Rv1314c Resolved · high auto-curated
H37Rv Rv1314c · MTBC0 mtbc0_001406 ·
193 aa · 1478699–1479280 (-) ·
RefSeq NP_215830.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cob(I)yrinic acid a,c-diamide adenosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | cob(I)yrinic acid a%2Cc-diamide adenosyltransferase |
| Revised (this work) | Cob(I)yrinic acid a%2Cc-diamide adenosyltransferase. Pfam: Cob_adeno_trans (PF01923.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP99
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Corrinoid adenosyltransferase |
| EC (curated) |
EC 2.5.1.17
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | yvqK |
| eggNOG description | adenosyltransferase |
| Orthologous group | COG2096 |
| EC number |
EC 2.5.1.17
|
| KEGG orthology |
K00798
|
| KEGG pathways |
map00860, map01100
|
| KEGG modules |
M00122
|
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, 2 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 |
|---|---|---|---|---|
Cob_adeno_trans | PF01923.24 | 4.6e-62 | 8–176 | Cobalamin adenosyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: murA (UDP-N-acetylglucosamine 1-carboxyvinyltransferase), high confidence from genomic context alone (score 786 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0255c cobQ1 |
cobyric acid synthase | 918 | 910 | database:900 |
Rv0254c cobU |
bifunctional cobinamide kinase/cobinamide phosphate guanylyltransferase | 933 | 908 | database:900 |
Rv2208 cobS |
adenosylcobinamide-GDP ribazoletransferase | 920 | 908 | database:900 |
Rv2236c cobD |
cobalamin biosynthesis transmembrane protein CobD | 915 | 908 | database:900 |
Rv2848c cobB |
cobyrinic acid A,C-diamide synthase | 915 | 908 | database:900 |
Rv2062c cobN |
cobalamin biosynthesis protein CobN | 933 | 907 | database:900 |
Rv2849c cobO |
cob(I)alamin adenosyltransferase | 932 | 906 | database:900 |
Rv1315 murA |
UDP-N-acetylglucosamine 1-carboxyvinyltransferase | 786 | 786 ctx | neighborhood:785 |
Rv1313c |
insertion sequence element IS1557 transposase | 469 | 469 ctx | neighborhood:467 |
Rv2124c metH |
methionine synthase | 590 | 430 | |
Rv1493 mutB |
methylmalonyl-CoA mutase large subunit | 457 | 422 | |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 479 | 313 | |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 505 | 301 | |
Rv2072c cobL |
precorrin-6Y C(5,15)-methyltransferase | 575 | 229 | textmining:472 |
Rv2718c nrdR |
transcriptional regulator NrdR | 440 | 99 | textmining:405 |
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: cob(I)yrinic acid a,c-diamide adenosyltransferase
- MTBC0 PGAP product: cob(I)yrinic acid a%2Cc-diamide adenosyltransferase
- Pfam (hmmscan --cut_ga): Cob_adeno_trans PF01923.24 (E=5e-62)
- (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_215830.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cob_adeno_trans (PF01923.24)
- 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
COG2096 - Curated reference: UniProt P9WP99 (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 —
15 functional partner(s); context anchor
murA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001406|Rv1314c| MAVHLTRIYTRTGDDGTTGLSDMSRVAKTDARLVAYADCDEANAAIGAALALGHPDTQITDVLRQIQNDLFDAGADLSTPIVENPKHPPLRIAQSYIDRLEGWCDAYNAGLPALKSFVLPGGSPLSALLHVARTVVRRAERSAWAAVDAHPEGVSVLPAKYLNRLSDLLFILSRVANPDGDVLWRPGGDRTAS