search

hallamlab / MetaPathways

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information
http://hallam.microbiology.ubc.ca/MetaPathways
12 stars 7 forks source link

Step 11 (annotate gff files) error #36

Closed maepz closed 7 years ago

maepz commented 10 years ago

Hi there, The pipeline seem to run fine until I reach step 11: Here is the error from the meta_paths_run_log.txt

screen shot 2014-02-25 at 3 23 21 pm

I run MetaPathways_1_0, on mac OS X 10.9

hallamlab commented 10 years ago

Hi, Have you tried our MetaPathways version 2.0? Let me know if you would like to try probably this issue will not be a problem. Otherwise, I can look into it if you share with me the input files for this step.

Regards Kishori

maepz commented 10 years ago

Hi Kishori, I did try to run the pipeline with the 2.0 version but for some obscure reason it doesn't work on my computer. Michael Wu and I exchanged emails last week about that but we were not able to find a solution the the problem. I attached the input file for this step:regression_test.unannot.gffregression_test.metacyc.blastout.parsed.txtregression_test.cog.blastout.parsed.txt And the python script for this step:MetaPathways_annotate_fast.py Let me know if you need anything else Yours. Maeva Date: Tue, 25 Feb 2014 16:49:55 -0800 From: notifications@github.com To: MetaPathways@noreply.github.com CC: maepz@hotmail.com Subject: Re: [MetaPathways] Step 11 (annotate gff files) error (#36)

Hi,

Have you tried our MetaPathways version 2.0? Let me know if you would like to try probably this issue will not be a problem. Otherwise, I can look into it if you share with me the input files for this step.

Regards

Kishori

— Reply to this email directly or view it on GitHub.

query q_length bitscore bsr expect aln_length identity ec product

regression_test_21_0 479 2061 0.802882742501 0.0 479.0 100.0
regression_test_21_0 476 1888 0.735488897546 0.0 476.0 100.0
regression_test_21_0 478 1846 0.719127386054 0.0 478.0 100.0
regression_test_21_0 423 905 0.352551616673 0.0 423.0 100.0
regression_test_21_0 373 853 0.332294507207 0.0 373.0 100.0
regression_test_7_0 223 820 0.605612998523 0.0 223.0 100.0
regression_test_7_0 191 773 0.570901033973 0.0 191.0 100.0
regression_test_7_0 191 765 0.564992614476 0.0 191.0 100.0
regression_test_7_0 191 765 0.564992614476 0.0 191.0 100.0
regression_test_7_0 191 765 0.564992614476 0.0 191.0 100.0
regression_test_11_0 257 693 0.491838183109 0.0 257.0 100.0
regression_test_11_0 257 693 0.491838183109 0.0 257.0 100.0
regression_test_19_0 279 648 0.46385110952 0.0 279.0 100.0
regression_test_19_0 272 625 0.447387258411 0.0 272.0 100.0
regression_test_19_0 287 623 0.445955619184 0.0 287.0 100.0
regression_test_19_0 271 612 0.438081603436 0.0 271.0 100.0
regression_test_19_0 265 586 0.419470293486 0.0 265.0 100.0
regression_test_14_0 186 518 0.483660130719 0.0 186.0 100.0
regression_test_14_0 204 501 0.467787114846 0.0 204.0 100.0
