MTBC Gene Atlas

Rv1371 Family assigned · medium auto-curated

H37Rv Rv1371 · MTBC0 mtbc0_001472 · 489 aa · 1552703–1554172 (+) · RefSeq NP_215887.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)membrane protein
MTBC0 PGAP re-annotationcytochrome b5 domain-containing protein
Revised (this work)Cytochrome b5 domain-containing protein. Pfam: Cyt-b5 (PF00173.34), FA_desaturase (PF00487.31).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt P71799 TrEMBL · unreviewed · Predicted
UniProt nameProbable conserved membrane protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category C Energy production and conversion
I Lipid transport and metabolism
eggNOG descriptionCytochrome b5-like Heme/Steroid binding domain
Orthologous groupCOG5274

Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.

Conservation & selection (intra-MTBC, 145 209 strains) pseudogene candidate

pN/pS 0.721 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 4 synonymous, 9 missense, 0 nonsense, 2 frameshift
Disruption 2 distinct premature-stop/frameshift site(s); most common in 9.81% of strains (14239) · clonal

pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.

Domains (Pfam, hmmscan --cut_ga)

PfamAccessioni-EvalueResiduesDescription
Cyt-b5PF00173.34 6.2e-1128–87 Cytochrome b5-like Heme/Steroid binding domain
FA_desaturasePF00487.31 1.7e-13172–403 Fatty acid desaturase

Functional interaction network (STRING v12, guilt-by-association)

Closest characterised functional partner: pks18 (alpha-pyrone synthesis polyketide synthase-like protein), high confidence from genomic context alone (score 948 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv1372 pks18 alpha-pyrone synthesis polyketide synthase-like protein 978 948 ctx neighborhood:882 cooccurence:448 textmining:601
Rv1373 glycolipid sulfotransferase 925 895 ctx neighborhood:881
Rv1937 oxygenase 964 876 coexpression:434 database:661 textmining:723
Rv1368 lprF lipoprotein LprF 819 819 ctx cooccurence:752
Rv2373c dnaJ2 chaperone protein DnaJ 804 779 experimental:777
Rv0352 dnaJ1 chaperone protein DnaJ 804 779 experimental:777
Rv0260c transcriptional regulator 769 761 coexpression:734
Rv0385 monooxygenase 835 751 database:661
Rv0018c pstP phosphoserine/threonine phosphatase PstP 760 740 experimental:739
Rv3529c hyp hypothetical protein 743 731 database:636
Rv0261c narK3 nitrate/nitrite transporter 753 730 coexpression:730
Rv2514c hyp hypothetical protein 707 707 ctx cooccurence:703
Rv2515c hyp hypothetical protein 846 698 ctx cooccurence:695 textmining:511
Rv0009 ppiA iron-regulated peptidyl-prolyl cis-trans isomerase PpiA 704 685 experimental:685
Rv2582 ppiB peptidyl-prolyl cis-trans isomerase B 704 685 experimental:685

STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.

Evidence

  • Legacy H37Rv annotation: membrane protein
  • MTBC0 PGAP product: cytochrome b5 domain-containing protein
  • Pfam (hmmscan --cut_ga): Cyt-b5 PF00173.34 (E=6e-11), FA_desaturase PF00487.31 (E=2e-13)
  • (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)

Sources

  • Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
  • Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215887.1)
  • Domains: Pfam-A via hmmscan --cut_ga — Cyt-b5 (PF00173.34), FA_desaturase (PF00487.31)
  • Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
  • Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021, doi:10.1093/molbev/msab293), eggNOG 5.0 DB (Huerta-Cepas et al. 2019) — OG COG5274
  • Curated reference: UniProt P71799 (TrEMBL, unreviewed; Predicted)
  • Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 114 functional partner(s); context anchor pks18
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001472|Rv1371|
MTNDLPDVRERDGGPRPAPPAGGPRLSDVWVYNGRAYDLSEWISKHPGGAFFIGRTKNRDITAIVKSYHRDPAIVERILQRRYALGRDATPRDIHPKHNAPAFLFKDDFNSWRDTPKYRFDDPNDLLHRVKARLAEPALAARIKRMDTLFNAIVAVLAVGYFAVQGVRLVEPSWMPLWAFVIAMVLLRSSLAGFGHYALHRAQRGLNRVFNNAFDLNYVALSLVTADGHTLLHHPYTQSEVDIKKNVFTMMMRLPWLYRVPVHTIHKFGHMLSGMAIRIVDVFRITRKVGVEESYGSWRAALPHFLGSAGVRLLLVSELVVFAIAGDFWPWALQFVATLWVSTFLVVASHEFEDDTQGGAVNGEDWGIDQLEHANDLTVIGNRYVDCFLSAGLSSHRVHHVLPFQRSGFANIVTEDVLREEAAKFGVEWLPAKGFITDRLPRLCRKYLLTPSRQAKERHWGFVREHCSPAALKASASYVVAGFVGIGSV