:WP_002817404.1,SO:0001217,UniParc:UPI0000E88D24,UniRef:UniRef100_A0NJY5,UniRef:UniRef50_Q04FX2,UniRef:UniRef90_Q04FX2;gene=sspJ 1183500002 Prodigal CDS 46927 47430 . + 0 ID=AEKKBH_00300;Name=Protein N-acetyltransferase%2C RimJ/RimL family;locus_tag=AEKKBH_00300;product=Protein N-acetyltransferase%2C RimJ/RimL family;Dbxref=COG:COG1670,COG:JO,RefSeq:WP_002820281.1,SO:0001217,UniParc:UPI0000391BA3,UniRef:UniRef100_A0A483BKX3,UniRef:UniRef50_A0A483BKX3,UniRef:UniRef90_A0A483BKX3;gene=rimL 1183500002 Prodigal CDS 47646 48005 . + 0 ID=AEKKBH_00305;Name=Helix-turn-helix domain-containing protein;locus_tag=AEKKBH_00305;product=Helix-turn-helix domain-containing protein;Dbxref=RefSeq:WP_002818567.1,SO:0001217,UniParc:UPI0000E5541F,UniRef:UniRef100_Q04FX0,UniRef:UniRef50_Q04FX0,UniRef:UniRef90_Q04FX0 1183500002 Prodigal CDS 48524 49795 . + 0 ID=AEKKBH_00310;Name=D-alanyl-D-alanine carboxypeptidase;locus_tag=AEKKBH_00310;product=D-alanyl-D-alanine carboxypeptidase;Dbxref=COG:COG1686,COG:M,RefSeq:WP_002822820.1,SO:0001217,UniParc:UPI000277B2AE,UniRef:UniRef100_UPI000277B2AE,UniRef:UniRef50_D3L8J5,UniRef:UniRef90_D3L8J5;gene=dacC 1183500002 Prodigal CDS 49893 50696 . + 0 ID=AEKKBH_00315;Name=S-formylglutathione hydrolase FrmB;locus_tag=AEKKBH_00315;product=S-formylglutathione hydrolase FrmB;Dbxref=COG:COG0627,COG:V,RefSeq:WP_002817398.1,SO:0001217,UniParc:UPI0000391BA0,UniRef:UniRef100_K6PS50,UniRef:UniRef50_A0A483BAC0,UniRef:UniRef90_A0A483BAC0;gene=frmB 1183500002 Prodigal CDS 51026 51190 . + 0 ID=AEKKBH_00320;Name=Mitochondrial import receptor subunit TOM5-like protein;locus_tag=AEKKBH_00320;product=Mitochondrial import receptor subunit TOM5-like protein;Dbxref=RefSeq:WP_002817397.1,SO:0001217,UniParc:UPI0000E88D25,UniRef:UniRef100_A0NJY1,UniRef:UniRef50_Q04FW7,UniRef:UniRef90_Q04FW7 1183500002 Prodigal CDS 51492 51758 . + 0 ID=AEKKBH_00325;Name=ATP-binding cassette domain-containing protein;locus_tag=AEKKBH_00325;product=ATP-binding cassette domain-containing protein;Dbxref=SO:0001217,UniRef:UniRef50_UPI000B0D47F2,UniRef:UniRef90_UPI000B0D47F2 1183500002 Prodigal CDS 51755 52378 . + 0 ID=AEKKBH_00330;Name=ABC superfamily ATP binding cassette transporter%2C ABC protein;locus_tag=AEKKBH_00330;product=ABC superfamily ATP binding cassette transporter%2C ABC protein;Dbxref=SO:0001217,UniRef:UniRef50_G0UHP3 1183500002 Prodigal CDS 52378 53250 . + 0 ID=AEKKBH_00335;Name=Transport permease protein;locus_tag=AEKKBH_00335;product=Transport permease protein;Dbxref=KEGG:K11051,RefSeq:WP_032811263.1,SO:0001217,UniParc:UPI00050F6A5F,UniRef:UniRef100_UPI00050F6A5F,UniRef:UniRef50_Q04FW5,UniRef:UniRef90_Q04FW5 1183500002 Prodigal CDS 53281 53730 . + 0 ID=AEKKBH_00340;Name=DNA-binding response regulator%2C LytR/AlgR family;locus_tag=AEKKBH_00340;product=DNA-binding response regulator%2C LytR/AlgR family;Dbxref=COG:COG3279,COG:KT,RefSeq:WP_002821602.1,SO:0001217,UniParc:UPI0000E55420,UniRef:UniRef100_Q04FW4,UniRef:UniRef50_D3L8K0,UniRef:UniRef90_D3L8K0;gene=lytT 1183500002 Prodigal CDS 53733 54134 . + 0 ID=AEKKBH_00345;Name=DUF3021 domain-containing protein;locus_tag=AEKKBH_00345;product=DUF3021 domain-containing protein;Dbxref=RefSeq:WP_002818576.1,SO:0001217,UniParc:UPI0000391B9B,UniRef:UniRef100_A0A6H3GJ84,UniRef:UniRef50_A0NJX7,UniRef:UniRef90_A0NJX7 1183500002 Prodigal CDS 54239 54871 . + 0 ID=AEKKBH_00350;Name=Lipoprotein-anchoring transpeptidase ErfK/SrfK;locus_tag=AEKKBH_00350;product=Lipoprotein-anchoring transpeptidase ErfK/SrfK;Dbxref=COG:COG1376,COG:M,RefSeq:WP_002822823.1,SO:0001217,UniParc:UPI000277BBF1,UniRef:UniRef100_A0NJX6,UniRef:UniRef50_A0A1A5VI15,UniRef:UniRef90_Q04FW2;gene=erfK 1183500002 Prodigal CDS 54913 55509 . - 0 ID=AEKKBH_00355;Name=Putative NADPH-quinone reductase (modulator of drug activity B);locus_tag=AEKKBH_00355;product=Putative NADPH-quinone reductase (modulator of drug activity B);Dbxref=COG:COG2249,COG:R,RefSeq:WP_002822824.1,SO:0001217,UniParc:UPI000277BBF2,UniRef:UniRef100_A0A483BD41,UniRef:UniRef50_A0A6L5A503,UniRef:UniRef90_A0A483BD41;gene=mdaB 1183500002 Prodigal CDS 55609 56076 . + 0 ID=AEKKBH_00360;Name=DNA-binding transcriptional regulator%2C MarR family;locus_tag=AEKKBH_00360;product=DNA-binding transcriptional regulator%2C MarR family;Dbxref=COG:COG1846,COG:K,RefSeq:WP_002818582.1,SO:0001217,UniParc:UPI00003C9949,UniRef:UniRef100_A0NJX4,UniRef:UniRef50_A0NJX4,UniRef:UniRef90_A0NJX4;gene=marR 1183500002 Prodigal CDS 56135 56542 . - 0 ID=AEKKBH_00365;Name=Polysacc-synt-C domain-containing protein;locus_tag=AEKKBH_00365;product=Polysacc-synt-C domain-containing protein;Dbxref=RefSeq:WP_002818583.1,SO:0001217,UniParc:UPI00003C9948,UniRef:UniRef100_A0A3S7H329,UniRef:UniRef50_A0NJX3,UniRef:UniRef90_A0NJX3 1183500002 Prodigal CDS 57056 57643 . + 0 ID=AEKKBH_00370;Name=Major Facilitator Superfamily protein;locus_tag=AEKKBH_00370;product=Major Facilitator Superfamily protein;Dbxref=RefSeq:WP_002818585.1,SO:0001217,UniParc:UPI0000391B98,UniRef:UniRef100_A0NJX2,UniRef:UniRef50_A0NJX2,UniRef:UniRef90_A0NJX2 1183500002 Prodigal CDS 58145 58504 . - 0 ID=AEKKBH_00375;Name=Putative fluoride ion transporter CrcB;locus_tag=AEKKBH_00375;product=Putative fluoride ion transporter CrcB;Dbxref=RefSeq:WP_002817386.1,SO:0001217,UniParc:UPI00003C9946,UniRef:UniRef100_A0NJX1,UniRef:UniRef50_A0NJX1,UniRef:UniRef90_A0NJX1;gene=crcB 1183500002 Prodigal CDS 58501 58887 . - 0 ID=AEKKBH_00380;Name=fluoride efflux transporter CrcB;locus_tag=AEKKBH_00380;product=fluoride efflux transporter CrcB;Dbxref=COG:COG0239,COG:DP,RefSeq:WP_002817385.1,SO:0001217,UniParc:UPI00003C9945,UniRef:UniRef100_A0NJX0,UniRef:UniRef50_A0NJX0,UniRef:UniRef90_A0NJX0;gene=crcB 1183500002 Prodigal CDS 59458 60006 . + 0 ID=AEKKBH_00385;Name=DNA-binding protein%2C AcrR family%2C includes nucleoid occlusion protein SlmA;locus_tag=AEKKBH_00385;product=DNA-binding protein%2C AcrR family%2C includes nucleoid occlusion protein SlmA;Dbxref=COG:COG1309,COG:K,RefSeq:WP_002817384.1,SO:0001217,UniParc:UPI0000391B97,UniRef:UniRef100_A0NJW9,UniRef:UniRef50_A0NJW9,UniRef:UniRef90_A0NJW9;gene=acrR 1183500002 Prodigal CDS 60008 61069 . + 0 ID=AEKKBH_00390;Name=ABC transporter permease;locus_tag=AEKKBH_00390;product=ABC transporter permease;Dbxref=RefSeq:WP_002818587.1,SO:0001217,UniParc:UPI0000E55421,UniRef:UniRef100_A0NJW8,UniRef:UniRef50_J9W189,UniRef:UniRef90_A0A3T0TNL0 1183500002 Prodigal CDS 61072 61746 . + 0 ID=AEKKBH_00395;Name=ABC-type lipoprotein export system%2C ATPase component;locus_tag=AEKKBH_00395;product=ABC-type lipoprotein export system%2C ATPase component;Dbxref=COG:COG1136,COG:M,RefSeq:WP_002817382.1,SO:0001217,UniParc:UPI0000E88D11,UniRef:UniRef100_A0NJW7,UniRef:UniRef50_A0A243PXX9,UniRef:UniRef90_Q04FV4;gene=lolD 1183500002 Prodigal CDS 61763 62422 . - 0 ID=AEKKBH_00400;Name=DNA-binding protein%2C AcrR family%2C includes nucleoid occlusion protein SlmA;locus_tag=AEKKBH_00400;product=DNA-binding protein%2C AcrR family%2C includes nucleoid occlusion protein SlmA;Dbxref=COG:COG1309,COG:K,RefSeq:WP_002817381.1,SO:0001217,UniParc:UPI00003C9944,UniRef:UniRef100_A0NJW6,UniRef:UniRef50_A0NJW6,UniRef:UniRef90_A0NJW6;gene=acrR 1183500002 Prodigal CDS 62424 63569 . - 0 ID=AEKKBH_00405;Name=ABC-type multidrug transport system%2C permease component;locus_tag=AEKKBH_00405;product=ABC-type multidrug transport system%2C permease component;Dbxref=COG:COG0842,COG:V,RefSeq:WP_002822826.1,SO:0001217,UniParc:UPI000277BBF4,UniRef:UniRef100_A0A6H3GJ90,UniRef:UniRef50_D3L8L5,UniRef:UniRef90_D3L8L5;gene=yadH 1183500002 Prodigal CDS 63547 64284 . - 0 ID=AEKKBH_00410;Name=ABC-type multidrug transport system%2C ATPase component;locus_tag=AEKKBH_00410;product=ABC-type multidrug transport system%2C ATPase component;Dbxref=COG:COG1131,COG:V,RefSeq:WP_002817380.1,SO:0001217,UniParc:UPI0000E88D13,UniRef:UniRef100_A0A483BH10,UniRef:UniRef50_A0A5E8F6Y6,UniRef:UniRef90_A0A483BH10;gene=ccmA 1183500002 Prodigal CDS 64560 65066 . + 0 ID=AEKKBH_00415;Name=RNA 2'%2C3'-cyclic phosphodiesterase (2'-5' RNA ligase);locus_tag=AEKKBH_00415;product=RNA 2'%2C3'-cyclic phosphodiesterase (2'-5' RNA ligase);Dbxref=COG:COG1514,COG:J,RefSeq:WP_143808576.1,SO:0001217,UniParc:UPI000AFB3DD7,UniRef:UniRef100_A0A6H3GVK3,UniRef:UniRef50_A0A3T0TSP8,UniRef:UniRef90_A0A6H3GVK3;gene=thpR 1183500002 Prodigal CDS 65269 65946 . + 0 ID=AEKKBH_00420;Name=Magnesium uptake protein YhiD/SapB%2C involved in acid resistance;locus_tag=AEKKBH_00420;product=Magnesium uptake protein YhiD/SapB%2C involved in acid resistance;Dbxref=COG:COG1285,COG:P,RefSeq:WP_002822828.1,SO:0001217,UniParc:UPI000277BBF6,UniRef:UniRef100_A0A6H3GWD7,UniRef:UniRef50_D3L8L8,UniRef:UniRef90_D3L8L8;gene=sapB 1183500002 Prodigal