Rv2041c Family assigned · medium auto-curated
H37Rv Rv2041c · MTBC0 mtbc0_002174 ·
439 aa · 2315140–2316459 (-) ·
RefSeq NP_216557.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sugar ABC transporter substrate-binding lipoprotein |
|---|---|
| MTBC0 PGAP re-annotation | sugar ABC transporter substrate-binding protein |
| Revised (this work) | Sugar ABC transporter substrate-binding protein. Pfam: SBP_bac_1 (PF01547.31), SBP_bac_8 (PF13416.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53485
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable sugar-binding lipoprotein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Bacterial extracellular solute-binding protein |
| Orthologous group | COG1653 |
| KEGG orthology |
K02027
|
| 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 | 0.881 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 |
|---|---|---|---|---|
SBP_bac_1 | PF01547.31 | 3.0e-49 | 52–351 | Bacterial extracellular solute-binding protein |
SBP_bac_8 | PF13416.12 | 8.7e-28 | 56–373 | Bacterial extracellular solute-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2039c (sugar ABC transporter permease), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2039c |
sugar ABC transporter permease | 999 | 998 ctx | neighborhood:881 cooccurence:759 coexpression:872 experimental:412 textmining:777 |
Rv2038c ugpC |
sugar ABC transporter ATP-binding protein | 998 | 992 ctx | neighborhood:800 cooccurence:570 coexpression:861 experimental:444 textmining:828 |
Rv2040c |
sugar ABC transporter permease | 995 | 987 ctx | neighborhood:785 cooccurence:755 coexpression:626 experimental:412 textmining:652 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 959 | 943 ctx | cooccurence:404 coexpression:449 experimental:828 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 948 | 930 ctx | cooccurence:431 coexpression:430 experimental:788 |
Rv2317 uspB |
sugar ABC transporter permease UspB | 956 | 919 ctx | cooccurence:741 coexpression:444 experimental:412 textmining:490 |
Rv2316 uspA |
sugar ABC transporter permease UspA | 937 | 908 ctx | cooccurence:733 coexpression:428 experimental:412 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 929 | 900 ctx | cooccurence:693 coexpression:449 experimental:412 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 917 | 900 ctx | cooccurence:708 coexpression:432 experimental:412 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 955 | 860 ctx | cooccurence:505 coexpression:468 experimental:444 textmining:695 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 879 | 833 ctx | cooccurence:444 coexpression:466 experimental:444 |
Rv2037c |
transmembrane protein | 827 | 827 ctx | neighborhood:774 |
Rv2042c hyp |
hypothetical protein | 804 | 804 ctx | neighborhood:684 |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 693 | 694 ctx | neighborhood:684 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 627 | 627 ctx | cooccurence:625 |
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 substrate-binding lipoprotein
- MTBC0 PGAP product: sugar ABC transporter substrate-binding protein
- Pfam (hmmscan --cut_ga): SBP_bac_1 PF01547.31 (E=3e-49), SBP_bac_8 PF13416.12 (E=9e-28)
- (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_216557.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBP_bac_1 (PF01547.31), SBP_bac_8 (PF13416.12)
- 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
COG1653 - Curated reference: UniProt O53485 (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 —
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_002174|Rv2041c| MVNKPFERRSLLRGAGALTAASLAPWAAGCAADDDDALTFFFAANPDELRPRMRVVNEFQRRYPDIKVRALLSGPGVMQQLATFCAGGKCPDVLMAWELTYAELADRGVLLDLNTLLARDQAFAAELKSDSIGALYETFTFNGGQYAFPEQWSGNFLFYNKQLFDDAGVPPPPGSWERPWSFAEFLDAAQALTKQGRSGRDRQWGFVNAWVSFYAAGLFAMNNGVPWSVPRMNPTHLNFDHDGFLEAVQFYADLTNKHKVAPSAAEQQSMSTADLFSVGKAGIALAGHWRYQTFDRADGLDFDVAPLPIGPRGRAACSDIGVTGLAIAATSRRKDQAWEFVKFATGPVGQALIGESRLFVPVLRSAINSHGFANAHRRVGNLAVLSEGPAYSEGLPVTPAWEKIAALMDRYFGPVLRGSRPATSLTGLSQAVDEVLRNP