Rv1906c Family assigned · medium auto-curated
H37Rv Rv1906c · MTBC0 mtbc0_002021 ·
156 aa · 2170535–2171005 (-) ·
RefSeq NP_216422.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains Rv1352 (PF27111.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07726
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 |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | ABC-type Fe3 transport system, periplasmic component |
| Orthologous group | COG1840 |
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 | 0.347 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
Rv1352 | PF27111.1 | 2.7e-27 | 43–114 | Rv1352-like extracellular domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aao (D-amino acid oxidase), high confidence from genomic context alone (score 722 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) |
|---|---|---|---|---|
Rv1905c aao |
D-amino acid oxidase | 942 | 722 ctx | neighborhood:717 textmining:803 |
Rv0941c hyp |
hypothetical protein | 716 | 716 ctx | cooccurence:715 |
Rv2721c hyp |
hypothetical protein | 674 | 674 ctx | cooccurence:666 |
Rv0538 |
membrane protein | 665 | 653 ctx | cooccurence:618 |
Rv1904 hyp |
hypothetical protein | 869 | 639 ctx | cooccurence:482 textmining:652 |
Rv3810 pirG |
cell surface protein | 620 | 621 ctx | cooccurence:617 |
Rv2015c hyp |
hypothetical protein | 603 | 603 ctx | cooccurence:600 |
Rv0479c |
membrane protein | 594 | 595 ctx | cooccurence:590 |
Rv2743c hyp |
hypothetical protein | 583 | 584 ctx | cooccurence:581 |
Rv1765c hyp |
hypothetical protein | 575 | 576 ctx | cooccurence:572 |
Rv1836c hyp |
hypothetical protein | 572 | 572 ctx | cooccurence:549 |
Rv2719c chiZ |
membrane protein | 564 | 564 ctx | cooccurence:545 |
Rv1648 |
transmembrane protein | 546 | 546 ctx | cooccurence:546 |
Rv1111c hyp |
hypothetical protein | 523 | 523 ctx | cooccurence:520 |
Rv1364c |
sigma factor regulatory protein | 524 | 519 | coexpression:505 |
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: hypothetical protein
- Pfam (hmmscan --cut_ga): Rv1352 PF27111.1 (E=3e-27)
- (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_216422.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv1352 (PF27111.1)
- 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
COG1840 - Curated reference: UniProt O07726 (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 —
57 functional partner(s); context anchor
aao - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002021|Rv1906c| MRLKPAPSPAAAFAVAGLILAGWAGSVGLAGADPEPAPTPKTAIDSDGTYAVGIDIAPGTYSSAGPVGDGTCYWKRMGNPDGALIDNALSKKPQVVTIEPTDKAFKTHGCQPWQNTGSEGAAPAGVPGPEAGAQLQNQLGILNGLLGPTGGRVPQP