CDS 66115 66396 . - 0 ID=AEKKBH_00425;Name=Nicotinamide mononucleotide transporter;locus_tag=AEKKBH_00425;product=Nicotinamide mononucleotide transporter;Dbxref=SO:0001217,UniRef:UniRef50_A0A1Q2T7B0 1183500002 Prodigal CDS 66433 66849 . - 0 ID=AEKKBH_00430;Name=Ribosyl nicotinamide transporter PnuC-like;locus_tag=AEKKBH_00430;product=Ribosyl nicotinamide transporter PnuC-like;Dbxref=SO:0001217,UniRef:UniRef50_A0A0V8EIY5 1183500002 Prodigal CDS 67024 68286 . - 0 ID=AEKKBH_00435;Name=Type II restriction endonuclease;locus_tag=AEKKBH_00435;product=Type II restriction endonuclease;Dbxref=SO:0001217,UniRef:UniRef50_Q04FU8,UniRef:UniRef90_Q04FU8 1183500002 Prodigal CDS 68557 69213 . - 0 ID=AEKKBH_00440;Name=Putative NADH-flavin reductase;locus_tag=AEKKBH_00440;product=Putative NADH-flavin reductase;Dbxref=COG:COG2910,COG:R,KEGG:K07118,RefSeq:WP_002818618.1,SO:0001217,UniParc:UPI0000391B8B,UniRef:UniRef100_Q04FU2,UniRef:UniRef50_A0A0R2MC66,UniRef:UniRef90_A0A3S7H3J2;gene=ywnB 1183500002 Prodigal CDS 69350 70096 . - 0 ID=AEKKBH_00445;Name=ABC-type polar amino acid transport system%2C ATPase component;locus_tag=AEKKBH_00445;product=ABC-type polar amino acid transport system%2C ATPase component;Dbxref=COG:COG1126,COG:E,RefSeq:WP_002818620.1,SO:0001217,UniParc:UPI0000391B8A,UniRef:UniRef100_Q04FU1,UniRef:UniRef50_A0A5E7KPZ1,UniRef:UniRef90_A0A483C062;gene=glnQ 1183500002 Prodigal CDS 70093 71700 . - 0 ID=AEKKBH_00450;Name=ABC-type amino acid transport/signal transduction system%2C periplasmic component/domain;locus_tag=AEKKBH_00450;product=ABC-type amino acid transport/signal transduction system%2C periplasmic component/domain;Dbxref=COG:COG0834,COG:ET,RefSeq:WP_002820607.1,SO:0001217,UniParc:UPI00027777B2,UniRef:UniRef100_Q04FU0,UniRef:UniRef50_A0A224XBN3,UniRef:UniRef90_Q04FU0;gene=hisJ 1183500002 Infernal regulatory_region 71806 71975 1.4e-11 - . ID=AEKKBHLLOK_53;Name=Lysine riboswitch;product=Lysine riboswitch;Dbxref=RFAM:RF00168,SO:0000035 1183500002 Prodigal CDS 72064 72222 . - 0 ID=AEKKBH_00455;Name=2-dehydropantoate 2-reductase;locus_tag=AEKKBH_00455;product=2-dehydropantoate 2-reductase;Dbxref=EC:1.1.1.169,KEGG:K00077,RefSeq:WP_002818626.1,SO:0001217,UniParc:UPI0000391B88,UniRef:UniRef100_A0A483CJ83,UniRef:UniRef50_I8R8H9,UniRef:UniRef90_A0A3T0TNR1 1183500002 Prodigal CDS 72259 73023 . - 0 ID=AEKKBH_00460;Name=2-dehydropantoate 2-reductase;locus_tag=AEKKBH_00460;product=2-dehydropantoate 2-reductase;Dbxref=EC:1.1.1.169,KEGG:K00077,SO:0001217,UniParc:UPI00030A6572,UniRef:UniRef100_UPI00030A6572,UniRef:UniRef50_D3L8N1,UniRef:UniRef90_D3L8N1 1183500002 Prodigal CDS 73206 74126 . + 0 ID=AEKKBH_00465;Name=Uncharacterized membrane protein YczE;locus_tag=AEKKBH_00465;product=Uncharacterized membrane protein YczE;Dbxref=COG:COG2364,COG:S,KEGG:K07149,RefSeq:WP_002817372.1,SO:0001217,UniParc:UPI0000391B86,UniRef:UniRef100_A0NJV9,UniRef:UniRef50_A0A3T0TSP6,UniRef:UniRef90_A0A3T0TSP6;gene=yczE 1183500002 Prodigal CDS 74129 75226 . - 0 ID=AEKKBH_00470;Name=AraC-type DNA-binding domain and AraC-containing proteins;locus_tag=AEKKBH_00470;product=AraC-type DNA-binding domain and AraC-containing proteins;Dbxref=COG:COG2207,COG:K,RefSeq:WP_002822831.1,SO:0001217,UniParc:UPI000277BBF9,UniRef:UniRef100_A0A6H3GZR2,UniRef:UniRef50_A0NJV8,UniRef:UniRef90_A0NJV8;gene=araC 1183500002 Prodigal CDS 75406 76143 . + 0 ID=AEKKBH_00475;Name=Nitroreductase;locus_tag=AEKKBH_00475;product=Nitroreductase;Dbxref=COG:C,COG:COG0778,RefSeq:WP_002817368.1,SO:0001217,UniParc:UPI0000391B84,UniRef:UniRef100_A0NJV7,UniRef:UniRef50_A0A483BTE8,UniRef:UniRef90_A0A483BTE8;gene=nfnB 1183500002 Prodigal CDS 76282 77289 . + 0 ID=AEKKBH_00480;Name=Uncharacterized membrane protein YadS%2C UPF0324 family;locus_tag=AEKKBH_00480;product=Uncharacterized membrane protein YadS%2C UPF0324 family;Dbxref=COG:COG2855,COG:S,SO:0001217,UniParc:UPI0000E88D28,UniRef:UniRef100_A0NJV6,UniRef:UniRef50_A0A285PLC4,UniRef:UniRef90_A0A483BCK2;gene=yeiH 1183500002 Prodigal CDS 77526 78374 . + 0 ID=AEKKBH_00485;Name=Short-chain dehydrogenase;locus_tag=AEKKBH_00485;product=Short-chain dehydrogenase;Dbxref=COG:COG0300,COG:R,RefSeq:WP_002822832.1,SO:0001217,UniParc:UPI000277B337,UniRef:UniRef100_A0NJV5,UniRef:UniRef50_A0A2N9K8B3,UniRef:UniRef90_A0A483BTD7;gene=yqjQ 1183500002 Prodigal CDS 78487 79068 . - 0 ID=AEKKBH_00490;Name=DNA-binding protein%2C AcrR family%2C includes nucleoid occlusion protein SlmA;locus_tag=AEKKBH_00490;product=DNA-binding protein%2C AcrR family%2C includes nucleoid occlusion protein SlmA;Dbxref=COG:COG1309,COG:K,RefSeq:WP_002822833.1,SO:0001217,UniParc:UPI000277BBFA,UniRef:UniRef100_A0A6H3GVL3,UniRef:UniRef50_A0A5P8M2R5,UniRef:UniRef90_Q04FT4;gene=acrR 1183500002 Prodigal CDS 79230 81074 . + 0 ID=AEKKBH_00495;Name=putative arabinose efflux permease AraJ%2C MFS family;locus_tag=AEKKBH_00495;product=putative arabinose efflux permease AraJ%2C MFS family;Dbxref=COG:COG2814,COG:G,RefSeq:WP_002822834.1,SO:0001217,UniParc:UPI000277BBFB,UniRef:UniRef100_A0A6H3GWE8,UniRef:UniRef50_K8Q7R1,UniRef:UniRef90_D3L8N8;gene=araJ 1183500002 Prodigal CDS 81067 81558 . + 0 ID=AEKKBH_00500;Name=ABC transporter%2C permease;locus_tag=AEKKBH_00500;product=ABC transporter%2C permease;Dbxref=RefSeq:WP_002817363.1,SO:0001217,UniParc:UPI0000391B7F,UniRef:UniRef100_A0NJV3,UniRef:UniRef50_A0NJV3,UniRef:UniRef90_A0NJV3 1183500002 Prodigal CDS 81561 81725 . + 0 ID=AEKKBH_00505;Name=Two-component response regulator (DesK);locus_tag=AEKKBH_00505;product=Two-component response regulator (DesK);Dbxref=KEGG:K07693,RefSeq:WP_002818638.1,SO:0001217,UniParc:UPI0000391B7E,UniRef:UniRef100_A0A6H3GSR6,UniRef:UniRef50_R3WK62,UniRef:UniRef90_A0A483BV05 1183500002 Prodigal CDS 81726 81878 . + 0 ID=AEKKBH_00510;Name=Response regulatory domain-containing protein;locus_tag=AEKKBH_00510;product=Response regulatory domain-containing protein;Dbxref=SO:0001217,UniParc:UPI0003105973,UniRef:UniRef100_A0A6H3GS75,UniRef:UniRef50_D3L8P2,UniRef:UniRef90_D3L8P2 1183500002 Bakta CDS 82087 82167 . + 0 ID=AEKKBH_00515;Name=DNA-binding response regulator;locus_tag=AEKKBH_00515;product=DNA-binding response regulator;Dbxref=SO:0001217,UniParc:UPI000E6D3750,UniRef:UniRef100_A0A6H3GVI6,UniRef:UniRef50_Q04FT0,UniRef:UniRef90_Q04FT0 1183500002 Prodigal CDS 82551 82691 . + 0 ID=AEKKBH_00520;Name=GFO-IDH-MocA domain-containing protein;locus_tag=AEKKBH_00520;product=GFO-IDH-MocA domain-containing protein;Dbxref=SO:0001217,UniParc:UPI0001C67121,UniRef:UniRef100_D3L8P4,UniRef:UniRef50_D3L8P4,UniRef:UniRef90_D3L8P4 1183500002 Prodigal CDS 82664 83674 . + 0 ID=AEKKBH_00525;Name=5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase;locus_tag=AEKKBH_00525;product=5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase;Dbxref=SO:0001217,UniRef:UniRef50_A0A386PR96,UniRef:UniRef90_A0A3T0TNJ6 1183500002 Prodigal CDS 83678 84787 . + 0 ID=AEKKBH_00530;Name=Cystathionine gamma-synthase and O-acetylhomoserine thiolyase;locus_tag=AEKKBH_00530;product=Cystathionine gamma-synthase and O-acetylhomoserine thiolyase;Dbxref=RefSeq:WP_002822837.1,SO:0001217,UniParc:UPI000277BBFC,UniRef:UniRef100_A0A6H3GVB6,UniRef:UniRef50_A0A483BA84,UniRef:UniRef90_A0A483BA84 1183500002 Prodigal CDS 84784 85920 . + 0 ID=AEKKBH_00535;Name=Cystathionine beta-lyase/cystathionine gamma-synthase;locus_tag=AEKKBH_00535;product=Cystathionine beta-lyase/cystathionine gamma-synthase;Dbxref=COG:COG0626,COG:E,RefSeq:WP_002822839.1,SO:0001217,UniParc:UPI000277BBFD,UniRef:UniRef100_A0A6H3GZS1,UniRef:UniRef50_A0A1W7LKJ6,UniRef:UniRef90_A0A483BQ86;gene=metC 1183500002 Prodigal CDS 85922 86734 . + 0 ID=AEKKBH_00540;Name=Homoserine O-succinyltransferase;locus_tag=AEKKBH_00540;product=Homoserine O-succinyltransferase;Dbxref=COG:COG1897,COG:E,EC:2.3.1.31,EC:2.3.1.46,KEGG:K00651,RefSeq:WP_002818647.1,SO:0001217,UniParc:UPI0000E55427,UniRef:UniRef100_A0A6H3GSK4,UniRef:UniRef50_A0NJV0,UniRef:UniRef90_A0NJV0;gene=metA 1183500002 Prodigal CDS 86828 87550 . + 0 ID=AEKKBH_00545;Name=YebC/PmpR family DNA-binding transcriptional regulator;locus_tag=AEKKBH_00545;product=YebC/PmpR family DNA-binding transcriptional regulator;Dbxref=COG:COG0217,COG:KJ,GO:0003677,GO:0005737,GO:0006355,RefSeq:WP_002822841.1,SO:0001217,UniParc:UPI000277BBFE,UniRef:UniRef100_A0A6H3GJB6,UniRef:UniRef50_Q8Y6Z5,UniRef:UniRef90_Q04FS7;gene=tACO1 1183500002 Prodigal CDS 87634 89295 . + 0 ID=AEKKBH_00550;Name=formate--tetrahydrofolate ligase;locus_tag=AEKKBH_00550;product=formate--tetrahydrofolate ligase;Dbxref=COG:COG2759,COG:F,EC:6.3.4.3,GO:0004329,GO:0005524,GO:0035999,RefSeq:WP_002822842.1,SO:0001217,UniParc:UPI000277B242,UniRef:UniRef100_A0A6H3GQC1,UniRef:UniRef50_Q04FS6,UniRef:UniRef90_Q04FS6;gene=fhs

