Rv1898 Family assigned · medium auto-curated
H37Rv Rv1898 · MTBC0 mtbc0_002012 ·
102 aa · 2163005–2163313 (+) ·
RefSeq NP_216414.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | MTH1187 family thiamine-binding protein |
| Revised (this work) | MTH1187 family thiamine-binding protein. Pfam: Thiamine_BP (PF01910.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFQ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UPF0045 thiamine-binding protein family member Rv1898 |
UniProt still lists this protein as UPF0045 thiamine-binding protein family member Rv1898; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Thiamine-binding protein |
| Orthologous group | COG0011 |
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
Thiamine_BP | PF01910.23 | 4.3e-29 | 5–95 | Thiamine-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dtd (D-tyrosyl-tRNA(Tyr) deacylase), high confidence from genomic context alone (score 787 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) |
|---|---|---|---|---|
Rv1897c dtd |
D-tyrosyl-tRNA(Tyr) deacylase | 786 | 787 ctx | neighborhood:787 |
Rv1896c |
S-adenosyl-L-methionine-dependent methyltransferase | 609 | 609 ctx | neighborhood:609 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 570 | 341 | |
Rv2671 ribD |
bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase | 500 | 156 | textmining:432 |
Rv2672 |
protease | 627 | 68 | textmining:617 |
Rv0552 hyp |
hypothetical protein | 808 | 67 | textmining:803 |
Rv0874c hyp |
hypothetical protein | 805 | 54 | textmining:803 |
Rv0842 |
integral membrane protein | 660 | 49 | textmining:658 |
Rv2724c fadE20 |
acyl-CoA dehydrogenase FadE20 | 803 | 41 | textmining:803 |
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: MTH1187 family thiamine-binding protein
- Pfam (hmmscan --cut_ga): Thiamine_BP PF01910.23 (E=4e-29)
- (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_216414.1)
- Domains: Pfam-A via hmmscan --cut_ga — Thiamine_BP (PF01910.23)
- 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
COG0011 - Curated reference: UniProt P9WFQ1 (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 —
9 functional partner(s); context anchor
dtd - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002012|Rv1898| MSVLVAFSVTPLGVGEGVGEIVTEAIRVVRDSGLPNQTDAMFTVIEGDTWAEVMAVVQRAVEAVAARAPRVSAVIKVDWRPGVTDAMTQKVATVERYLLRPE