Rv2531c Resolved · high auto-curated
H37Rv Rv2531c · MTBC0 - ·
947 aa · 2854938–2857781 (-) ·
RefSeq YP_177889.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | amino acid decarboxylase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Amino acid decarboxylase. Pfam: OKR_DC_1 (PF01276.27). |
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 |
I6X4K0
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable amino acid decarboxylase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | adi |
| eggNOG description | Orn Lys Arg decarboxylase |
| Orthologous group | COG1982 |
| EC number |
EC 4.1.1.19
|
| KEGG orthology |
K01584
|
| KEGG pathways |
map00330, map01100
|
| KEGG modules |
M00133
|
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 | 0.48 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 13 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 5.31% of strains (7704) · convergent |
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 |
|---|---|---|---|---|
OKR_DC_1 | PF01276.27 | 2.8e-49 | 290–515 | Orn/Lys/Arg decarboxylase, major domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB39 (antitoxin VapB39), high confidence from genomic context alone (score 830 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2530A vapB39 |
antitoxin VapB39 | 829 | 830 ctx | neighborhood:828 |
Rv1001 arcA |
arginine deiminase | 901 | 806 | database:800 textmining:513 |
Rv1659 argH |
argininosuccinate lyase | 823 | 803 | database:800 |
Rv1722 |
carboxylase | 777 | 777 ctx | cooccurence:758 |
Rv2530c vapC39 |
ribonuclease VapC39 | 803 | 699 ctx | neighborhood:695 |
Rv1561 vapC11 |
ribonuclease VapC11 | 687 | 687 | coexpression:687 |
Rv2533c nusB |
N utilization substance protein B | 687 | 668 ctx | neighborhood:652 |
Rv2532c hyp |
hypothetical protein | 666 | 666 ctx | neighborhood:651 |
Rv2534c efp |
elongation factor P | 835 | 662 ctx | neighborhood:651 textmining:532 |
Rv2535c pepQ |
cytoplasmic peptidase PepQ | 700 | 628 ctx | neighborhood:596 |
Rv0392c ndhA |
NADH dehydrogenase NdhA | 548 | 548 ctx | neighborhood:544 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 561 | 542 | experimental:405 |
Rv2536 |
transmembrane protein | 447 | 448 ctx | neighborhood:447 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 459 | 436 | experimental:405 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 431 | 431 ctx | cooccurence: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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): amino acid decarboxylase
- Pfam (hmmscan --cut_ga): OKR_DC_1 PF01276.27 (E=3e-49)
- (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 YP_177889.1)
- Domains: Pfam-A via hmmscan --cut_ga — OKR_DC_1 (PF01276.27)
- 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
COG1982 - Curated reference: UniProt I6X4K0 (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 —
42 functional partner(s); context anchor
vapB39 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2531c| MNPNSVRPRRLHVSALAAVANPSYTRLDTWNLLDDACRHLAEVDLAGLDTTHDVARAKRLMDRIGAYERYWLYPGAQNLATFRAHLDSHSTVRLTEEVSLAVRLLSEYGDRTALFDTSASLAEQELVAQAKQQQFYTVLLADDSPATAPDSLAECLRQLRNPADEVQFELLVVASIEDAITAVALNGEIQAAIIRHDLPLRSRDRVPLMTTLLGTDGDEAVANETHDWVECAEWIRELRPHIDLYLLTDESIAAETQDEPDVYDRTFYRLNDVTDLHSTVLAGLRNRYATPFFDALRAYAAAPVGQFHALPVARGASIFNSKSLHDMGEFYGRNIFMAETSTTSGGLDSLLDPHGNIKTAMDKAAVTWNANQTYFVTNGTSTANKIVVQALTRPGDIVLIDRNCHKSHHYGLVLAGAYPMYLDAYPLPQYAIYGAVPLRTIKQALLDLEAAGQLHRVRMLLLTNCTFDGVVYNPRRVMEEVLAIKPDICFLWDEAWYAFATAVPWARQRTAMIAAERLEQMLSTAEYAEEYRNWCASMDGVDRSEWVDHRLLPDPNRARVRVYATHSTHKSLSALRQASMIHVRDQDFKALTRDAFGEAFLTHTSTSPNQQLLASLDLARRQVDIEGFELVRHVYNMALVFRHRVRKDRLISKWFRILDESDLVPDAFRSSTVSSYRQVRQGALADWNEAWRSDQFVLDPTRLTLFIGATGMNGYDFREKILMERFGIQINKTSINSVLLIFTIGVTWSSVHYLLDVLRRVAIDLDRSQKAASGADLALHRRHVEEITQDLPHLPDFSEFDLAFRPDDASSFGDMRSAFYAGYEEADREYVQIGLAGRRLAEGKTLVSTTFVVPYPPGFPVLVPGQLVSKEIIYFLAQLDVKEIHGYNPDLGLSVFTQAALARMEAARNAVATVGAALPAFEVPRDASALNGTVNGDSVLQGVAEDA