sequence-region 1183500003 1 5945

1183500003 Bakta region 1 5945 . + . ID=1183500003;Name=1183500003 1183500003 Prodigal CDS 549 1544 . - 0 ID=AEKKBH_00555;Name=site-specific DNA-methyltransferase (adenine-specific);locus_tag=AEKKBH_00555;product=site-specific DNA-methyltransferase (adenine-specific);Dbxref=SO:0001217,UniRef:UniRef50_Q1J4R6 1183500003 Prodigal CDS 1516 2136 . - 0 ID=AEKKBH_00560;Name=type I restriction-modification system subunit M N-terminal domain-containing protein;locus_tag=AEKKBH_00560;product=type I restriction-modification system subunit M N-terminal domain-containing protein;Dbxref=SO:0001217,UniRef:UniRef50_A0A0E2RCQ6,UniRef:UniRef90_UPI0015D67442 1183500003 Prodigal CDS 2437 2907 . - 0 ID=AEKKBH_00565;Name=DUF3021 domain-containing protein;locus_tag=AEKKBH_00565;product=DUF3021 domain-containing protein;Dbxref=RefSeq:WP_002822778.1,SO:0001217,UniParc:UPI000277B9F5,UniRef:UniRef100_A0A6H3GHT4,UniRef:UniRef50_A0A0R1VT88,UniRef:UniRef90_A0A6H3GHT4 1183500003 Prodigal CDS 2904 3347 . - 0 ID=AEKKBH_00570;Name=LytTR family transcriptional regulator;locus_tag=AEKKBH_00570;product=LytTR family transcriptional regulator;Dbxref=RefSeq:WP_002822777.1,SO:0001217,UniParc:UPI000277B9F4,UniRef:UniRef100_A0A6H3GNP9,UniRef:UniRef50_A0A0R1VK08,UniRef:UniRef90_A0A6H3GNP9 1183500003 Prodigal CDS 3544 4653 . - 0 ID=AEKKBH_00575;Name=L-aminopeptidase/D-esterase;locus_tag=AEKKBH_00575;product=L-aminopeptidase/D-esterase;Dbxref=COG:COG3191,COG:E,RefSeq:WP_032820016.1,SO:0001217,UniParc:UPI000510419A,UniRef:UniRef100_UPI000510419A,UniRef:UniRef50_J9W459,UniRef:UniRef90_A0A483BJ07;gene=dmpA 1183500003 Prodigal CDS 4744 5766 . - 0 ID=AEKKBH_00580;Name=putative dehydrogenase;locus_tag=AEKKBH_00580;product=putative dehydrogenase;Dbxref=COG:COG0673,COG:R,RefSeq:WP_002822774.1,SO:0001217,UniParc:UPI000277B9F2,UniRef:UniRef100_A0A6H3GUT8,UniRef:UniRef50_A0A0P8Z6B6,UniRef:UniRef90_Q04HL8;gene=mviM

sequence-region 1183500004 1 1709

1183500004 Bakta region 1 1709 . + . ID=1183500004;Name=1183500004 1183500004 Prodigal CDS 46 666 . + 0 ID=AEKKBH_00585;Name=Restriction endonuclease subunit S;locus_tag=AEKKBH_00585;product=Restriction endonuclease subunit S;Dbxref=EC:3.1.21.3,KEGG:K01154,RefSeq:WP_239643627.1,SO:0001217,UniParc:UPI000B0E3F28,UniRef:UniRef100_UPI00050F1029,UniRef:UniRef50_A0A5C7F3Q9,UniRef:UniRef90_A0A650C616 1183500004 Prodigal CDS 751 1680 . + 0 ID=AEKKBH_00590;Name=Tyr recombinase domain-containing protein;locus_tag=AEKKBH_00590;product=Tyr recombinase domain-containing protein;Dbxref=RefSeq:WP_032820012.1,SO:0001217,UniParc:UPI00050E3C41,UniRef:UniRef100_UPI00050E3C41,UniRef:UniRef50_A0A0M9FJ04,UniRef:UniRef90_A0A6N4RMJ8

sequence-region 1183500005 1 1882

1183500005 Bakta region 1 1882 . + . ID=1183500005;Name=1183500005 1183500005 Prodigal CDS 48 572 . + 0 ID=AEKKBH_00595;Name=Glycosyltransferase;locus_tag=AEKKBH_00595;product=Glycosyltransferase;Dbxref=SO:0001217,UniRef:UniRef50_A0A0R1VFN9