regression_test_17_0 231 499 0.39666136725 0.0 231.0 100.0
regression_test_17_0 236 497 0.39507154213 0.0 236.0 100.0
regression_test_17_0 239 496 0.394276629571 0.0 239.0 100.0
regression_test_16_0 226 490 0.419520547945 0.0 226.0 100.0
regression_test_9_0 265 488 0.341497550735 0.0 265.0 100.0
regression_test_16_0 224 485 0.415239726027 0.0 224.0 100.0
regression_test_16_0 223 484 0.414383561644 0.0 223.0 100.0
regression_test_17_0 236 483 0.383942766296 0.0 236.0 100.0
regression_test_17_0 231 482 0.383147853736 0.0 231.0 100.0
regression_test_22_0 117 480 0.774193548387 0.0 117.0 100.0
regression_test_22_0 117 479 0.772580645161 0.0 117.0 100.0
regression_test_9_0 265 477 0.333799860042 0.0 265.0 100.0
regression_test_16_0 229 475 0.406678082192 0.0 229.0 100.0
regression_test_16_0 224 473 0.404965753425 0.0 224.0 100.0
regression_test_9_0 279 472 0.330300909727 0.0 279.0 100.0
regression_test_9_0 277 471 0.329601119664 0.0 277.0 100.0
regression_test_15_0 215 469 0.426751592357 0.0 215.0 100.0
regression_test_9_0 261 467 0.326801959412 0.0 261.0 100.0
regression_test_22_0 117 466 0.751612903226 0.0 117.0 100.0
regression_test_14_0 207 459 0.428571428571 0.0 207.0 100.0
regression_test_15_0 210 459 0.417652411283 0.0 210.0 100.0
regression_test_14_0 204 459 0.428571428571 0.0 204.0 100.0
regression_test_22_0 117 458 0.738709677419 0.0 117.0 100.0
regression_test_14_0 205 456 0.425770308123 0.0 205.0 100.0
regression_test_18_0 213 454 0.391042204996 0.0 213.0 100.0
regression_test_15_0 217 452 0.411282984531 0.0 217.0 100.0
regression_test_15_0 210 452 0.411282984531 0.0 210.0 100.0
regression_test_18_0 212 449 0.386735572782 0.0 212.0 100.0
regression_test_15_0 215 448 0.407643312102 0.0 215.0 100.0
regression_test_18_0 213 444 0.382428940568 0.0 213.0 100.0
regression_test_22_0 116 442 0.712903225806 0.0 116.0 100.0
regression_test_11_0 251 442 0.313697657913 0.0 251.0 100.0
regression_test_18_0 210 441 0.37984496124 0.0 210.0 100.0
regression_test_18_0 213 437 0.376399655469 0.0 213.0 100.0
regression_test_11_0 255 390 0.2767920511 0.0 255.0 100.0
regression_test_11_0 245 378 0.268275372605 0.0 245.0 100.0
regression_test_5_0 105 371 0.661319073084 0.0 105.0 100.0
regression_test_8_0 184 371 0.378958120531 0.0 184.0 100.0
regression_test_5_0 105 289 0.515151515152 0.0 105.0 100.0
regression_test_12_0 192 280 0.258064516129 0.0 192.0 100.0
regression_test_5_1 74 198 0.409090909091 0.0 74.0 100.0
regression_test_8_0 143 178 0.181818181818 0.0 143.0 100.0
regression_test_8_0 160 177 0.180796731359 0.0 160.0 100.0
regression_test_8_0 162 160 0.163432073544 0.0 162.0 100.0
regression_test_8_0 140 146 0.149131767109 0.0 140.0 100.0
regression_test_5_0 99 135 0.24064171123 0.0 99.0 100.0
regression_test_5_0 99 122 0.217468805704 0.0 99.0 100.0
regression_test_12_0 63 106 0.0976958525346 0.0 63.0 100.0
regression_test_5_0 107 105 0.187165775401 0.0 107.0 100.0
regression_test_12_0 60 104 0.0958525345622 0.0 60.0 100.0

