Rv1610 Family assigned · medium auto-curated
H37Rv Rv1610 · MTBC0 mtbc0_001716 ·
235 aa · 1821407–1822114 (+) ·
RefSeq NP_216126.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | TIGR02234 family membrane protein |
| Revised (this work) | TIGR02234 family membrane protein. Pfam: Trp_oprn_chp (PF09534.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06128
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Trp region conserved |
| Orthologous group | 2EGC7 |
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 | 0.758 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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 |
|---|---|---|---|---|
Trp_oprn_chp | PF09534.16 | 1.0e-43 | 23–224 | Tryptophan-associated transmembrane protein (Trp_oprn_chp) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpE (anthranilate synthase component I), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1609 trpE |
anthranilate synthase component I | 884 | 884 ctx | neighborhood:881 |
Rv1611 trpC |
indole-3-glycerol phosphate synthase | 781 | 781 ctx | neighborhood:778 |
Rv1608c bcpB |
peroxiredoxin | 773 | 773 ctx | neighborhood:773 |
Rv1125 hyp |
hypothetical protein | 766 | 766 ctx | cooccurence:764 |
Rv3843c |
transmembrane protein | 763 | 763 ctx | cooccurence:760 |
Rv0383c ttfA hyp |
hypothetical protein | 761 | 761 ctx | cooccurence:761 |
Rv1274 lprB |
lipoprotein LprB | 755 | 755 ctx | cooccurence:754 |
Rv0817c lmeA hyp |
hypothetical protein | 752 | 753 ctx | cooccurence:752 |
Rv3850 hyp |
hypothetical protein | 750 | 751 ctx | cooccurence:747 |
Rv3802c |
membrane protein | 748 | 749 ctx | cooccurence:747 |
Rv1100 hyp |
hypothetical protein | 747 | 748 ctx | cooccurence:746 |
Rv3035 hyp |
hypothetical protein | 747 | 748 ctx | cooccurence:744 |
Rv1275 lprC |
lipoprotein LprC | 746 | 747 ctx | cooccurence:745 |
Rv2342 hyp |
hypothetical protein | 741 | 741 ctx | cooccurence:740 |
Rv3794 embA |
arabinosyltransferase A | 739 | 740 ctx | cooccurence:733 |
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: membrane protein
- MTBC0 PGAP product: TIGR02234 family membrane protein
- Pfam (hmmscan --cut_ga): Trp_oprn_chp PF09534.16 (E=1e-43)
- (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_216126.1)
- Domains: Pfam-A via hmmscan --cut_ga — Trp_oprn_chp (PF09534.16)
- 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
2EGC7 - Curated reference: UniProt O06128 (TrEMBL, unreviewed; Predicted)
- 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 —
113 functional partner(s); context anchor
trpE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001716|Rv1610| MAANAGSVRPNRRARPMIGIAQLLLVVAAGALWMAARLPWVVIGSFDELGPPKEVTLTGASWSTALLPLALLMLAAAVAALAVRGWPLRALAVLLAAASFAVGYLGISLWVVPDVAARGADLAHVPVVTLVGSARHYWGAVAAVLAAVCALLAAVFLMSSAAIRGSAGEDMARYAAPRARRSIARRQHSNAAGRAAPQDDGPDMGPRMSERMIWEALDEGRDPTDREQESDTEGR