sequence-region 1183500006 1 138628

1183500006 Bakta region 1 138628 . + . ID=1183500006;Name=1183500006 1183500006 Prodigal CDS 2228 2497 . - 0 ID=AEKKBH_00600;Name=DUF1797 domain-containing protein;locus_tag=AEKKBH_00600;product=DUF1797 domain-containing protein;Dbxref=COG:COG4703,COG:S,RefSeq:WP_257610525.1,SO:0001217,UniParc:UPI0000391DD8,UniRef:UniRef100_Q04G30,UniRef:UniRef50_Q04G30,UniRef:UniRef90_Q04G30;gene=ykuJ 1183500006 Prodigal CDS 2472 3500 . - 0 ID=AEKKBH_00605;Name=putative membrane flippase AglD2/YbhN%2C UPF0104 family;locus_tag=AEKKBH_00605;product=putative membrane flippase AglD2/YbhN%2C UPF0104 family;Dbxref=COG:COG0392,COG:M,RefSeq:WP_002822898.1,SO:0001217,UniParc:UPI000277B89C,UniRef:UniRef100_A0A650C797,UniRef:UniRef50_Q04G31,UniRef:UniRef90_Q04G31;gene=aglD2 1183500006 Prodigal CDS 3497 4528 . - 0 ID=AEKKBH_00610;Name=Glycosyltransferase involved in cell wall bisynthesis;locus_tag=AEKKBH_00610;product=Glycosyltransferase involved in cell wall bisynthesis;Dbxref=COG:COG0438,COG:M,EC:2.4.1.208,KEGG:K13677,RefSeq:WP_002816498.1,SO:0001217,UniParc:UPI0000391DDA,UniRef:UniRef100_A0A483B981,UniRef:UniRef50_A0A223XF79,UniRef:UniRef90_A0A483B981;gene=rfaB 1183500006 Prodigal CDS 4542 5837 . - 0 ID=AEKKBH_00615;Name=Glycosyltransferase involved in cell wall bisynthesis;locus_tag=AEKKBH_00615;product=Glycosyltransferase involved in cell wall bisynthesis;Dbxref=COG:COG0438,COG:M,RefSeq:WP_002816499.1,SO:0001217,UniParc:UPI0000E88578,UniRef:UniRef100_A0NHU9,UniRef:UniRef50_A0A0J5PA36,UniRef:UniRef90_Q04G33;gene=rfaB 1183500006 Prodigal CDS 5881 7608 . - 0 ID=AEKKBH_00620;Name=Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria);locus_tag=AEKKBH_00620;product=Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria);Dbxref=COG:COG1080,COG:G,RefSeq:WP_032820298.1,SO:0001217,UniParc:UPI0005102A5B,UniRef:UniRef100_A0A483B9K8,UniRef:UniRef50_Q9ZAD8,UniRef:UniRef90_A0A3T0TS85;gene=ptsP 1183500006 Prodigal CDS 7866 8669 . - 0 ID=AEKKBH_00625;Name=Hydroxymethylpyrimidine pyrophosphatase and other HAD family phosphatases;locus_tag=AEKKBH_00625;product=Hydroxymethylpyrimidine pyrophosphatase and other HAD family phosphatases;Dbxref=COG:COG0561,COG:HR,RefSeq:WP_002818509.1,SO:0001217,UniParc:UPI0000E55411,UniRef:UniRef100_Q04G35,UniRef:UniRef50_A0A1C4BH04,UniRef:UniRef90_A0A483BG01;gene=cof 1183500006 Prodigal CDS 8852 9055 . - 0 ID=AEKKBH_00630;Name=Phosphotransferase system cellobiose-specific component IIB;locus_tag=AEKKBH_00630;product=Phosphotransferase system cellobiose-specific component IIB;Dbxref=COG:COG1440,COG:G,RefSeq:WP_002818507.1,SO:0001217,UniParc:UPI00003C9986,UniRef:UniRef100_A0A6H3GRK1,UniRef:UniRef50_A0A6H3GRK1,UniRef:UniRef90_A0A6H3GRK1;gene=celA 1183500006 Prodigal CDS 9291 10001 . + 0 ID=AEKKBH_00635;Name=glucosamine-6-phosphate deaminase;locus_tag=AEKKBH_00635;product=glucosamine-6-phosphate deaminase;Dbxref=COG:COG0363,COG:G,EC:3.5.99.6,GO:0004342,GO:0005975,GO:0006044,GO:0019262,KEGG:K02564,RefSeq:WP_002818506.1,SO:0001217,UniParc:UPI0000391DDE,UniRef:UniRef100_Q04G36,UniRef:UniRef50_O35000,UniRef:UniRef90_Q04G36;gene=nagB 1183500006 Prodigal CDS 10170 10433 . - 0 ID=AEKKBH_00640;Name=phosphocarrier protein HPr;locus_tag=AEKKBH_00640;product=phosphocarrier protein HPr;Dbxref=COG:COG1925,COG:TG,RefSeq:WP_002816503.1,SO:0001217,UniParc:UPI0000391DDF,UniRef:UniRef100_A0A483BK41,UniRef:UniRef50_P24366,UniRef:UniRef90_A0A483BK41;gene=ptsH 1183500006 Prodigal CDS 10546 10734 . - 0 ID=AEKKBH_00645;Name=CYTH domain-containing protein;locus_tag=AEKKBH_00645;product=CYTH domain-containing protein;Dbxref=RefSeq:WP_002818505.1,SO:0001217,UniParc:UPI00003C9987,UniRef:UniRef100_A0A3S7H403,UniRef:UniRef50_G9WI57,UniRef:UniRef90_A0A3S7H403 1183500006 Prodigal CDS 10734 11426 . - 0 ID=AEKKBH_00650;Name=Lipoprotein;locus_tag=AEKKBH_00650;product=Lipoprotein;Dbxref=RefSeq:WP_002818504.1,SO:0001217,UniParc:UPI0000391DE0,UniRef:UniRef100_Q04G39,UniRef:UniRef50_Q04G39,UniRef:UniRef90_Q04G39 1183500006 Prodigal CDS 11604 13739 . + 0 ID=AEKKBH_00655;Name=ATP-dependent Clp protease%2C ATP-binding subunit ClpA;locus_tag=AEKKBH_00655;product=ATP-dependent Clp protease%2C ATP-binding subunit ClpA;Dbxref=COG:COG0542,COG:O,SO:0001217,UniRef:UniRef50_A0A0D1A4U2,UniRef:UniRef90_D3L8B2;gene=clpA 1183500006 Prodigal CDS 13819 14172 . + 0 ID=AEKKBH_00660;Name=Cytochrome;locus_tag=AEKKBH_00660;product=Cytochrome;Dbxref=RefSeq:WP_002816508.1,SO:0001217,UniParc:UPI0000E88574,UniRef:UniRef100_A0A6H3GUX1,UniRef:UniRef50_Q04G41,UniRef:UniRef90_Q04G41 1183500006 Prodigal CDS 14229 15443 . - 0 ID=AEKKBH_00665;Name=Phosphoglycerate kinase;locus_tag=AEKKBH_00665;product=Phosphoglycerate kinase;Dbxref=COG:COG0126,COG:G,EC:2.7.2.3,GO:0004618,GO:0005524,GO:0005737,GO:0006096,KEGG:K00927,RefSeq:WP_002816509.1,SO:0001217,UniParc:UPI0000E88580,UniRef:UniRef100_A0A6H3GVS0,UniRef:UniRef50_Q04LZ5,UniRef:UniRef90_Q04G42;gene=pgk 1183500006 Prodigal CDS 15495 15812 . - 0 ID=AEKKBH_00670;Name=UPF0145 protein OEOE_0637;locus_tag=AEKKBH_00670;product=UPF0145 protein OEOE_0637;Dbxref=COG:COG0393,COG:S,RefSeq:WP_002816510.1,SO:0001217,UniParc:UPI0000391DE3,UniRef:UniRef100_Q04G43,UniRef:UniRef50_Q9CH08,UniRef:UniRef90_Q04G43;gene=ybjQ 1183500006 Prodigal CDS 15855 17171 . - 0 ID=AEKKBH_00675;Name=glucose-6-phosphate isomerase;locus_tag=AEKKBH_00675;product=glucose-6-phosphate isomerase;Dbxref=COG:COG0166,COG:G,EC:5.3.1.9,GO:0004347,GO:0005737,GO:0006094,GO:0006096,GO:0097367,RefSeq:WP_002816511.1,SO:0001217,UniParc:UPI0000E88575,UniRef:UniRef100_A0NHW0,UniRef:UniRef50_P80860,UniRef:UniRef90_Q04G44;gene=pgi 1183500006 Prodigal CDS 17185 18990 . - 0 ID=AEKKBH_00680;Name=glutamine--fructose-6-phosphate transaminase (isomerizing);locus_tag=AEKKBH_00680;product=glutamine--fructose-6-phosphate transaminase (isomerizing);Dbxref=COG:COG0449,COG:M,EC:2.6.1.16,KEGG:K00820,RefSeq:WP_002816512.1,SO:0001217,UniParc:UPI0000E8857E,UniRef:UniRef100_A0A6H3GRL0,UniRef:UniRef50_P0CI73,UniRef:UniRef90_A0A6H3GRL0;gene=glmS 1183500006 Prodigal CDS 19100 20002 . - 0 ID=AEKKBH_00685;Name=Permease of the drug/metabolite transporter (DMT) superfamily;locus_tag=AEKKBH_00685;product=Permease of the drug/metabolite transporter (DMT) superfamily;Dbxref=COG:COG0697,COG:GER,RefSeq:WP_002816513.1,SO:0001217,UniParc:UPI0000E88581,UniRef:UniRef100_A0NHW2,UniRef:UniRef50_D3L8A6,UniRef:UniRef90_D3L8A6;gene=rhaT 1183500006 Prodigal CDS 20002 21093 . - 0 ID=AEKKBH_00690;Name=Spermidine/putrescine-binding periplasmic protein;locus_tag=AEKKBH_00690;product=Spermidine/putrescine-binding periplasmic protein;Dbxref=COG:COG0687,COG:E,RefSeq:WP_002816514.1,SO:0001217,UniParc:UPI0000E8857B,UniRef:UniRef100_A0A3S7H159,UniRef:UniRef50_U4TY46,UniRef:UniRef90_Q04G47;gene=potD 1183500006 Prodigal CDS 21090 21896 . - 0 ID=AEKKBH_00695;Name=ABC-type spermidine/putrescine transport system%2C permease component II;locus_tag=AEKKBH_00695;product=ABC-type spermidine/putrescine transport system%2C permease component II;Dbxref=COG:COG1177,COG:E,RefSeq:WP_002822906.1,SO:0001217,UniParc:UPI000277B8A2,UniRef:UniRef100_A0A483BBX1,UniRef:UniRef50_A0A224X4H8,UniRef:UniRef90_Q04G48;gene=potC 1183500006 Prodigal CDS 21896 22714 . - 0 ID=AEKKBH_00700;Name=ABC-type spermidine/putrescine transport system%2C permease component I;locus_tag=AEKKBH_00700;product=ABC-type spermidine/putrescine transport system%2C permease component I;Dbxref=COG:COG1176,COG:E,RefSeq:WP_002822907.1,SO:0001217,UniParc:UPI000277B8A3,UniRef:UniRef100_A0A6H3GIP9,UniRef:UniRef50_A0A387BP51,UniRef:UniRef90_A0NHF5;gene=potB 1183500006 Prodigal CDS 22714 23817 . - 0 ID=AEKKBH_00705;Name=Spermidine/putrescine import ATP-binding protein PotA;locus_tag=AEKKBH_00705;product=Spermidine/putrescine import ATP-binding protein PotA;Dbxref=COG:COG3842,COG:E,EC:7.6.2.11,GO:0005524,GO:0015417,GO:0043190,RefSeq:WP_032804491.1,SO:0001217,UniParc:UPI00014F7B54,UniRef:UniRef100_Q04G50,UniRef:UniRef50_Q04G50,UniRef:UniRef90_Q04G50;gene=potA 1183500006 Prodigal CDS 23932 24324 . - 0 ID=AEKKBH_00710;Name=30S ribosomal protein S9;locus_tag=AEKKBH_00710;product=30S ribosomal protein S9;Dbxref=COG:COG0103,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:1990904,KEGG:K02996,RefSeq:WP_002816342.1,SO:0001217,UniParc:UPI0000E886C5,UniRef:UniRef100_A0A483B9K0,UniRef:UniRef50_P80374,UniRef:UniRef90_Q04G51;gene=rpsI 1183500006 Prodigal CDS 24343 24789 . - 0 ID=AEKKBH_00715;Name=50S ribosomal protein L13;locus_tag=AEKKBH_00715;product=50S ribosomal protein L13;Dbxref=COG:COG0102,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:1990904,RefSeq:WP_002818489.1,SO:0001217,UniParc:UPI00003C998F,UniRef:UniRef100_Q04G52,UniRef:UniRef50_Q04G52,UniRef:UniRef90_Q04G52;gene=rplM 1183500006 Prodigal CDS 24883 25731 . - 0 ID=AEKKBH_00720;Name=SseB domain-containing protein;locus_tag=AEKKBH_00720;product=SseB domain-containing protein;Dbxref=RefSeq:WP_002822908.1,SO:0001217,UniParc:UPI000277B93B,UniRef:UniRef100_A0A483BCM9,UniRef:UniRef50_G9WI42,UniRef:UniRef90_Q04G53;gene=sseB 1183500006 Prodigal CDS 25715 26473 . - 0 ID=AEKKBH_00725;Name=tRNA pseudouridine(38-40) synthase TruA;locus_tag=AEKKBH_00725;product=tRNA pseudouridine(38-40) synthase TruA;Dbxref=COG:COG0101,COG:J,EC:5.4.99.12,GO:0003723,GO:0031119,GO:0106029,KEGG:K06173,RefSeq:WP_002818487.1,SO:0001217,UniParc:UPI0000391DF0,UniRef:UniRef100_Q04G54,UniRef:UniRef50_Q88XU9,UniRef:UniRef90_Q04G54;gene=truA 1183500006 Prodigal CDS 26460 27269 . - 0 ID=AEKKBH_00730;Name=ECF-type transporter transmembrane protein EcfT;locus_tag=AEKKBH_00730;product=ECF-type transporter transmembrane protein EcfT;Dbxref=COG:COG0619,COG:H,KEGG:K16785,RefSeq:WP_002822909.1,SO:0001217,UniParc:UPI000277B93C,UniRef:UniRef100_A0NHE5,UniRef:UniRef50_Q04G55,UniRef:UniRef90_Q04G55;gene=ecfT 1183500006 Prodigal CDS 27262 28086 . - 0 ID=AEKKBH_00735;Name=Energy-coupling factor transporter ATP-binding protein EcfA2;locus_tag=AEKKBH_00735;product=Energy-coupling factor transporter ATP-binding protein EcfA2;Dbxref=COG:COG1122,COG:PR,RefSeq:WP_002822911.1,SO:0001217,UniParc:UPI000277B93D,UniRef:UniRef100_A0A483B9E5,UniRef:UniRef50_A0A483B9E5,UniRef:UniRef90_A0A483B9E5;gene=ecfA2 1183500006 Prodigal CDS 28062 28865 . - 0 ID=AEKKBH_00740;Name=Energy-coupling factor transporter ATP-binding protein EcfA2;locus_tag=AEKKBH_00740;product=Energy-coupling factor transporter ATP-binding protein EcfA2;Dbxref=COG:COG1122,COG:PR,RefSeq:WP_011677527.1,SO:0001217,UniParc:UPI0000391DF3,UniRef:UniRef100_Q04G57,UniRef:UniRef50_A0A483BIE1,UniRef:UniRef90_A0A483BIE1;gene=ecfA2 1183500006 Prodigal CDS 28986 29381 . - 0 ID=AEKKBH_00745;Name=50S ribosomal protein L17;locus_tag=AEKKBH_00745;product=50S ribosomal protein L17;Dbxref=COG:COG0203,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:1990904,KEGG:K02879,RefSeq:WP_032805401.1,SO:0001217,UniParc:UPI00050FF368,UniRef:UniRef100_UPI00050FF368,UniRef:UniRef50_Q8ETV8,UniRef:UniRef90_Q04G59;gene=rplQ 1183500006 Prodigal CDS 29412 30356 . - 0 ID=AEKKBH_00750;Name=DNA-directed RNA polymerase subunit alpha;locus_tag=AEKKBH_00750;product=DNA-directed RNA polymerase subunit alpha;Dbxref=COG:COG0202,COG:K,EC:2.7.7.6,GO:0000428,GO:0003677,GO:0003899,GO:0005737,GO:0006351,GO:0046983,RefSeq:WP_032805404.1,SO:0001217,UniParc:UPI0004A0B5E9,UniRef:UniRef100_UPI0004A0B5E9,UniRef:UniRef50_A1USR8,UniRef:UniRef90_Q04G60;gene=rpoA 1183500006 Prodigal CDS 30381 30779 . - 0 ID=AEKKBH_00755;Name=30S ribosomal protein S11;locus_tag=AEKKBH_00755;product=30S ribosomal protein S11;Dbxref=COG:COG0100,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,KEGG:K02948,RefSeq:WP_002820374.1,SO:0001217,UniParc:UPI0000391DF6,UniRef:UniRef100_Q04G61,UniRef:UniRef50_P44379,UniRef:UniRef90_Q04G61;gene=rpsK 1183500006 Prodigal CDS 30801 31172 . - 0 ID=AEKKBH_00760;Name=30S ribosomal protein S13;locus_tag=AEKKBH_00760;product=30S ribosomal protein S13;Dbxref=COG:COG0099,COG:J,GO:0000049,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,KEGG:K02952,RefSeq:WP_002816335.1,SO:0001217,UniParc:UPI0000391DF7,UniRef:UniRef100_Q04G62,UniRef:UniRef50_B2UNG5,UniRef:UniRef90_Q04G62;gene=rpsM 1183500006 Prodigal CDS 31391 31627 . - 0 ID=AEKKBH_00765;Name=translation initiation factor IF-1;locus_tag=AEKKBH_00765;product=translation initiation factor