query q_length bitscore bsr expect aln_length identity ec product

regression_test_21_0 482 1851 0.721075185041 0.0 482.0 100.0 1.18.6.1 Nitrogenase molybdenum-iron protein alpha chain OS=Rhizobium sp. (strain NGR234) GN=nifD1 PE=3 SV=2 # UNIPROT # P19066 # NITROGENASE-RXN # # 1.18.6.1 regression_test_21_0 379 902 0.351382937281 0.0 379.0 100.0 1.18.6.1 Nitrogenase molybdenum-iron protein alpha chain OS=Methanosarcina barkeri GN=nifD2 PE=3 SV=1 # UNIPROT # P55170 # NITROGENASE-RXN # # 1.18.6.1 regression_test_21_0 457 819 0.319049474094 0.0 457.0 100.0 1.18.6.1 # UNIPROT # P71526 # NITROGENASE-RXN # # 1.18.6.1 regression_test_21_0 454 807 0.314374756525 0.0 454.0 100.0 1.18.6.1 Nitrogenase molybdenum-iron protein alpha chain OS=Methanococcus thermolithotrophicus GN=nifD PE=3 SV=1 # UNIPROT # P20620 # NITROGENASE-RXN # # 1.18.6.1 regression_test_21_0 375 788 0.306973120374 0.0 375.0 100.0 1.18.6.1 Nitrogenase molybdenum-iron protein alpha chain OS=Clostridium pasteurianum GN=nifD PE=1 SV=2 # UNIPROT # P00467 # NITROGENASE-RXN # MetaCyc:NIFDCP-MONOMER # 1.18.6.1 regression_test_19_0 274 617 0.441660701503 0.0 274.0 100.0 2.3.1.61 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex OS=Bartonella vinsonii subsp. berkhofii GN=sucB PE=3 SV=1 # UNIPROT # Q8GCY1 # RXN0-1147 # # 2.3.1.61 regression_test_12_0 191 538 0.495852534562 0.0 191.0 100.0 4.1.1.31 Phosphoenolpyruvate carboxylase OS=Synechococcus sp. (strain WH8102) GN=ppc PE=3 SV=1 # UNIPROT # Q7U4M0 # PEPCARBOX-RXN # SSP84588:SYNW2047OR2767-MONOMER # 4.1.1.31 regression_test_19_0 277 514 0.367931281317 0.0 277.0 100.0 2.3.1.61 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex OS=Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) GN=sucB PE=3 SV=1 # UNIPROT # P52993 # RXN0-1147 # REUT381666:H16_A2324-MONOMER # 2.3.1.61 regression_test_17_0 231 507 0.403020667727 0.0 231.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Rickettsia typhi GN=ppdK PE=3 SV=1 # UNIPROT # Q68WP2 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # RTYP257363:RT0478-MONOMER # 2.7.9.1 regression_test_16_0 226 498 0.426369863014 0.0 226.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Rickettsia typhi GN=ppdK PE=3 SV=1 # UNIPROT # Q68WP2 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # RTYP257363:RT0478-MONOMER # 2.7.9.1 regression_test_9_0 257 489 0.342197340798 0.0 257.0 100.0 6.2.1.13 Branched-chain acyl-CoA synthetase (ADP-forming) alpha subunit ;acetyl-CoA synthetase (ADP-forming) alpha subunit OS=Ignisphaera aggregans (strain DSM 17230 / JCM 13409 / AQ1.S1) GN=Igag_1585 PE=4 SV=1 # UNIPROT # E0SRD3 # ACETATE--COA-LIGASE-ADP-FORMING-RXN # # 6.2.1.13 regression_test_22_0 117 474 0.764516129032 0.0 117.0 100.0 1.18.6.1 Nitrogenase iron protein OS=Cyanothece sp. (strain ATCC 51142) GN=nifH PE=3 SV=1 # UNIPROT # O07641 # NITROGENASE-RXN # # 1.18.6.1 regression_test_17_0 237 472 0.37519872814 0.0 237.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase 1, chloroplastic OS=Arabidopsis thaliana GN=PPDK PE=1 SV=2 # UNIPROT # O23404 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_9_0 254 467 0.326801959412 0.0 254.0 100.0 6.2.1.13 Acetyl-CoA synthetase (ADP forming), alpha chain (AcdA) OS=Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) GN=acdA-2 PE=4 SV=1 # UNIPROT # C5A3H6 # ACETATE--COA-LIGASE-ADP-FORMING-RXN # # 6.2.1.13 regression_test_15_0 209 464 0.42220200182 0.0 209.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Rickettsia typhi GN=ppdK PE=3 SV=1 # UNIPROT # Q68WP2 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # RTYP257363:RT0478-MONOMER # 2.7.9.1 regression_test_16_0 226 464 0.397260273973 0.0 226.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase 1, chloroplastic OS=Arabidopsis thaliana GN=PPDK PE=1 SV=2 # UNIPROT # O23404 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_18_0 212 457 0.393626184324 0.0 212.