Rv3041c Family assigned · medium auto-curated
H37Rv Rv3041c · MTBC0 mtbc0_003233 ·
287 aa · 3422365–3423228 (-) ·
RefSeq NP_217557.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ABC transporter ATP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter ATP-binding protein |
| Revised (this work) | ABC transporter ATP-binding protein. Pfam: ABC_tran (PF00005.34), AAA_21 (PF13304.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YF11
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved ATP-binding protein ABC transporter |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | ylmA |
| eggNOG description | ABC transporter |
| Orthologous group | COG1119 |
| EC number |
EC 3.6.3.34
|
| KEGG orthology |
K02013
|
| KEGG pathways |
map02010
|
| KEGG modules |
M00240
|
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 | 0.255 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
ABC_tran | PF00005.34 | 1.2e-24 | 40–188 | ABC transporter |
AAA_21 | PF13304.13 | 5.6e-06 | 147–223 | AAA domain, putative AbiEii toxin, Type IV TA system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA17 (enoyl-CoA hydratase EchA17), high confidence from genomic context alone (score 900 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3040c hyp |
hypothetical protein | 905 | 905 ctx | neighborhood:881 |
Rv3039c echA17 |
enoyl-CoA hydratase EchA17 | 899 | 900 ctx | neighborhood:881 |
Rv3038c hyp |
hypothetical protein | 879 | 880 ctx | neighborhood:879 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 871 | 871 ctx | neighborhood:869 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 820 | 820 ctx | neighborhood:819 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 577 | 577 | database:540 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 571 | 571 | database:540 |
Rv3859c gltB |
glutamate synthase large subunit | 546 | 547 ctx | neighborhood:544 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 545 | 545 | database:540 |
Rv2326c |
ABC transporter ATP-binding protein | 542 | 543 | database:540 |
Rv3036c TB22.2 hyp |
hypothetical protein | 539 | 539 ctx | neighborhood:539 |
Rv2995c leuB |
3-isopropylmalate dehydrogenase | 510 | 511 ctx | cooccurence:455 |
Rv3037c |
S-adenosylmethionine-dependent methyltransferase | 492 | 493 ctx | neighborhood:490 |
Rv1559 ilvA |
threonine dehydratase IlvA | 477 | 478 | |
Rv3044 fecB |
FeIII-dicitrate-binding periplasmic lipoprotein | 468 | 467 ctx | neighborhood:438 |
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: ABC transporter ATP-binding protein
- MTBC0 PGAP product: ABC transporter ATP-binding protein
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=1e-24), AAA_21 PF13304.13 (E=6e-06)
- (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_217557.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34), AAA_21 (PF13304.13)
- 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
COG1119 - Curated reference: UniProt I6YF11 (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 —
18 functional partner(s); context anchor
echA17 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003233|Rv3041c| MRHDSRVLDNGGPDAADPDLLIDFRNVSLRRNGRTLVGPLDWAVELDERWVIVGPNGAGKTSLLRIAAAAEHPSSGVAFVLGERLGRVDVSELRARVGLSSSALAERVPGDERVRDLVVSAGYAVLGRWRERYEAVDYHRAIDMLESLGAEHLANRTYGTLSEGERKRVLIARALMTDPELLLLDEPAAGLDLGGREELVARLADLAADPDAPALVLVTHHVEEIPPGFSHCLLLSEARVVAAGLLPDALTAENLSTAFGQEITLEVADGRYFARRRRSRAAHRRQS