IF-1;Dbxref=COG:COG0361,COG:J,GO:0003743,GO:0005737,GO:0019843,GO:0043022,RefSeq:WP_002816336.1,SO:0001217,UniParc:UPI0000391DF8,UniRef:UniRef100_A0A483BCL9,UniRef:UniRef50_Q8DS34,UniRef:UniRef90_Q04G64;gene=infA 1183500006 Prodigal CDS 31677 32243 . - 0 ID=AEKKBH_00770;Name=adenylate kinase;locus_tag=AEKKBH_00770;product=adenylate kinase;Dbxref=COG:COG0563,COG:F,EC:2.7.4.3,GO:0004017,GO:0005524,GO:0005737,GO:0016310,GO:0044209,RefSeq:WP_002822916.1,SO:0001217,UniParc:UPI000277B940,UniRef:UniRef100_A0A6H3GS96,UniRef:UniRef50_Q03ZM5,UniRef:UniRef90_Q04G65;gene=adk 1183500006 Prodigal CDS 32245 33591 . - 0 ID=AEKKBH_00775;Name=preprotein translocase subunit SecY;locus_tag=AEKKBH_00775;product=preprotein translocase subunit SecY;Dbxref=COG:COG0201,COG:U,RefSeq:WP_002822918.1,SO:0001217,UniParc:UPI000277B941,UniRef:UniRef100_A0A483BBV3,UniRef:UniRef50_F6CD01,UniRef:UniRef90_Q04G66;gene=secY 1183500006 Prodigal CDS 33597 34061 . - 0 ID=AEKKBH_00780;Name=50S ribosomal protein L15;locus_tag=AEKKBH_00780;product=50S ribosomal protein L15;Dbxref=COG:COG0200,COG:J,GO:0003735,GO:0005737,GO:0006412,GO:0015934,GO:0019843,KEGG:K02876,RefSeq:WP_002822922.1,SO:0001217,UniParc:UPI000277B441,UniRef:UniRef100_A0A650C775,UniRef:UniRef50_P19946,UniRef:UniRef90_Q04G67;gene=rplO 1183500006 Prodigal CDS 34061 34246 . - 0 ID=AEKKBH_00785;Name=50S ribosomal protein L30;locus_tag=AEKKBH_00785;product=50S ribosomal protein L30;Dbxref=COG:COG1841,COG:J,GO:0003735,GO:0005737,GO:0006412,GO:0015934,RefSeq:WP_002816353.1,SO:0001217,UniParc:UPI0000391DFC,UniRef:UniRef100_Q04G68,UniRef:UniRef50_A6W5V6,UniRef:UniRef90_Q04G68;gene=rpmD 1183500006 Prodigal CDS 34256 34753 . - 0 ID=AEKKBH_00790;Name=30S ribosomal protein S5;locus_tag=AEKKBH_00790;product=30S ribosomal protein S5;Dbxref=COG:COG0098,COG:J,GO:0003735,GO:0006412,GO:0015935,GO:0019843,KEGG:K02988,RefSeq:WP_002818468.1,SO:0001217,UniParc:UPI0000391DFD,UniRef:UniRef100_Q04G69,UniRef:UniRef50_Q839E7,UniRef:UniRef90_Q04G69;gene=rpsE 1183500006 Prodigal CDS 34771 35127 . - 0 ID=AEKKBH_00795;Name=50S ribosomal protein L18;locus_tag=AEKKBH_00795;product=50S ribosomal protein L18;Dbxref=COG:COG0256,COG:J,GO:0003735,GO:0005737,GO:0005840,GO:0006412,GO:0019843,GO:1990904,RefSeq:WP_002818467.1,SO:0001217,UniParc:UPI0000391DFE,UniRef:UniRef100_Q04G70,UniRef:UniRef50_Q8DS29,UniRef:UniRef90_Q04G70;gene=rplR 1183500006 Prodigal CDS 35159 35695 . - 0 ID=AEKKBH_00800;Name=50S ribosomal protein L6;locus_tag=AEKKBH_00800;product=50S ribosomal protein L6;Dbxref=COG:COG0097,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,KEGG:K02933,RefSeq:WP_002816351.1,SO:0001217,UniParc:UPI0000391DFF,UniRef:UniRef100_Q04G71,UniRef:UniRef50_Q8DML8,UniRef:UniRef90_Q04G71;gene=rplF 1183500006 Prodigal CDS 35735 36136 . - 0 ID=AEKKBH_00805;Name=30S ribosomal protein S8;locus_tag=AEKKBH_00805;product=30S ribosomal protein S8;Dbxref=COG:COG0096,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,KEGG:K02994,RefSeq:WP_032820303.1,SO:0001217,UniParc:UPI00050FDE16,UniRef:UniRef100_UPI00050FDE16,UniRef:UniRef50_Q46IS2,UniRef:UniRef90_Q04G72;gene=rpsH 1183500006 Prodigal CDS 36258 36800 . - 0 ID=AEKKBH_00810;Name=50S ribosomal protein L5;locus_tag=AEKKBH_00810;product=50S ribosomal protein L5;Dbxref=COG:COG0094,COG:J,GO:0000049,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,KEGG:K02931,RefSeq:WP_002816349.1,SO:0001217,UniParc:UPI0000391E01,UniRef:UniRef100_Q04G73,UniRef:UniRef50_Q50306,UniRef:UniRef90_Q04G73;gene=rplE 1183500006 Prodigal CDS 36819 37088 . - 0 ID=AEKKBH_00815;Name=50S ribosomal protein L24;locus_tag=AEKKBH_00815;product=50S ribosomal protein L24;Dbxref=COG:COG0198,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,RefSeq:WP_002816348.1,SO:0001217,UniParc:UPI0000391E02,UniRef:UniRef100_Q04G74,UniRef:UniRef50_A4TEC6,UniRef:UniRef90_Q04G74;gene=rplX 1183500006 Prodigal CDS 37099 37467 . - 0 ID=AEKKBH_00820;Name=50S ribosomal protein L14;locus_tag=AEKKBH_00820;product=50S ribosomal protein L14;Dbxref=COG:COG0093,COG:J,GO:0003735,GO:0006412,GO:0015934,GO:0019843,RefSeq:WP_002818465.1,SO:0001217,UniParc:UPI0000391E03,UniRef:UniRef100_Q04G75,UniRef:UniRef50_Q5SHP8,UniRef:UniRef90_Q04G75;gene=rplN 1183500006 Prodigal CDS 37489 37755 . - 0 ID=AEKKBH_00825;Name=30S ribosomal protein S17;locus_tag=AEKKBH_00825;product=30S ribosomal protein S17;Dbxref=COG:COG0186,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,RefSeq:WP_002822923.1,SO:0001217,UniParc:UPI000277B942,UniRef:UniRef100_A0A483B9I0,UniRef:UniRef50_Q839F5,UniRef:UniRef90_Q04G76;gene=rpsQ 1183500006 Prodigal CDS 37766 37975 . - 0 ID=AEKKBH_00830;Name=50S ribosomal protein L29;locus_tag=AEKKBH_00830;product=50S ribosomal protein L29;Dbxref=COG:COG0255,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:1990904,RefSeq:WP_002822925.1,SO:0001217,UniParc:UPI000277B527,UniRef:UniRef100_A0A483BFN0,UniRef:UniRef50_Q9Z9K6,UniRef:UniRef90_Q04G77;gene=rpmC 1183500006 Prodigal CDS 37975 38406 . - 0 ID=AEKKBH_00835;Name=50S ribosomal protein L16;locus_tag=AEKKBH_00835;product=50S ribosomal protein L16;Dbxref=COG:COG0197,COG:J,GO:0000049,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,KEGG:K02878,RefSeq:WP_002818461.1,SO:0001217,UniParc:UPI0000E5540A,UniRef:UniRef100_Q04G78,UniRef:UniRef50_Q9RXJ5,UniRef:UniRef90_Q04G78;gene=rplP 1183500006 Prodigal CDS 38406 39191 . - 0 ID=AEKKBH_00840;Name=30S ribosomal protein S3;locus_tag=AEKKBH_00840;product=30S ribosomal protein S3;Dbxref=GO:0003729,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,RefSeq:WP_032820304.1,SO:0001217,UniParc:UPI00050E9349,UniRef:UniRef100_UPI00050E9349,UniRef:UniRef50_Q04G79,UniRef:UniRef90_Q04G79;gene=rpsC 1183500006 Prodigal CDS 39194 39556 . - 0 ID=AEKKBH_00845;Name=50S ribosomal protein L22;locus_tag=AEKKBH_00845;product=50S ribosomal protein L22;Dbxref=COG:COG0091,COG:J,GO:0003735,GO:0006412,GO:0015934,GO:0019843,KEGG:K02890,RefSeq:WP_002818459.1,SO:0001217,UniParc:UPI0000E55408,UniRef:UniRef100_Q04G80,UniRef:UniRef50_Q1GBL3,UniRef:UniRef90_Q04G80;gene=rplV 1183500006 Prodigal CDS 39567 39848 . - 0 ID=AEKKBH_00850;Name=30S ribosomal protein S19;locus_tag=AEKKBH_00850;product=30S ribosomal protein S19;Dbxref=COG:COG0185,COG:J,GO:0003735,GO:0005737,GO:0006412,GO:0015935,GO:0019843,RefSeq:WP_002818458.1,SO:0001217,UniParc:UPI0000E55407,UniRef:UniRef100_Q04G81,UniRef:UniRef50_Q3ZJ86,UniRef:UniRef90_Q04G81;gene=rpsS 1183500006 Prodigal CDS 39861 40700 . - 0 ID=AEKKBH_00855;Name=50S ribosomal protein L2;locus_tag=AEKKBH_00855;product=50S ribosomal protein L2;Dbxref=COG:COG0090,COG:J,GO:0003735,GO:0006412,GO:0015934,GO:0016740,GO:0019843,RefSeq:WP_002817274.1,SO:0001217,UniParc:UPI0000E8822E,UniRef:UniRef100_A0A483B9Q3,UniRef:UniRef50_Q7NM65,UniRef:UniRef90_Q04G82;gene=rplB 1183500006 Prodigal CDS 40722 41021 . - 0 ID=AEKKBH_00860;Name=50S ribosomal protein L23;locus_tag=AEKKBH_00860;product=50S ribosomal protein L23;Dbxref=COG:COG0089,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,RefSeq:WP_002817273.1,SO:0001217,UniParc:UPI0000E55405,UniRef:UniRef100_Q04G83,UniRef:UniRef50_Q88XY4,UniRef:UniRef90_Q04G83;gene=rplW 1183500006 Prodigal CDS 41021 41644 . - 0 ID=AEKKBH_00865;Name=50S ribosomal protein L4;locus_tag=AEKKBH_00865;product=50S ribosomal protein L4;Dbxref=COG:COG0088,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,KEGG:K02926,RefSeq:WP_002822926.1,SO:0001217,UniParc:UPI000277B943,UniRef:UniRef100_A0A483B936,UniRef:UniRef50_P42921,UniRef:UniRef90_Q04G84;gene=rplD 1183500006 Prodigal CDS 41659 42402 . - 0 ID=AEKKBH_00870;Name=50S ribosomal protein L3;locus_tag=AEKKBH_00870;product=50S ribosomal protein L3;Dbxref=COG:COG0087,COG:J,GO:0003735,GO:0005840,GO:0006412,GO:0019843,GO:1990904,RefSeq:WP_002822927.1,SO:0001217,UniParc:UPI000277B944,UniRef:UniRef100_A0A6H3GSB4,UniRef:UniRef50_Q04G85,UniRef:UniRef90_Q04G85;gene=rplC 1183500006 Prodigal CDS 42428 42736 . - 0 ID=AEKKBH_00875;Name=30S ribosomal protein S10;locus_tag=AEKKBH_00875;product=30S ribosomal protein S10;Dbxref=COG:COG0051,COG:J,GO:0000049,GO:0003735,GO:0005840,GO:0006412,GO:1990904,RefSeq:WP_002817271.1,SO:0001217,UniParc:UPI0000E55402,UniRef:UniRef100_Q04G86,UniRef:UniRef50_Q7VA06,UniRef:UniRef90_Q04G86;gene=rpsJ 1183500006 Prodigal CDS 42963 43784 . - 0 ID=AEKKBH_00880;Name=Peptidoglycan-binding protein LysM;locus_tag=AEKKBH_00880;product=Peptidoglycan-binding protein LysM;Dbxref=RefSeq:WP_002822928.1,SO:0001217,UniParc:UPI000277B945,UniRef:UniRef100_UPI000277B945,UniRef:UniRef50_A0A6H3GUR8,UniRef:UniRef90_A0A6N4A894;gene=lysM 1183500006 Prodigal CDS 43941 45827 . - 0 ID=AEKKBH_00885;Name=Putative peptidoglycan O-acetyltransferase;locus_tag=AEKKBH_00885;product=Putative peptidoglycan O-acetyltransferase;Dbxref=RefSeq:WP_032811133.1,SO:0001217,UniParc:UPI00050F107F,UniRef:UniRef100_UPI00050F107F,UniRef:UniRef50_A0A483BFH8,UniRef:UniRef90_A0A483BFH8 1183500006 Prodigal CDS 45895 47670 . - 0 ID=AEKKBH_00890;Name=aspartate--tRNA ligase;locus_tag=AEKKBH_00890;product=aspartate--tRNA ligase;Dbxref=COG:COG0173,COG:J,RefSeq:WP_032821398.1,SO:0001217,UniParc:UPI00050F71E6,UniRef:UniRef100_UPI00050F71E6,UniRef:UniRef50_Q74IX4,UniRef:UniRef90_Q04G89;gene=aspS 1183500006 Prodigal CDS 47667 48935 . - 0 ID=AEKKBH_00895;Name=histidine--tRNA ligase;locus_tag=AEKKBH_00895;product=histidine--tRNA ligase;Dbxref=COG:COG0124,COG:J,EC:6.1.1.21,KEGG:K01892,RefSeq:WP_002822932.1,SO:0001217,UniParc:UPI000277B948,UniRef:UniRef100_A0A6H3GPU4,UniRef:UniRef50_Q04G90,UniRef:UniRef90_Q04G90;gene=hisS 1183500006 Prodigal CDS 48997 49926 . + 0 ID=AEKKBH_00900;Name=N-acetylmuramoyl-L-alanine amidase;locus_tag=AEKKBH_00900;product=N-acetylmuramoyl-L-alanine amidase;Dbxref=COG:COG0860,COG:M,EC:3.5.1.28,KEGG:K01448,RefSeq:WP_002822934.1,SO:0001217,UniParc:UPI000277B949,UniRef:UniRef100_A0A6H3GV26,UniRef:UniRef50_D3L859,UniRef:UniRef90_D3L859;gene=amiC 1183500006 Prodigal CDS 49975 52221 . - 0 ID=AEKKBH_00905;Name=(p)ppGpp synthase/hydrolase%2C HD superfamily;locus_tag=AEKKBH_00905;product=(p)ppGpp synthase/hydrolase%2C HD superfamily;Dbxref=COG:COG0317,COG:TK,RefSeq:WP_032820305.1,SO:0001217,UniParc:UPI00050EDC79,UniRef:UniRef100_UPI00050EDC79,UniRef:UniRef50_Q931Q4,UniRef:UniRef90_A0A483BBS2;gene=spoT 1183500006 Prodigal CDS 52208 52624 . - 0 ID=AEKKBH_00910;Name=Lipoprotein;locus_tag=AEKKBH_00910;product=Lipoprotein;Dbxref=RefSeq:WP_002818444.1,SO:0001217,UniParc:UPI0000E553FE,UniRef:UniRef100_A0A6H3GNV0,UniRef:UniRef50_G9WFG9,UniRef:UniRef90_A0A6H3GNV0 1183500006 Prodigal CDS 52631 53392 . - 0 ID=AEKKBH_00915;Name=16S rRNA U1498 N3-methylase RsmE;locus_tag=AEKKBH_00915;product=16S rRNA U1498 N3-methylase RsmE;Dbxref=COG:COG1385,COG:J,RefSeq:WP_002822939.1,SO:0001217,UniParc:UPI000277B94B,UniRef:UniRef100_A0A650C733,UniRef:UniRef50_A0A6N4RLE8,UniRef:UniRef90_Q04G94;gene=rsmE 1183500006 Prodigal CDS 53389 54468 . - 0 ID=AEKKBH_00920;Name=NADPH:quinone reductase or related Zn-dependent oxidoreductase;locus_tag=AEKKBH_00920;product=NADPH:quinone reductase or related Zn-dependent oxidoreductase;Dbxref=COG:COG0604,COG:CR,RefSeq:WP_002817262.1,SO:0001217,UniParc:UPI0000E8823B,UniRef:UniRef100_A0NJL7,UniRef:UniRef50_Q04G95,UniRef:UniRef90_Q04G95;gene=qor 1183500006 Prodigal CDS 54458 55159 . - 0 ID=AEKKBH_00925;Name=Efflux RND transporter periplasmic adaptor subunit;locus_tag=AEKKBH_00925;product=Efflux RND transporter periplasmic adaptor subunit;Dbxref=RefSeq:WP_002822940.1,SO:0001217,UniParc:UPI000277B94C,UniRef:UniRef100_UPI000277B94C,UniRef:UniRef50_Q04G97,UniRef:UniRef90_Q04G97 1183500006 Prodigal CDS 55156 57066 . - 0 ID=AEKKBH_00930;Name=translation elongation factor 4;locus_tag=AEKKBH_00930;product=translation elongation factor 4;Dbxref=COG:COG0481,COG:J,SO:0001217,UniRef:UniRef50_B7G816,UniRef:UniRef90_Q04G98;gene=lepA 1183500006 Prodigal CDS 57063 58046 . - 0 ID=AEKKBH_00935;Name=Penicillin V acylase or related amidase%2C Ntn superfamily;locus_tag=AEKKBH_00935;product=Penicillin V acylase or related amidase%2C Ntn superfamily;Dbxref=COG:COG3049,COG:MR,RefSeq:WP_002817259.1,SO:0001217,UniParc:UPI0000E8822F,UniRef:UniRef100_A0NJL4,UniRef:UniRef50_Q04G99,UniRef:UniRef90_Q04G99;gene=yxeI 1183500006 Prodigal CDS 58102 59181 . - 0 ID=AEKKBH_00940;Name=tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA;locus_tag=AEKKBH_00940;product=tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA;Dbxref=EC:2.4.99.17,KEG

