MTBC Gene Atlas

Rv0264c Family assigned · medium

H37Rv Rv0264c · MTBC0 mtbc0_000280 · 210 aa · 316165–316797 (-) · RefSeq NP_214778.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationallophanate hydrolase subunit 1
Revised (this work)Allophanate hydrolase / 5-oxoprolinase (C/D) subunit (Pfam CT_C_D PF02682). With Rv0263c forms a urea-amidolyase / 5-oxoprolinase-type complex that hydrolyses amide bonds (e.g. allophanate or 5-oxoproline).

Curated reference (UniProt)

UniProt P95221 TrEMBL · unreviewed · Evidence at protein level
UniProt nameCarboxyltransferase domain-containing protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category E Amino acid transport and metabolism
Preferred namekipI
eggNOG descriptionAllophanate hydrolase subunit 1
Orthologous groupCOG2049

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)

pN/pS 0.719 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 2 missense, 0 nonsense, 0 frameshift

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
CT_C_DPF02682.22 3.1e-509–199 Carboxyltransferase domain, subdomain C and D

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

Closest characterised functional partner: aac (aminoglycoside 2'-N-acetyltransferase), high confidence from genomic context alone (score 899 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.

PartnerProductScoreNo text-miningChannels (≥400)
Rv0263c hyp hypothetical protein 999 1000 ctx neighborhood:865 fusion:899 cooccurence:774 coexpression:975 experimental:997 textmining:929
Rv0262c aac aminoglycoside 2'-N-acetyltransferase 979 899 ctx neighborhood:865 textmining:804
Rv0265c iron ABC transporter substrate-binding lipoprotein 954 778 ctx neighborhood:776 textmining:803
Rv1249c membrane protein 814 778 coexpression:760
Rv0516c oprA anti-anti-sigma factor 716 716 coexpression:716
Rv1773c transcriptional regulator 714 715 coexpression:655
Rv1719 transcriptional regulator 710 711 coexpression:656
Rv2989 transcriptional regulator 667 668 coexpression:656
Rv0266c oplA 5-oxoprolinase OplA 748 564 ctx neighborhood:564 textmining:445
Rv0269c hyp hypothetical protein 531 532 ctx neighborhood:529
Rv0261c narK3 nitrate/nitrite transporter 496 496 ctx neighborhood:493
Rv0924c mntH divalent metal cation transporter MntH 509 491 coexpression:405
Rv0319 pcp pyrrolidone-carboxylate peptidase 467 448
Rv2230c GTP cyclohydrolase 463 440 coexpression:421
Rv3063 cstA carbon starvation protein A 400 401

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

  • MTBC0 PGAP product: 'allophanate hydrolase subunit 1'
  • Pfam: CT_C_D PF02682 (E=3.1e-50)

ESM Atlas signal (exploratory)

Ancestral protein hash 7f6a123950adb9eb789880d463d33e84 · 10 ESM-space neighbours (max similarity 0.911). SAE features are orienting indices, not validated domains.

#IndexActivationInterpretation
15326 1.29 Conserved His/Asp catalytic landmark
26102 1.25 Active-site glycine-rich phosphate-binding loops
38028 1.06 Catalytic-core active-site belt
47104 0.82 C-terminal beta-to-alpha module
511781 0.67 Anionic cofactor-binding α/β cores
613388 0.57 Generic N-terminal segment detector
714837 0.55 N-terminal beta-1 edge motifs
88703 0.53 Terminal helical scaffold detector

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_214778.1)
  • Domains: Pfam-A via hmmscan --cut_ga — CT_C_D (PF02682.22)
  • 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 COG2049
  • Curated reference: UniProt P95221 (TrEMBL, unreviewed; Evidence at protein level)
  • 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 — 25 functional partner(s); context anchor aac
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000280|Rv0264c|
MDAALACTVLDYGDHALMLQCDSTADAMAWTDALRAAALPGVVDIVAASRTVLVKLDAPRYQGVTRQRLRRLRVTPEAVAAADHRCDLVIDVVYDGPDLAEVARCTGLTTAAVINAHTATGWRAGFSGSAPGFAYLIDGDPSLRVPRRPERRTSMPPGSVALADGFSAIYPSQAPSDWQIIGHTDAVLWDVDRPQPALLTPGMWVQFRAA