Rv1995 Family assigned · medium auto-curated
H37Rv Rv1995 · MTBC0 mtbc0_002122 ·
255 aa · 2261754–2262521 (+) ·
RefSeq NP_216511.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hemerythrin domain-containing protein |
| Revised (this work) | Hemerythrin domain-containing protein. Pfam: Hemerythrin (PF01814.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLP3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1995 |
UniProt still lists this protein as Uncharacterized protein Rv1995; 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 | Hemerythrin HHE cation binding domain |
| Orthologous group | COG3945 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 1.632 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 3.34% of strains (4843) · 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 |
|---|---|---|---|---|
Hemerythrin | PF01814.29 | 2.2e-15 | 69–201 | Hemerythrin HHE cation binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1996 (universal stress protein), medium confidence from genomic context alone (score 580 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) |
|---|---|---|---|---|
Rv1996 |
universal stress protein | 706 | 580 ctx | neighborhood:578 |
Rv0470A hyp |
hypothetical protein | 543 | 544 ctx | cooccurence:543 |
Rv1994c cmtR |
HTH-type transcriptional regulator CmtR | 732 | 539 ctx | neighborhood:528 textmining:443 |
Rv0665 vapC8 |
ribonuclease VapC8 | 484 | 484 ctx | cooccurence:484 |
Rv3479 |
transmembrane protein | 464 | 464 ctx | cooccurence:464 |
Rv2337c hyp |
hypothetical protein | 452 | 452 ctx | cooccurence:446 |
Rv1992c ctpG |
cation transporter ATPase G | 636 | 445 ctx | neighborhood:440 |
Rv0626 vapB5 |
antitoxin VapB5 | 436 | 436 ctx | cooccurence:436 |
Rv1993c hyp |
hypothetical protein | 918 | 430 ctx | neighborhood:425 textmining:862 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 427 | 427 ctx | cooccurence:427 |
Rv1979c |
permease | 434 | 194 | |
Rv1673c hyp |
hypothetical protein | 613 | 180 | textmining:548 |
Rv1521 fadD25 |
fatty-acid--CoA ligase FadD25 | 511 | 164 | textmining:440 |
Rv2075c hyp |
hypothetical protein | 602 | 159 | textmining:547 |
Rv2434c |
transmembrane protein | 563 | 71 | textmining:549 |
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: hemerythrin domain-containing protein
- Pfam (hmmscan --cut_ga): Hemerythrin PF01814.29 (E=2e-15)
- (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_216511.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hemerythrin (PF01814.29)
- 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
COG3945 - Curated reference: UniProt P9WLP3 (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 —
18 functional partner(s); context anchor
Rv1996 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002122|Rv1995| MVASGAATKGVTVMKQTPPAAVGRRHLLEISASAAGVIALSACSGSPPEPGKGRPDTTPEQEVPVTAPEDLMREHGVLKRILLIYREGIRRLQADDQSPAPALNESAQIIRRFIEDYHGQLEEQYVFPKLEQAGKLTDITSVLRTQHQRGRVLTDRVLAATTAAAAFDQPARDTLAQDMAAYIRMFEPHEAREDTVVFPALRDVMSAVEFRDMAETFEDEEHRRFGEAGFQSVVDKVADIEKSLGIYDLSQFTPS