lauriebelch commented 1 month ago

Hi Olivier,

I can run this GFF fine on my system (I saved it in a file and have attached it here bakta.gff.zip

Are you able to send an actual file, or email it to laurencebelcher@gmail.com , and I can take a look

Laurie

lauriebelch commented 1 month ago

OK so the problem is that the GFF file has the sequence at the end, which is breaking the code

##FASTA
>1183500001
TCTGTCATTTCGCCCTCGTATACCTGCTTAATTATAATGATCGAGTCAGTCGGCAGACAA
ATCCTGTGAGGATAATTAACACGAATCAAAGCAATCGTTAAAGTCGTAGGCTGGGCAAAA

I have an idea to fix it:

Open the script SOC_mine.py Go to lines 95-96 They are currently:

for line in open(gff):
    if line.startswith("#"):

You can try changing them to

for line in open(gff):
    if line.startswith("##FASTA"):
        break
    if line.startswith("#"):

This will tell the code to ignore any part of the GFF that is just the sequence

oclaisse commented 1 month ago

Thanks a lot, for parse part I have not completely understand about -k and -a options they are installed and I have to ask to Véronique were did she install them or not?

OK so the problem is that the GFF file has the sequence at the end, which is breaking the code

FASTA

1183500001 TCTGTCATTTCGCCCTCGTATACCTGCTTAATTATAATGATCGAGTCAGTCGGCAGACAA ATCCTGTGAGGATAATTAACACGAATCAAAGCAATCGTTAAAGTCGTAGGCTGGGCAAAA

I have an idea to fix it:

Open the script SOC_mine.py Go to lines 95-96 They are currently: for line in open(gff): if line.startswith("#"):

You can try changing them to for line in open(gff): if line.startswith("##FASTA"): break if line.startswith("#"):

This will tell the code to ignore any part of the GFF that is just the sequence

oclaisse commented 1 month ago

thanks, the code have modified and mine works

and now I want to parse and you can the issue below

SOC_parse.py -i /home/oclaisse/work/socfinder/IOEB9805_mine/ -k /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/SOCIAL_KO.csv -a /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/antismash_types.csv /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py:117: FutureWarning: The 'delim_whitespace' keyword in pd.read_table is deprecated and will be removed in a future version. Use sep='\s+' instead data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) Traceback (most recent call last): File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py", line 117, in data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1405, in read_table return _read(filepath_or_buffer, kwds) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init self._engine = self._make_engine(f, self.engine) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine return mapping[engine](f, self.options) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init self._reader = parsers.TextReader(src, **kwds) File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

Could you understand? in blast_outputs, the 3 PSORT files are empty and kofam is 5Mo

De: "lauriebelch" @.> À: "lauriebelch/SOCfinder" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Mercredi 7 Août 2024 15:28:49 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

OK so the problem is that the GFF file has the sequence at the end, which is breaking the code

FASTA

1183500001 TCTGTCATTTCGCCCTCGTATACCTGCTTAATTATAATGATCGAGTCAGTCGGCAGACAA ATCCTGTGAGGATAATTAACACGAATCAAAGCAATCGTTAAAGTCGTAGGCTGGGCAAAA

I have an idea to fix it:

Open the script SOC_mine.py Go to lines 95-96 They are currently: for line in open(gff): if line.startswith("#"):

You can try changing them to for line in open(gff): if line.startswith("##FASTA"): break if line.startswith("#"):

This will tell the code to ignore any part of the GFF that is just the sequence

— Reply to this email directly, [ https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273477599 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AXUIJN7EVUZCIVFFQVTOLEDZQIOJDAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGQ3TONJZHE | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

lauriebelch commented 1 month ago

Hi Olivier,

For this error, try rebuilding the blast databases

Go to the SOCfinder folder, and

cd blast_files unzip Archive.zipcd .. chmod +x ./SOC_MakeBlastDB.py ./SOC_MakeBlastDB.py

On Wed, 7 Aug 2024 at 15:29, oclaisse @.***> wrote:

thanks, the code have modified and mine works

and now I want to parse and you can the issue below

SOC_parse.py -i /home/oclaisse/work/socfinder/IOEB9805_mine/ -k /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/SOCIAL_KO.csv -a /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/antismash_types.csv

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py:117: FutureWarning: The 'delim_whitespace' keyword in pd.read_table is deprecated and will be removed in a future version. Use sep='\s+' instead data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) Traceback (most recent call last): File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py", line 117, in data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1405, in read_table return _read(filepath_or_buffer, kwds) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init self._engine = self._make_engine(f, self.engine) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine return mapping[engine](f, self.options) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init self._reader = parsers.TextReader(src, **kwds) File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

Could you understand? in blast_outputs, the 3 PSORT files are empty and kofam is 5Mo

De: "lauriebelch" @.> À: "lauriebelch/SOCfinder" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Mercredi 7 Août 2024 15:28:49 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

OK so the problem is that the GFF file has the sequence at the end, which is breaking the code

FASTA

1183500001 TCTGTCATTTCGCCCTCGTATACCTGCTTAATTATAATGATCGAGTCAGTCGGCAGACAA ATCCTGTGAGGATAATTAACACGAATCAAAGCAATCGTTAAAGTCGTAGGCTGGGCAAAA

I have an idea to fix it:

Open the script SOC_mine.py Go to lines 95-96 They are currently: for line in open(gff): if line.startswith("#"):

You can try changing them to for line in open(gff): if line.startswith("##FASTA"): break if line.startswith("#"):

This will tell the code to ignore any part of the GFF that is just the sequence

— Reply to this email directly, [ https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273477599 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AXUIJN7EVUZCIVFFQVTOLEDZQIOJDAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGQ3TONJZHE | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273615415, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFRKNHJI3REOMQ5RKXRFBZDZQIVMNAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGYYTKNBRGU . You are receiving this because you commented.Message ID: @.***>

oclaisse commented 1 month ago

Hi Laurence, we made the process and try again to mine, this produce the same results. Veronique suggest to add the path of the blast file?

