Rv1156 Resolved · high auto-curated
H37Rv Rv1156 · MTBC0 mtbc0_001243 ·
195 aa · 1290747–1291334 (+) ·
RefSeq NP_215672.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | HhH-GPD-type base excision DNA repair protein |
| Revised (this work) | HhH-GPD-type base excision DNA repair protein. Pfam: HhH-GPD (PF00730.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06554
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | HhH-GPD family |
| Orthologous group | COG0177 |
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 | 0.486 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
HhH-GPD | PF00730.32 | 5.4e-12 | 25–185 | HhH-GPD superfamily base excision DNA repair protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ligC (DNA ligase C), medium confidence from genomic context alone (score 578 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 818 | 799 | experimental:403 database:641 |
Rv2828A hyp |
hypothetical protein | 615 | 615 ctx | cooccurence:615 |
Rv3731 ligC |
DNA ligase C | 602 | 578 ctx | cooccurence:564 |
Rv0393 hyp |
hypothetical protein | 568 | 569 ctx | cooccurence:564 |
Rv0670 end |
endonuclease IV | 605 | 562 | experimental:441 |
Rv1155 |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 528 | 529 ctx | neighborhood:521 |
Rv2074 |
pyridoxamine 5'-phosphate oxidase | 506 | 506 ctx | cooccurence:500 |
Rv0944 fpg2 |
formamidopyrimidine-DNA glycosylase | 530 | 503 | coexpression:414 |
Rv2618 hyp |
hypothetical protein | 442 | 442 ctx | cooccurence:442 |
Rv3394c hyp |
hypothetical protein | 471 | 439 | |
Rv2090 |
5'-3' exonuclease | 471 | 437 | |
Rv1613 trpA |
tryptophan synthase subunit alpha | 434 | 435 | coexpression:428 |
Rv2464c nei1 |
DNA glycosylase | 448 | 417 | coexpression:417 |
Rv3297 nei |
endonuclease VIII | 446 | 415 | coexpression:415 |
Rv2924c fpg |
formamidopyrimidine-DNA glycosylase | 445 | 414 | coexpression:414 |
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: hypothetical protein
- MTBC0 PGAP product: HhH-GPD-type base excision DNA repair protein
- Pfam (hmmscan --cut_ga): HhH-GPD PF00730.32 (E=5e-12)
- (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_215672.1)
- Domains: Pfam-A via hmmscan --cut_ga — HhH-GPD (PF00730.32)
- 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
COG0177 - Curated reference: UniProt O06554 (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 —
19 functional partner(s); context anchor
ligC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001243|Rv1156| MPNLQLVQEPAADALLNANPFALLVGMLLDQQVPMETAFAGPKKIADRMGSFDAGDIADYDPDKFVALCSERPAIHRFPGSMAKRIQALAQIIVDRYDGDAAALWTAGEPDGNELLRRLKGLPGFGEQKARIFLALLGKQYGVTPKGWQVAAGEFGQPGTYLSVADIVDAGSLGQVRSHKRQRKAAAKAEGKAPT