Rv1977 Family assigned · medium auto-curated
H37Rv Rv1977 · MTBC0 mtbc0_002099 ·
348 aa · 2243367–2244413 (+) ·
RefSeq NP_216493.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | M48 family metallopeptidase |
| Revised (this work) | M48 family metallopeptidase. Pfam: Peptidase_M48 (PF01435.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53978
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 |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | Peptidase family M48 |
| Orthologous group | COG0501 |
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 | 0.171 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 17.54% of strains (25468) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Peptidase_M48 | PF01435.25 | 1.6e-33 | 67–263 | Peptidase family M48 |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0342 iniA |
isoniazid inductible protein IniA | 664 | 644 | database:643 |
Rv1978 hyp |
hypothetical protein | 631 | 526 ctx | neighborhood:519 |
Rv3610c ftsH |
zinc metalloprotease FtsH | 615 | 484 | coexpression:407 |
Rv0966c hyp |
hypothetical protein | 441 | 441 ctx | cooccurence:439 |
Rv0351 grpE |
stress response protein GrpE | 492 | 437 | coexpression:418 |
Rv1286 cysC |
adenylyl-sulfate kinase | 418 | 418 | coexpression:418 |
Rv0384c clpB |
chaperone protein ClpB | 464 | 350 | |
Rv3617 ephA |
epoxide hydrolase EphA | 436 | 176 | |
Rv1979c |
permease | 403 | 148 | |
Rv2869c rip |
zinc metalloprotease | 507 | 86 | textmining:484 |
Rv1976c hyp |
hypothetical protein | 557 | 57 | textmining:550 |
Rv2467 pepN |
aminopeptidase PepN | 562 | 53 | textmining:557 |
Rv1974 |
membrane protein | 454 | 52 | textmining:448 |
Rv1975 hyp |
hypothetical protein | 554 | 50 | textmining:550 |
Rv1993c hyp |
hypothetical protein | 546 | 50 | textmining:542 |
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: M48 family metallopeptidase
- Pfam (hmmscan --cut_ga): Peptidase_M48 PF01435.25 (E=2e-33)
- (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_216493.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M48 (PF01435.25)
- 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
COG0501 - Curated reference: UniProt O53978 (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)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002099|Rv1977| MSQTPATTRKTFPEISSRAWEHPADRTALSALRRLKGFDQILKLMSGMLRERQHRLLYLASAARVGPRQFADLDALLDECVDVLDASAKPELYVMQSPIADAFTIGMGKPFTVITSGLYDLVTHDEMRFVMGHELGHALSGHAVYRTMMMHLLRLARSFGVLPVGGWALRAIVAALLEWQRKSELSGDRAGLLCAQDLDTALRVEMKLAGGCRLDKLDSEAFLAQAREYETSGDMRDGVLKLLNLELQTHPFSVLRAAALTHWVDTGGYAKVIAGEYPRRADDGNAKFADDLGAAARYYRDGFDQSNDPLIKGIRDGFGGIVEGVGRAASNAADSLGRKITEWRQPSK