Rv2040c Family assigned · medium auto-curated
H37Rv Rv2040c · MTBC0 mtbc0_002173 ·
300 aa · 2314241–2315143 (-) ·
RefSeq NP_216556.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sugar ABC transporter permease |
|---|---|
| MTBC0 PGAP re-annotation | sugar ABC transporter permease |
| Revised (this work) | Sugar ABC transporter permease. Pfam: BPD_transp_1 (PF00528.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53484
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable sugar-transport integral membrane protein ABC transporter |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | Binding-protein-dependent transport system inner membrane component |
| Orthologous group | COG1175 |
| KEGG orthology |
K02025
|
| KEGG modules |
M00207
|
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 | 0.256 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 |
|---|---|---|---|---|
BPD_transp_1 | PF00528.28 | 2.0e-15 | 86–290 | Binding-protein-dependent transport system inner membrane component |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2039c (sugar ABC transporter permease), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2039c |
sugar ABC transporter permease | 999 | 1000 ctx | neighborhood:801 cooccurence:774 coexpression:906 experimental:412 database:900 textmining:831 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 999 | 1000 ctx | neighborhood:801 cooccurence:772 coexpression:878 experimental:458 database:900 textmining:699 |
Rv2041c |
sugar ABC transporter substrate-binding lipoprotein | 995 | 987 ctx | neighborhood:785 cooccurence:755 coexpression:626 experimental:412 textmining:652 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 953 | 932 ctx | cooccurence:771 coexpression:470 experimental:458 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 940 | 932 ctx | cooccurence:771 coexpression:466 experimental:458 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 987 | 930 ctx | cooccurence:774 coexpression:486 experimental:412 textmining:830 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 972 | 929 ctx | cooccurence:774 coexpression:480 experimental:412 textmining:627 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 949 | 925 ctx | cooccurence:765 coexpression:486 experimental:412 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 864 | 835 ctx | cooccurence:520 coexpression:431 experimental:412 |
Rv2037c |
transmembrane protein | 785 | 786 ctx | neighborhood:781 |
Rv2318 uspC |
sugar ABC transporter substrate-binding lipoprotein UspC | 812 | 763 | coexpression:430 experimental:412 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 758 | 744 | coexpression:429 experimental:412 |
Rv2042c hyp |
hypothetical protein | 680 | 680 ctx | neighborhood:666 |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 670 | 671 ctx | neighborhood:666 |
Rv2044c hyp |
hypothetical protein | 569 | 568 ctx | neighborhood:558 |
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: sugar ABC transporter permease
- MTBC0 PGAP product: sugar ABC transporter permease
- Pfam (hmmscan --cut_ga): BPD_transp_1 PF00528.28 (E=2e-15)
- (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_216556.1)
- Domains: Pfam-A via hmmscan --cut_ga — BPD_transp_1 (PF00528.28)
- 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
COG1175 - Curated reference: UniProt O53484 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
20 functional partner(s); context anchor
Rv2039c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002173|Rv2040c| MTRRRGRRAWAGRMFVAPNLAAVVVFMLFPLGFSLYMSFQKWDLFTHATFVRLDNFRNLFTSDPLFLIAVVNTAVYTVGTVVPTVIVSLVVAAFLNRKIKGISLFRTVVFLPLAISSVVMAVVWQFVFNTDNGLLNIMLGWLGIGPIPWLIEPRWAMVSLCLVSVWRSVPFATVVLLAAMQGVPETVYEAARIDGAGEIRQFVSITVPLIRGALSFVVVISIIHAFQAFDLVYVLTGANGGPETATYVLGIMLFQHAFSFLEFGYASALAWVMFAILLVLTVLQLRITHRRSWEASRGLG