Rv1417 Family assigned · medium auto-curated
H37Rv Rv1417 · MTBC0 mtbc0_001517 ·
154 aa · 1601494–1601958 (+) ·
RefSeq NP_215933.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | PH domain-containing protein |
| Revised (this work) | PH domain-containing protein. Pfam: bPH_6 (PF10756.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLY1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1417 |
UniProt still lists this protein as Uncharacterized protein Rv1417; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bacterial PH domain |
| Orthologous group | 2E71H |
| Gene Ontology (34) |
GO:0005575, GO:0005623, GO:0005886, GO:0006766, GO:0006767, GO:0006771, GO:0006807, GO:0008150, GO:0008152, GO:0009058, GO:0009110, GO:0009231 +22 more
|
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, 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 |
|---|---|---|---|---|
bPH_6 | PF10756.16 | 1.0e-25 | 72–141 | Bacterial PH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ribA2 (bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase), high confidence from genomic context alone (score 902 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 902 | 902 ctx | neighborhood:881 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 976 | 885 ctx | neighborhood:881 textmining:803 |
Rv1418 lprH |
lipoprotein LprH | 849 | 850 ctx | neighborhood:846 |
Rv1388 mihF |
integration host factor MihF | 825 | 825 | experimental:436 database:540 |
Rv0705 rpsS |
30S ribosomal protein S19 | 817 | 818 | experimental:463 database:574 |
Rv0682 rpsL |
30S ribosomal protein S12 | 814 | 806 | experimental:463 database:573 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 804 | 798 | experimental:463 database:578 |
Rv0707 rpsC |
30S ribosomal protein S3 | 803 | 796 | experimental:463 database:578 |
Rv0721 rpsE |
30S ribosomal protein S5 | 799 | 792 | experimental:463 database:575 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 788 | 788 | experimental:436 database:548 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 787 | 788 | experimental:436 database:548 |
Rv0718 rpsH |
30S ribosomal protein S8 | 794 | 787 | experimental:463 database:578 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 789 | 785 | experimental:463 database:557 |
Rv2785c rpsO |
30S ribosomal protein S15 | 784 | 782 | experimental:463 database:573 |
Rv0702 rplD |
50S ribosomal protein L4 | 788 | 781 | experimental:463 database:575 |
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: PH domain-containing protein
- Pfam (hmmscan --cut_ga): bPH_6 PF10756.16 (E=1e-25)
- (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_215933.1)
- Domains: Pfam-A via hmmscan --cut_ga — bPH_6 (PF10756.16)
- 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
2E71H - Curated reference: UniProt P9WLY1 (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 —
135 functional partner(s); context anchor
ribA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001517|Rv1417| MTAAPNDWDVVLRPHWTPLFAYAAAFLIAVAHVAGGLLLKVGSSGVVFQTADQVAMGALGLVLAGAVLLFARPRLRVGSAGLSVRNLLGDRIVGWSEVIGVSFPGGSRWARIDLADDEYIPVMAIQAVDKDRAVAAMDTVRSLLARYRPDLCAR