finding expected missing small genes (example, nce1,and missing list)

[ValWood]

Finding expected missing small genes example, nce1 (this should work for most small, reasonably conserved proteins even if we don't have a clue about the location)

Pombe. SPAC12G12.17 /nce1

clearly missing from japonicus

tbalxstN identifies 2 fragments in region:

create CDS and FASTA/adjust until matches orthologs:

CDS - 1322452: 1322658 MW: 6130.2935 MNLISKRLDPVFGLAVGVYAYILYERKQPRPAGRSLRELLARAWLRPSSKPSST 10 20 30 40 50

[ValWood]

These are some of the small missing proteins we need to look for. There are more, but this is some of the major obvious missing ones:

• [x] rpl4101 60S ribosomal protein L41 25
• [x] rpl4102 60S ribosomal protein L41 (predicted) 25
• [x] BC10 family small membrane protein, unknown biological role, human BLCAP ortholog 108
• [x] cox9 cytochrome c oxidase subunit VIIa (predicted) 58
• [ ] cox8 cytochrome c oxidase subunit VIII (predicted) 66 (CAN'T FIND!)
• [ ] cytosine deaminase (predicted) 162. (CAN'T FIND!)
• [x] ER membrane integral protein, implicated in sterol metabolism (predicted) 183
• [ ] glm1 Glomulin, ubiquitin-protein transferase inhibitor Glm1 (predicted) 227 (CAN'T FIND)
• [x] gna1 glucosamine-phosphate N-acetyltransferase (predicted) 111
• [x] hot13 helper of TIM Hot13 (predicted)
• [ ] hry1 HHE domain cation binding protein (predicted) 203. (CAN'T FIND!)
• [ ] mug105 K48-linkage specific deubiquitinase 244 (CAN'T FIND)
• [x] sdc1 Lid2 complex Dpy-30 domain subunit Sdc1 109
• [ ] moa1 meiosis-specific kinetochore regulator (Meikin) Moa1 172.
  SJAG_04630 candidate
• [ ] rrg8 mitochondrial conserved fungal protein Rrg8 (predicted) 234
  candidate>SJAG_02925.1 length:235
• [ ] mitochondrial DUF1772 family protein, multimembrane spanning anthrone oxygenase-like 160 (CAN'T FIND)
• [ ] mrx11 mitochondrial expression network (MIOREX) component Mrx11 179 (CAN'T FIND)
• [x] ina17 mitochondrial F1-FO ATP synthase peripheral stalk assembly factor Ina17 (predicted) 112
• [ ] cmc4 mitochondrial / mature-T-Cell Proliferation I type ortholog70 (CAN'T FIND)
• [ ] mitochondrial proton-transporting ATP synthase complex assembly protein (predicted) 178. (CAN'T FIND) cant fit at syntenic location
• [x] new15 mitochondrial ribosomal protein subunit L35 (predicted) 86
• [ ] img2 mitochondrial ribosomal protein subunit L49 (predicted) 105 (CAN'T FIND)
• [ ] mitochondrial ribosomal protein subunit L9 (predicted) 101 (CAN'T FIND)
• [ ] rrg9 mitochondrial ribosome assembly protein Rrg9 (predicted) 117 (CAN'T FIND)
• [ ] mitochondrial thioredoxin-related protein (predicted) 121
• [ ] mzt1 mitotic spindle organizing protein Mzt1 64. (CAN'T FIND)
• [x] nat2 N alpha-acetylation related protein Nat2 (predicted) 167
• [ ] pcm2 protein-L-isoaspartate O-methyltransferase Pcm2 (predicted) 230 (CAN'T FIND)
• [ ] saw1 recombination protein Saw1 (predicted) 120 (CAN'T FIND)
• [ ] Siva family protein 124
• [ ] gem6 SMN complex subunit Gem6 93 (part of tandem fusion, see below)
• [ ] ubiquitin family protein, human UBTD1 homolog 239. (CAN'T FIND)
• [ ] ctr6 vacuolar copper exporter Ctr6 148
• [x] vps55 vacuolar sorting protein Vps55 (predicted) 128
• [ ] wwm3 WW domain containing conserved fungal protein Wwm3 204

[ValWood]

SJAG_02161 phosphatidylglycerol phospholipase C Pgc1 /SMN complex subunit Gem6 tandem fusion (I can't see a way to split. May be a sequence error)