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Rickettsia typhi GN=ppdK PE=3 SV=1 # UNIPROT # Q68WP2 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # RTYP257363:RT0478-MONOMER # 2.7.9.1 regression_test_14_0 205 452 0.422035480859 0.0 205.0 100.0 1.1.1.40 NADP-dependent malic enzyme OS=Salmonella typhimurium GN=maeB PE=3 SV=2 # UNIPROT # Q9ZFV8 # MALIC-NADP-RXN # STYP99287:STM2472-MONOMER # 1.1.1.40 regression_test_9_0 276 452 0.316305108467 0.0 276.0 100.0 6.2.1.13 Acetyl-CoA synthetase (ADP forming), alpha chain (AcdA) OS=Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) GN=acdA-4 PE=4 SV=1 # UNIPROT # C5A4T1 # ACETATE--COA-LIGASE-ADP-FORMING-RXN # # 6.2.1.13 regression_test_9_0 261 452 0.316305108467 0.0 261.0 100.0 6.2.1.13 Acetyl-CoA synthetase (ADP-forming) alpha subunit / branched-chain acyl-CoA synthetase (ADP-forming) alpha subunit OS=Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / F1) GN=Smar_0449 PE=4 SV=1 # UNIPROT # A3DLQ0 # ACETATE--COA-LIGASE-ADP-FORMING-RXN # SMAR399550:SMAR_0449-MONOMER # 6.2.1.13 regression_test_14_0 207 445 0.415499533147 0.0 207.0 100.0 1.1.1.40 Probable NADP-dependent malic enzyme OS=Rickettsia prowazekii GN=RP373 PE=3 SV=1 # UNIPROT # Q9ZDF6 # MALIC-NADP-RXN # RPRO272947:RP373-MONOMER # 1.1.1.40 regression_test_15_0 213 440 0.400363967243 0.0 213.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase 1, chloroplastic OS=Arabidopsis thaliana GN=PPDK PE=1 SV=2 # UNIPROT # O23404 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_14_0 207 433 0.404295051354 0.0 207.0 100.0 1.1.1.40 NADP-dependent malic enzyme OS=Rhizobium meliloti GN=tme PE=1 SV=2 # UNIPROT # O30808 # MALIC-NADP-RXN # SMEL266834:SMC01126-MONOMER # 1.1.1.40 regression_test_18_0 215 432 0.372093023256 0.0 215.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase 1, chloroplastic OS=Arabidopsis thaliana GN=PPDK PE=1 SV=2 # UNIPROT # O23404 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_9_0 265 424 0.296710986704 0.0 265.0 100.0 6.2.1.13 Probable acetyl-CoA synthetase OS=uncultured archaeon GN=C4_0042 PE=4 SV=1 # UNIPROT # Q2Y4P6 # ACETATE--COA-LIGASE-ADP-FORMING-RXN # # 6.2.1.13 regression_test_17_0 236 414 0.329093799682 0.0 236.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Giardia intestinalis PE=3 SV=1 # UNIPROT # P51776 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_17_0 231 406 0.322734499205 0.0 231.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Entamoeba histolytica GN=PPDK PE=3 SV=1 # UNIPROT # P37213 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_16_0 223 405 0.346746575342 0.0 223.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Giardia intestinalis PE=3 SV=1 # UNIPROT # P51776 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_11_0 253 402 0.285308729595 0.0 253.0 100.0 1.18.6.1 Nitrogenase iron protein 2 OS=Paenibacillus durus GN=nifH2 PE=3 SV=1 # UNIPROT # Q9AKT4 # NITROGENASE-RXN # # 1.18.6.1 regression_test_16_0 224 394 0.337328767123 0.0 224.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Entamoeba histolytica GN=PPDK PE=3 SV=1 # UNIPROT # P37213 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_11_0 269 391 0.277501774308 0.0 269.0 100.0 1.18.6.1 Nitrogenase iron protein 2 OS=Methanococcus thermolithotrophicus GN=nifH2 PE=3 SV=2 # UNIPROT # P08625 # NITROGENASE-RXN # # 1.18.6.1 regression_test_19_0 291 391 0.279885468862 0.0 291.0 100.0 2.3.1.61 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex OS=Mycobacterium tuberculosis GN=dlaT PE=1 SV=1 # UNIPROT # P65633 # RXN0-1147 # # 2.3.1.61 regression_test_15_0 217 385 0.350318471338 0.0 217.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Giardia intestinalis PE=3 SV=1 # UNIPROT # P51776 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_19_0 285 383 0.274158911954 0.0 285.0 100.0 2.3.1.61 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex OS=Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) GN=odhB PE=3 SV=1 # UNIPROT # Q49XM4 # RXN0-1147 # SSAP342451:SSP1326-MONOMER # 2.3.1.61 regression_test_11_0 254 381 0.270404542229 0.0 254.0 100.0 1.18.6.1 Nitrogenase iron protein OS=Methanospirillum hungatei (strain JF-1 / DSM 864) GN=nifH PE=3 SV=1 # UNIPROT # Q2FUB7 # NITROGENASE-RXN # MHUN323259:MHUN_0793-MONOMER # 1.18.6.1 regression_test_5_0 105 378 0.673796791444 0.0 105.0 100.0 Coenzyme PQQ synthesis protein E OS=Klebsiella pneumoniae GN=pqqE PE=3 SV=1 # UNIPROT # P27507 # RXN-11176 # MetaCyc:MONOMER-15350 # regression_test_18_0 209 376 0.323858742463 0.0 209.