Rv1227c Family assigned · medium auto-curated
H37Rv Rv1227c · MTBC0 mtbc0_001315 ·
177 aa · 1378736–1379269 (-) ·
RefSeq NP_215743.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | PH domain-containing protein |
| Revised (this work) | PH domain-containing protein. Pfam: bPH_2 (PF03703.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33223
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bacterial PH domain |
| Orthologous group | COG3402 |
| KEGG orthology |
K09167
|
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 | 0.268 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
bPH_2 | PF03703.21 | 1.6e-16 | 87–164 | Bacterial PH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1226c (transmembrane protein), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1226c |
transmembrane protein | 989 | 988 ctx | neighborhood:882 cooccurence:772 coexpression:580 |
Rv3278c |
transmembrane protein | 633 | 585 | coexpression:561 |
Rv1225c hyp |
hypothetical protein | 573 | 574 ctx | neighborhood:571 |
Rv1228 lpqX |
lipoprotein LpqX | 549 | 550 ctx | neighborhood:547 |
Rv0438c moeA2 |
molybdopterin molybdenumtransferase | 545 | 546 ctx | neighborhood:544 |
Rv0436c pssA |
CDP-diacylglycerol--serine O-phosphatidyltransferase | 519 | 519 ctx | neighborhood:444 |
Rv0487 hyp |
hypothetical protein | 506 | 506 ctx | cooccurence:506 |
Rv0724 sppA |
protease IV SppA | 452 | 453 | coexpression:436 |
Rv0435c |
ATPase | 440 | 441 ctx | neighborhood:439 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 809 | 46 | textmining:809 |
Rv2943 |
insertion sequence element IS1533 transposase | 768 | 46 | textmining:767 |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 544 | 45 | textmining:543 |
Rv2014 |
Transposase; Rv2014, (MTCY39.03c), len: 196 aa. Transposase,similar to insertion elements; possibly made by frameshifting with respect to Rv | 809 | 41 | textmining:809 |
Rv3691 hyp |
hypothetical protein | 809 | 41 | textmining:809 |
Rv0255c cobQ1 |
cobyric acid synthase | 659 | 41 | textmining:659 |
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: transmembrane protein
- MTBC0 PGAP product: PH domain-containing protein
- Pfam (hmmscan --cut_ga): bPH_2 PF03703.21 (E=2e-16)
- (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_215743.1)
- Domains: Pfam-A via hmmscan --cut_ga — bPH_2 (PF03703.21)
- 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
COG3402 - Curated reference: UniProt O33223 (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 —
16 functional partner(s); context anchor
Rv1226c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001315|Rv1227c| MDHARNVPSATGPQRNHLALAEPAHRPSSQAPVMWALSASLGWILPVIAQLVWWAVHPQPPWPHLAAAALTAVAMVVHIGVVPLWRYRVHRWEISPQAVFTRTGWLVQERRITPISRVQTVDTYRGPMDRLFGLANVTVTTASSAGAVHIEALDTDVADRVVAQLTDIAALRGEDAT