De: "lauriebelch" @.> À: "lauriebelch" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Jeudi 8 Août 2024 14:21:35 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

Hi Olivier,

For this error, try rebuilding the blast databases

Go to the SOCfinder folder, and

cd blast_files unzip Archive.zipcd .. chmod +x ./SOC_MakeBlastDB.py ./SOC_MakeBlastDB.py

On Wed, 7 Aug 2024 at 15:29, oclaisse @.***> wrote:

thanks, the code have modified and mine works

and now I want to parse and you can the issue below

SOC_parse.py -i /home/oclaisse/work/socfinder/IOEB9805_mine/ -k /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/SOCIAL_KO.csv -a /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/antismash_types.csv

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py:117: FutureWarning: The 'delim_whitespace' keyword in pd.read_table is deprecated and will be removed in a future version. Use sep='\s+' instead data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) Traceback (most recent call last): File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py", line 117, in data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1405, in read_table return _read(filepath_or_buffer, kwds) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init self._engine = self._make_engine(f, self.engine) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine return mapping[engine](f, self.options) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init self._reader = parsers.TextReader(src, **kwds) File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

Could you understand? in blast_outputs, the 3 PSORT files are empty and kofam is 5Mo

De: "lauriebelch" @.> À: "lauriebelch/SOCfinder" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Mercredi 7 Août 2024 15:28:49 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

OK so the problem is that the GFF file has the sequence at the end, which is breaking the code

FASTA

1183500001 TCTGTCATTTCGCCCTCGTATACCTGCTTAATTATAATGATCGAGTCAGTCGGCAGACAA ATCCTGTGAGGATAATTAACACGAATCAAAGCAATCGTTAAAGTCGTAGGCTGGGCAAAA

I have an idea to fix it:

Open the script SOC_mine.py Go to lines 95-96 They are currently: for line in open(gff): if line.startswith("#"):

You can try changing them to for line in open(gff): if line.startswith("##FASTA"): break if line.startswith("#"):

This will tell the code to ignore any part of the GFF that is just the sequence

— Reply to this email directly, [ https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273477599 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AXUIJN7EVUZCIVFFQVTOLEDZQIOJDAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGQ3TONJZHE | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273615415, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFRKNHJI3REOMQ5RKXRFBZDZQIVMNAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGYYTKNBRGU . You are receiving this because you commented.Message ID: @.***>

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oclaisse commented 1 month ago

We have try to do it but it doesn't work either

De: "Olivier Claisse" @.> À: "lauriebelch" @.> Cc: "veronique martin" @.***> Envoyé: Jeudi 8 Août 2024 15:18:36 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

Hi Laurence, we made the process and try again to mine, this produce the same results. Veronique suggest to add the path of the blast file?

De: "lauriebelch" @.> À: "lauriebelch" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Jeudi 8 Août 2024 14:21:35 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

Hi Olivier,

For this error, try rebuilding the blast databases

Go to the SOCfinder folder, and

cd blast_files unzip Archive.zipcd .. chmod +x ./SOC_MakeBlastDB.py ./SOC_MakeBlastDB.py

On Wed, 7 Aug 2024 at 15:29, oclaisse @.***> wrote:

thanks, the code have modified and mine works

and now I want to parse and you can the issue below

SOC_parse.py -i /home/oclaisse/work/socfinder/IOEB9805_mine/ -k /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/SOCIAL_KO.csv -a /usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/antismash_types.csv

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py:117: FutureWarning: The 'delim_whitespace' keyword in pd.read_table is deprecated and will be removed in a future version. Use sep='\s+' instead data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) Traceback (most recent call last): File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py", line 117, in data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1405, in read_table return _read(filepath_or_buffer, kwds) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init self._engine = self._make_engine(f, self.engine) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine return mapping[engine](f, self.options) File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init self._reader = parsers.TextReader(src, **kwds) File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

Could you understand? in blast_outputs, the 3 PSORT files are empty and kofam is 5Mo

De: "lauriebelch" @.> À: "lauriebelch/SOCfinder" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Mercredi 7 Août 2024 15:28:49 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

OK so the problem is that the GFF file has the sequence at the end, which is breaking the code

FASTA

1183500001 TCTGTCATTTCGCCCTCGTATACCTGCTTAATTATAATGATCGAGTCAGTCGGCAGACAA ATCCTGTGAGGATAATTAACACGAATCAAAGCAATCGTTAAAGTCGTAGGCTGGGCAAAA

I have an idea to fix it:

Open the script SOC_mine.py Go to lines 95-96 They are currently: for line in open(gff): if line.startswith("#"):

You can try changing them to for line in open(gff): if line.startswith("##FASTA"): break if line.startswith("#"):

This will tell the code to ignore any part of the GFF that is just the sequence

— Reply to this email directly, [ https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273477599 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AXUIJN7EVUZCIVFFQVTOLEDZQIOJDAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGQ3TONJZHE | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273615415, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFRKNHJI3REOMQ5RKXRFBZDZQIVMNAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGYYTKNBRGU . You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, [ https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2275686876 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AXUIJNZG5E3HTDDJDURTDPTZQNPE7AVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZVGY4DMOBXGY | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

lauriebelch commented 1 month ago

lets try just the blast command on its own

blastp -db blast_databases/blastdbCExtra -query bakta/IOEB_9805.faa -evalue 10e-8 -outfmt "6 sseqid qacc qlen evalue bitscore sstart send slen" -out test1/blast_outputs/file_PSORT_E.txt -num_threads 16

replacing the inout bakta/IOEB_9805.faa an d the output test1/blast_outputs/file_PSORT_E.txt

On Thu, 8 Aug 2024 at 15:11, oclaisse @.***> wrote:

We have try to do it but it doesn't work either

De: "Olivier Claisse" @.> À: "lauriebelch" @.> Cc: "veronique martin" @.***> Envoyé: Jeudi 8 Août 2024 15:18:36 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

Hi Laurence, we made the process and try again to mine, this produce the same results. Veronique suggest to add the path of the blast file?

De: "lauriebelch" @.> À: "lauriebelch" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Jeudi 8 Août 2024 14:21:35 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

Hi Olivier,

For this error, try rebuilding the blast databases

Go to the SOCfinder folder, and

cd blast_files unzip Archive.zipcd .. chmod +x ./SOC_MakeBlastDB.py ./SOC_MakeBlastDB.py

On Wed, 7 Aug 2024 at 15:29, oclaisse @.***> wrote:

thanks, the code have modified and mine works

and now I want to parse and you can the issue below

SOC_parse.py -i /home/oclaisse/work/socfinder/IOEB9805_mine/ -k

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/SOCIAL_KO.csv

-a

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/antismash_types.csv

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py:117: FutureWarning: The 'delim_whitespace' keyword in pd.read_table is deprecated and will be removed in a future version. Use sep='\s+' instead data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) Traceback (most recent call last): File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py", line 117, in data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py",

line 1405, in read_table return _read(filepath_or_buffer, kwds) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py",

line 620, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py",

line 1620, in init self._engine = self._make_engine(f, self.engine) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py",

line 1898, in _make_engine return mapping[engine](f, **self.options) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py",

line 93, in init self._reader = parsers.TextReader(src, **kwds) File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

Could you understand? in blast_outputs, the 3 PSORT files are empty and kofam is 5Mo

De: "lauriebelch" @.> À: "lauriebelch/SOCfinder" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Mercredi 7 Août 2024 15:28:49 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

OK so the problem is that the GFF file has the sequence at the end, which is breaking the code

FASTA

1183500001 TCTGTCATTTCGCCCTCGTATACCTGCTTAATTATAATGATCGAGTCAGTCGGCAGACAA ATCCTGTGAGGATAATTAACACGAATCAAAGCAATCGTTAAAGTCGTAGGCTGGGCAAAA

I have an idea to fix it:

Open the script SOC_mine.py Go to lines 95-96 They are currently: for line in open(gff): if line.startswith("#"):

You can try changing them to for line in open(gff): if line.startswith("##FASTA"): break if line.startswith("#"):

This will tell the code to ignore any part of the GFF that is just the sequence

— Reply to this email directly, [

https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273477599 | view it on GitHub ] , or [

https://github.com/notifications/unsubscribe-auth/AXUIJN7EVUZCIVFFQVTOLEDZQIOJDAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGQ3TONJZHE | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

— Reply to this email directly, view it on GitHub < https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273615415>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/AFRKNHJI3REOMQ5RKXRFBZDZQIVMNAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGYYTKNBRGU>

. You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, [ https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2275686876 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AXUIJNZG5E3HTDDJDURTDPTZQNPE7AVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZVGY4DMOBXGY | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2275934687, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFRKNHPP6W6GORUQMN6G3WLZQN4CXAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZVHEZTINRYG4 . You are receiving this because you commented.Message ID: @.***>

oclaisse commented 1 month ago

Hi Laurence, here you can find the output Sincerely

De: "lauriebelch" @.> À: "lauriebelch" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Jeudi 8 Août 2024 16:22:30 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

lets try just the blast command on its own

blastp -db blast_databases/blastdbCExtra -query bakta/IOEB_9805.faa -evalue 10e-8 -outfmt "6 sseqid qacc qlen evalue bitscore sstart send slen" -out test1/blast_outputs/file_PSORT_E.txt -num_threads 16

replacing the inout bakta/IOEB_9805.faa an d the output test1/blast_outputs/file_PSORT_E.txt

On Thu, 8 Aug 2024 at 15:11, oclaisse @.***> wrote:

We have try to do it but it doesn't work either

De: "Olivier Claisse" @.> À: "lauriebelch" @.> Cc: "veronique martin" @.***> Envoyé: Jeudi 8 Août 2024 15:18:36 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

Hi Laurence, we made the process and try again to mine, this produce the same results. Veronique suggest to add the path of the blast file?