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Giardia intestinalis PE=3 SV=1 # UNIPROT # P51776 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_18_0 213 371 0.31955211025 0.0 213.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Entamoeba histolytica GN=PPDK PE=3 SV=1 # UNIPROT # P37213 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_15_0 214 370 0.336669699727 0.0 214.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Entamoeba histolytica GN=PPDK PE=3 SV=1 # UNIPROT # P37213 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # # 2.7.9.1 regression_test_11_0 257 366 0.259758694109 0.0 257.0 100.0 1.18.6.1 Nitrogenase iron protein OS=Cyanothece sp. (strain ATCC 51142) GN=nifH PE=3 SV=1 # UNIPROT # O07641 # NITROGENASE-RXN # # 1.18.6.1 regression_test_12_0 214 363 0.334562211982 0.0 214.0 100.0 4.1.1.31 Phosphoenolpyruvate carboxylase OS=Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) GN=ppc PE=3 SV=1 # UNIPROT # P06516 # PEPCARBOX-RXN # SELO269084:SYC1846_D-MONOMER # 4.1.1.31 regression_test_14_0 207 361 0.337068160598 0.0 207.0 100.0 1.1.1.38 Probable NAD-dependent malic enzyme 4 OS=Bacillus subtilis GN=ytsJ PE=3 SV=1 # UNIPROT # O34962 # MALIC-NAD-RXN # BSUB:BSU29220-MONOMER # 1.1.1.38 regression_test_14_0 188 352 0.328664799253 0.0 188.0 100.0 1.1.1.38 NAD-dependent malic enzyme OS=Geobacillus stearothermophilus PE=3 SV=1 # UNIPROT # P16468 # MALIC-NAD-RXN # # 1.1.1.38 regression_test_19_0 153 339 0.242662848962 0.0 153.0 100.0 2.3.1.61 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex 1, mitochondrial OS=Arabidopsis thaliana GN=At5g55070 PE=1 SV=1 # UNIPROT # Q9FLQ4 # RXN0-1147 # # 2.3.1.61 regression_test_22_0 115 338 0.545161290323 0.0 115.0 100.0 1.18.6.1 Nitrogenase iron protein OS=Methanospirillum hungatei (strain JF-1 / DSM 864) GN=nifH PE=3 SV=1 # UNIPROT # Q2FUB7 # NITROGENASE-RXN # MHUN323259:MHUN_0793-MONOMER # 1.18.6.1 regression_test_22_0 116 292 0.470967741935 0.0 116.0 100.0 1.18.6.1 Nitrogenase iron protein 2 OS=Paenibacillus durus GN=nifH2 PE=3 SV=1 # UNIPROT # Q9AKT4 # NITROGENASE-RXN # # 1.18.6.1 regression_test_12_0 192 280 0.258064516129 0.0 192.0 100.0 4.1.1.31 Phosphoenolpyruvate carboxylase OS=Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1) GN=ppc PE=3 SV=1 # UNIPROT # P74299 # PEPCARBOX-RXN # SSP1148:SLL0920-MONOMER # 4.1.1.31 regression_test_22_0 129 272 0.438709677419 0.0 129.0 100.0 1.18.6.1 Nitrogenase iron protein 2 OS=Methanococcus thermolithotrophicus GN=nifH2 PE=3 SV=2 # UNIPROT # P08625 # NITROGENASE-RXN # # 1.18.6.1 regression_test_17_0 245 252 0.200317965024 0.0 245.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Treponema pallidum GN=ppdK PE=3 SV=1 # UNIPROT # O83728 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # TPAL243276:TP_0746-MONOMER # 2.7.9.1 regression_test_16_0 233 249 0.213184931507 0.0 233.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Treponema pallidum GN=ppdK PE=3 SV=1 # UNIPROT # O83728 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # TPAL243276:TP_0746-MONOMER # 2.7.9.1 regression_test_15_0 224 247 0.22474977252 0.0 224.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Treponema pallidum GN=ppdK PE=3 SV=1 # UNIPROT # O83728 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # TPAL243276:TP_0746-MONOMER # 2.7.9.1 regression_test_18_0 219 214 0.184323858742 0.0 219.0 100.0 2.7.9.1 Pyruvate, phosphate dikinase OS=Treponema pallidum GN=ppdK PE=3 SV=1 # UNIPROT # O83728 # PYRUVATEORTHOPHOSPHATE-DIKINASE-RXN # TPAL243276:TP_0746-MONOMER # 2.7.9.1 regression_test_12_0 144 196 0.18064516129 0.0 144.0 100.0 4.1.1.31 Phosphoenolpyruvate carboxylase OS=Gloeobacter violaceus GN=ppc PE=3 SV=1 # UNIPROT # Q7NNJ7 # PEPCARBOX-RXN # GVIO251221:GLL0414-MONOMER # 4.1.1.31 regression_test_12_0 87 102 0.0940092165899 0.0 87.0 100.0 4.1.1.31 Phosphoenolpyruvate carboxylase OS=Xanthomonas campestris pv. campestris (strain 8004) GN=ppc PE=3 SV=1 # UNIPROT # Q4UR00 # PEPCARBOX-RXN # XCAM314565:XC_3479-MONOMER # 4.1.1.31

hallamlab commented 7 years ago

Please use the newest version of MP on GitHub