Rv0628c Family assigned · medium auto-curated
H37Rv Rv0628c · MTBC0 mtbc0_000661 ·
383 aa · 722314–723465 (-) ·
RefSeq NP_215142.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | FIST N-terminal domain-containing protein |
| Revised (this work) | FIST N-terminal domain-containing protein. Pfam: FIST (PF08495.16), FIST_C (PF10442.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKS7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0628c |
UniProt still lists this protein as Uncharacterized protein Rv0628c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | FIST C domain |
| Orthologous group | COG4398 |
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.786 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
FIST | PF08495.16 | 1.1e-29 | 35–219 | FIST N domain |
FIST_C | PF10442.15 | 1.8e-24 | 224–364 | FIST C domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recD (exonuclease V subunit alpha RecD), medium confidence from genomic context alone (score 558 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) |
|---|---|---|---|---|
Rv0629c recD |
exonuclease V subunit alpha RecD | 557 | 558 ctx | neighborhood:554 |
Rv0631c recC |
exonuclease V subunit gamma RecC | 557 | 557 ctx | neighborhood:553 |
Rv0630c recB |
exonuclease V subunit beta RecB | 554 | 554 ctx | neighborhood:553 |
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: FIST N-terminal domain-containing protein
- Pfam (hmmscan --cut_ga): FIST PF08495.16 (E=1e-29), FIST_C PF10442.15 (E=2e-24)
- (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_215142.1)
- Domains: Pfam-A via hmmscan --cut_ga — FIST (PF08495.16), FIST_C (PF10442.15)
- 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
COG4398 - Curated reference: UniProt P9WKS7 (SwissProt, reviewed; 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 —
3 functional partner(s); context anchor
recD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000661|Rv0628c| MRIGVGVSTAPDVRRAAAEAAAHAREELAGGTPALAVLLGSRSHTDQAVDLLAAVQASVEPAALIGCVAQGIVAGRHELENEPAVAVWLASGPPAETFHLDFVRTGSGALITGYRFDRTAHDLHLLLPDPYSFPSNLLIEHLNTDLPGTTVVGGVVSGGRRRGDTRLFRDRDVLTSGLVGVRLPGAHSVSVVSQGCRPIGEPYIVTGADGAVITELGGRPPLHRLREIVLGMAPDEQELVSRGLQIGIVVDEHLAVPGQGDFLIRGLLGADPTTGAIGIGEVVEVGATVQFQVRDAAAADKDLRLAVERAAAELPGPPVGGLLFTCNGRGRRMFGVTDHDASTIEDLLGGIPLAGFFAAGEIGPVAGHNALHGFTASMALFVD