De: "lauriebelch" @.> À: "lauriebelch" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Jeudi 8 Août 2024 14:21:35 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

Hi Olivier,

For this error, try rebuilding the blast databases

Go to the SOCfinder folder, and

cd blast_files unzip Archive.zipcd .. chmod +x ./SOC_MakeBlastDB.py ./SOC_MakeBlastDB.py

On Wed, 7 Aug 2024 at 15:29, oclaisse @.***> wrote:

thanks, the code have modified and mine works

and now I want to parse and you can the issue below

SOC_parse.py -i /home/oclaisse/work/socfinder/IOEB9805_mine/ -k

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/SOCIAL_KO.csv

-a

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/SOCfinder/inputs/antismash_types.csv

/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py:117: FutureWarning: The 'delim_whitespace' keyword in pd.read_table is deprecated and will be removed in a future version. Use sep='\s+' instead data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) Traceback (most recent call last): File "/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/bin/SOC_parse.py", line 117, in data = pd.read_table(blaste_output_filename, header=None, delim_whitespace=True) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py",

line 1405, in read_table return _read(filepath_or_buffer, kwds) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py",

line 620, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py",

line 1620, in init self._engine = self._make_engine(f, self.engine) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/readers.py",

line 1898, in _make_engine return mapping[engine](f, **self.options) File

"/usr/local/genome/Anaconda3/envs/socfinder-1.0.1/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py",

line 93, in init self._reader = parsers.TextReader(src, **kwds) File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

Could you understand? in blast_outputs, the 3 PSORT files are empty and kofam is 5Mo

De: "lauriebelch" @.> À: "lauriebelch/SOCfinder" @.> Cc: "Olivier Claisse" @.>, "Author" @.> Envoyé: Mercredi 7 Août 2024 15:28:49 Objet: Re: [lauriebelch/SOCfinder] not enough value (Issue #6)

OK so the problem is that the GFF file has the sequence at the end, which is breaking the code

FASTA

1183500001 TCTGTCATTTCGCCCTCGTATACCTGCTTAATTATAATGATCGAGTCAGTCGGCAGACAA ATCCTGTGAGGATAATTAACACGAATCAAAGCAATCGTTAAAGTCGTAGGCTGGGCAAAA

I have an idea to fix it:

Open the script SOC_mine.py Go to lines 95-96 They are currently: for line in open(gff): if line.startswith("#"):

You can try changing them to for line in open(gff): if line.startswith("##FASTA"): break if line.startswith("#"):

This will tell the code to ignore any part of the GFF that is just the sequence

— Reply to this email directly, [

https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273477599 | view it on GitHub ] , or [

https://github.com/notifications/unsubscribe-auth/AXUIJN7EVUZCIVFFQVTOLEDZQIOJDAVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGQ3TONJZHE | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

— Reply to this email directly, view it on GitHub < https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2273615415>,

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— Reply to this email directly, [ https://github.com/lauriebelch/SOCfinder/issues/6#issuecomment-2275686876 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AXUIJNZG5E3HTDDJDURTDPTZQNPE7AVCNFSM6AAAAABMEGLZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZVGY4DMOBXGY | unsubscribe ] . You are receiving this because you authored the thread. Message ID: @.***>

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sp|P49331| AEKKBH_01120 1100 0.0 1132 6 1087 1462 sp|P08987| AEKKBH_01120 1100 0.0 1001 2 1058 1476 sp|P11001| AEKKBH_01120 1100 0.0 995 6 1059 1597 sp|P27470| AEKKBH_01120 1100 0.0 986 2 1052 1592 sp|P13470| AEKKBH_01120 1100 0.0 985 110 1082 1455 sp|P08987| AEKKBH_01125 376 1.07e-98 315 1106 1471 1476 sp|P08987| AEKKBH_01125 376 1.28e-65 221 1169 1473 1476 sp|P08987| AEKKBH_01125 376 3.56e-56 193 1072 1341 1476 sp|P49331| AEKKBH_01125 376 6.71e-78 256 1105 1437 1462 sp|P49331| AEKKBH_01125 376 1.40e-77 255 1136 1447 1462 sp|P49331| AEKKBH_01125 376 8.43e-61 207 1099 1375 1462 sp|P49331| AEKKBH_01125 376 2.87e-33 126 1087 1308 1462 sp|P11001| AEKKBH_01125 376 3.47e-69 231 1108 1570 1597 sp|P11001| AEKKBH_01125 376 1.10e-53 186 1079 1343 1597 sp|P11001| AEKKBH_01125 376 1.62e-51 180 1080 1456 1597 sp|P11001| AEKKBH_01125 376 2.22e-51 179 1171 1592 1597 sp|P11001| AEKKBH_01125 376 9.68e-30 116 1079 1279 1597 sp|P27470| AEKKBH_01125 376 7.31e-68 227 1102 1565 1592 sp|P27470| AEKKBH_01125 376 1.88e-53 186 1050 1452 1592 sp|P27470| AEKKBH_01125 376 7.54e-52 181 1166 1587 1592 sp|P27470| AEKKBH_01125 376 5.81e-26 105 1095 1277 1592 sp|P13470| AEKKBH_01125 376 2.10e-63 214 1107 1410 1455 sp|P13470| AEKKBH_01125 376 1.59e-62 212 1135 1409 1455 sp|P13470| AEKKBH_01125 376 6.27e-52 181 1101 1368 1455 sp|P39046| AEKKBH_01580 291 1.12e-20 87.0 65 214 666 sp|Q9ZEU2| AEKKBH_02020 548 2.84e-25 105 118 301 636 sp|P26827| AEKKBH_02020 548 8.59e-17 78.6 38 259 710 sp|Q05884| AEKKBH_02020 548 2.44e-14 70.9 98 467 919 sp|P21543| AEKKBH_02020 548 1.52e-13 68.6 783 1080 1196 sp|P17692| AEKKBH_02020 548 2.08e-13 67.8 38 258 713 sp|Q60053| AEKKBH_02020 548 2.82e-13 67.4 217 306 666 dbj|BAB18101| AEKKBH_02020 548 6.06e-13 66.2 42 266 739 sp|P39046| AEKKBH_02160 430 2.86e-08 50.8 549 665 666 sp|P39046| AEKKBH_02160 430 3.29e-08 50.4 473 607 666 sp|P39046| AEKKBH_02160 430 5.03e-08 50.1 407 531 666 sp|P39046| AEKKBH_03235 208 1.79e-20 84.0 73 197 666 sp|P21130| AEKKBH_03820 956 3.07e-80 264 43 470 472 sp|P11701| AEKKBH_03820 956 3.44e-79 270 5 634 795 sp|P05655| AEKKBH_03820 956 7.02e-79 260 44 470 473 sp|Q55242| AEKKBH_03820 956 4.57e-76 264 93 682 969 sp|P94468| AEKKBH_03820 956 4.57e-75 249 44 470 473 sp|Q46654| AEKKBH_03820 956 3.16e-17 80.1 129 398 415 sp|O52408| AEKKBH_03820 956 6.35e-17 79.3 129 397 415 sp|Q60114| AEKKBH_03820 956 1.72e-16 77.8 46 390 423 sp|O68609| AEKKBH_03820 956 3.97e-15 73.9 145 413 431 sp|Q43998| AEKKBH_03820 956 1.85e-11 62.8 34 489 584 sp|Q04707| AEKKBH_04000 646 2.40e-59 207 55 631 719 sp|Q07259| AEKKBH_04000 646 3.29e-28 108 50 217 231 sp|P13692| AEKKBH_04600 423 4.81e-36 134 416 513 516 sp|P21171| AEKKBH_04600 423 2.24e-16 75.9 384 467 484 sp|P39046| AEKKBH_04600 423 2.99e-14 69.7 322 451 666 sp|P39046| AEKKBH_04600 423 1.11e-12 64.7 484 620 666 sp|P39046| AEKKBH_04600 423 9.41e-11 58.5 554 660 666 sp|P39046| AEKKBH_04600 423 6.42e-09 52.8 259 375 666 sp|P30234| AEKKBH_05040 392 2.68e-27 106 13 323 371 sp|P15555| AEKKBH_05110 337 3.10e-11 58.9 82 229 406 sp|P39046| AEKKBH_05265 218 3.48e-23 92.0 65 214 666 sp|O25001| AEKKBH_05545 275 7.95e-11 56.2 29 240 250 sp|Q04707| AEKKBH_06170 881 7.52e-141 431 3 651 719 sp|Q07259| AEKKBH_06170 881 3.07e-33 123 48 226 231 sp|P21158| AEKKBH_07020 224 3.94e-09 49.3 13 148 166 sp|P82593| AEKKBH_07080 507 3.89e-14 70.1 223 441 825 sp|Q9ZEU2| AEKKBH_07760 556 7.85e-19 85.1 118 304 636 sp|P21543| AEKKBH_07760 556 6.84e-16 76.3 783 950 1196 sp|Q60053| AEKKBH_07760 556 2.70e-15 73.9 158 334 666 sp|Q05884| AEKKBH_07760 556 5.38e-15 73.2 98 186 919 sp|P17692| AEKKBH_07760 556 5.43e-15 72.8 33 258 713 sp|P26827| AEKKBH_07760 556 8.44e-14 68.9 33 259 710 sp|P36175| AEKKBH_08240 341 1.64e-66 208 3 319 325 sp|P36175| AEKKBH_08250 241 2.97e-10 54.3 1 99 325 sp|Q93M42| AEKKBH_08305 795 1.03e-126 392 17 755 759 sp|P13692| AEKKBH_08440 415 1.52e-16 76.3 406 502 516 sp|P21171| AEKKBH_08440 415 4.41e-08 50.1 373 457 484 sp|Q9KJT6| AEKKBH_08445 370 1.77e-13 65.1 150 257 257 sp|P39046| AEKKBH_08445 370 2.84e-11 59.7 259 377 666 sp|P39046| AEKKBH_08445 370 1.54e-10 57.4 488 613 666 sp|P39046| AEKKBH_08445 370 4.69e-10 55.8 339 487 666 sp|P39046| AEKKBH_08445 370 4.47e-09 52.8 566 665 666 sp|P39046| AEKKBH_08620 520 6.36e-14 69.3 534 664 666 sp|P39046| AEKKBH_08620 520 2.70e-13 67.4 304 455 666 sp|P39046| AEKKBH_08620 520 7.29e-13 65.9 403 530 666 sp|P39046| AEKKBH_08620 520 1.32e-12 65.1 472 601 666 sp|P34020| AEKKBH_09035 354 4.50e-10 55.1 1 180 324 sp|P25310| AEKKBH_09035 354 1.70e-09 53.1 82 290 294 sp|P0C1R4| AEKKBH_09355 231 1.18e-45 157 221 387 1255 sp|P52081| AEKKBH_09355 231 7.46e-45 155 204 388 1256 sp|O33635| AEKKBH_09355 231 2.35e-43 150 287 485 1335

lauriebelch commented 1 month ago

Hi Olivier,

Hmm those blast files look completely normal, SOC_parse should work fine on those. Perhaps if you send me the whole output folder that you get from SOC_mine, I could take a look

Laurie

oclaisse commented 1 month ago

I can send you the kofam.txt (5Mo) if it can help? but in the blast_outputs the 3 .txt files PSORT, PSORT_E and PSORT_NE are completly empty

Hi Olivier,

Hmm those blast files look completely normal, SOC_parse should work fine on those. Perhaps if you send me the whole output folder that you get from SOC_mine, I could take a look

Laurie

lauriebelch commented 1 month ago

That's strange, because the output from the command before shows that the blast is working. I think I would need to see the full output folder, and the command that was run

lauriebelch commented 1 month ago

We can try and manually make those files

blast to gram

blastp -db blast_databases/blastdbP -query /home/oclaisse/work/bakta/selected_vepivici_output_bakta/IOEB_9805/IOEB_9805.faa -evalue 10e-8 -outfmt "6 sseqid qacc qlen evalue bitscore sstart send slen" -out home/oclaisse/work/socfinder/IOEB9805_mine/file_PSORT.txt -num_threads 16

blast to proven extracellular

blastp -db blast_databases/blastdbCExtra -query /home/oclaisse/work/bakta/selected_vepivici_output_bakta/IOEB_9805/IOEB_9805.faa -evalue 10e-8 -outfmt "6 sseqid qacc qlen evalue bitscore sstart send slen" -out home/oclaisse/work/socfinder/IOEB9805_mine/file_PSORT_E.txt -num_threads 16

blast to proven non-extracellular

blastp -db blast_databases/blastdbCNonExtra -query /home/oclaisse/work/bakta/selected_vepivici_output_bakta/IOEB_9805/IOEB_9805.faa -evalue 10e-8 -outfmt "6 sseqid qacc qlen evalue bitscore sstart send slen" -out home/oclaisse/work/socfinder/IOEB9805_mine/file_PSORT_NE.txt -num_threads 16

lauriebelch commented 1 month ago

OK I think this is getting closer

try running conda install -c bioconda diamond=0.9.14

and then do the SOC_mine step again, and then the SOC_parse step

oclaisse commented 1 month ago

it was done but it do not change anything :(