Rv1413 Family assigned · medium auto-curated
H37Rv Rv1413 · MTBC0 - ·
171 aa · 1589386–1589901 (+) ·
RefSeq NP_215929.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Ala_racemase_N (PF01168.27) 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WLY5
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv1413 |
UniProt still lists this protein as Uncharacterized protein Rv1413; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | Alanine racemase |
| Orthologous group | COG3616 |
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 | 0.361 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.35% of strains (510) · 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 |
|---|---|---|---|---|
Ala_racemase_N | PF01168.27 | 9.6e-14 | 29–156 | Alanine racemase, N-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ribH (6,7-dimethyl-8-ribityllumazine synthase), medium confidence from genomic context alone (score 564 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) |
|---|---|---|---|---|
Rv1414 hyp |
hypothetical protein | 997 | 997 ctx | neighborhood:882 fusion:899 cooccurence:774 |
Rv3470c ilvB2 |
acetolactate synthase large subunit | 679 | 679 | coexpression:654 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 564 | 564 ctx | neighborhood:561 |
Rv1417 |
membrane protein | 540 | 540 ctx | neighborhood:535 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 537 | 536 ctx | neighborhood:535 |
Rv1418 lprH |
lipoprotein LprH | 478 | 478 ctx | neighborhood:475 |
Rv1412 ribC |
riboflavin synthase | 469 | 470 ctx | neighborhood:468 |
Rv0342 iniA |
isoniazid inductible protein IniA | 411 | 412 ctx | cooccurence:411 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): Ala_racemase_N PF01168.27 (E=1e-13)
- (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_215929.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ala_racemase_N (PF01168.27)
- 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
COG3616 - Curated reference: UniProt P9WLY5 (SwissProt, reviewed; 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 —
8 functional partner(s); context anchor
ribH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1413| MATIGEVEVFVDHGADDVFITYPLWIGTRQADRLRQLADRARIAVGAGTAEGASNTGARLADAAGAIDVLIEIDSGHHRSGVRAEQVLEVAHAVGEAGLHLVGVFTFPGHSYAPGKPGEAGEQERRALNDAANALVAVGFPISCRSGGSTPTALLTAADGASETSRRLCAR