Rv3226c Resolved · high auto-curated
H37Rv Rv3226c · MTBC0 mtbc0_003435 ·
252 aa · 3624706–3625464 (-) ·
RefSeq NP_217743.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SOS response-associated peptidase |
| Revised (this work) | SOS response-associated peptidase. Pfam: SRAP (PF02586.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05872
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Abasic site processing protein |
| EC (curated) |
EC 3.4.-.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | yedK |
| eggNOG description | Belongs to the SOS response-associated peptidase family |
| Orthologous group | COG2135 |
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 | 0.341 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
SRAP | PF02586.20 | 2.3e-67 | 1–231 | SOS response associated peptidase (SRAP) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aroA (3-phosphoshikimate 1-carboxyvinyltransferase), high confidence from genomic context alone (score 788 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) |
|---|---|---|---|---|
Rv3227 aroA |
3-phosphoshikimate 1-carboxyvinyltransferase | 886 | 788 ctx | neighborhood:787 textmining:485 |
Rv3228 rsgA hyp |
hypothetical protein | 886 | 787 ctx | neighborhood:787 textmining:489 |
Rv2894c xerC |
tyrosine recombinase XerC | 775 | 767 | coexpression:767 |
Rv3225c |
GCN5-like N-acetyltransferase | 525 | 524 ctx | neighborhood:507 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 469 | 470 | |
Rv3242c hyp |
hypothetical protein | 457 | 457 | coexpression:457 |
Rv2646 |
integrase | 456 | 436 | coexpression:436 |
Rv2309c |
Rv2309c, (MTCY3G12.25), len: 151 aa. Possible integrase (fragment), similar to others e.g. Q48908 integrase (fragment) from Mycobacterium pa | 456 | 436 | coexpression:436 |
Rv2659c |
prophage integrase | 455 | 435 | coexpression:435 |
Rv1054 |
Rv1054, (MTV017.07), len: 104 aa. Probable integrase (fragment), similar to Rv2309c|MTCY3G12_25|Z79702 hypothetical protein (shows similarit | 454 | 434 | coexpression:434 |
Rv3751 |
Rv3751, (MTV025.099), len: 71 aa. Probable integrase (fragment), similar to part of many e.g. Q48908 integrase (fragment) from Mycobacterium | 454 | 434 | coexpression:434 |
Rv1701 xerD |
tyrosine recombinase XerD | 454 | 434 | coexpression:434 |
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: SOS response-associated peptidase
- Pfam (hmmscan --cut_ga): SRAP PF02586.20 (E=2e-67)
- (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_217743.1)
- Domains: Pfam-A via hmmscan --cut_ga — SRAP (PF02586.20)
- 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
COG2135 - Curated reference: UniProt O05872 (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 —
12 functional partner(s); context anchor
aroA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003435|Rv3226c| MCGRFAVTTDPAQLAEKITAIDEATGCGGGKTSYNVAPTDTIATVVSRHSEPDDEPTRRVRLMRWGLIPSWIKAGPGGAPDAKGPPLINARADKVATSPAFRSAVRSKRCLVPMDGWYEWRVDPDATPGRPNAKTPFFLHRHDGALLFTAGLWSVWKSYRSAPPLLSCTVITTDAVGELAEIHDRMPLLLAEEDWDDWLNPDAPPDPELLARPPDVRDIALRQVSTLVNNVRNNGPELLEPARSQPEQIQLL