Rv2585c Family assigned · medium auto-curated
H37Rv Rv2585c · MTBC0 mtbc0_002752 ·
557 aa · 2934548–2936221 (-) ·
RefSeq NP_217101.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein |
|---|---|
| MTBC0 PGAP re-annotation | ABC transporter substrate-binding protein |
| Revised (this work) | ABC transporter substrate-binding protein. Pfam: SBP_bac_5 (PF00496.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL77
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized lipoprotein Rv2585c |
UniProt still lists this protein as Uncharacterized lipoprotein Rv2585c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | ABC-type dipeptide transport system, periplasmic component |
| Orthologous group | COG0747 |
| KEGG orthology |
K02035
|
| KEGG pathways |
map02024
|
| KEGG modules |
M00239
|
| Gene Ontology (13) |
GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0030288, GO:0030313, GO:0031975, GO:0042597, GO:0044424, GO:0044444 +1 more
|
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 | 0.162 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 13 synonymous, 6 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_5 | PF00496.28 | 1.1e-17 | 101–462 | Bacterial extracellular solute-binding proteins, family 5 Middle |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: secD (protein translocase subunit SecD), high confidence from genomic context alone (score 885 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1282c oppC |
oligopeptide ABC transporter permease OppC | 962 | 957 | coexpression:438 database:900 |
Rv1283c oppB |
oligopeptide ABC transporter permease OppB | 967 | 956 | coexpression:459 database:900 |
Rv3663c dppD |
dipeptide ABC transporter ATP-binding protein DppD | 944 | 922 | database:900 |
Rv1281c oppD |
oligopeptide ABC transporter ATP-binding protein OppD | 916 | 916 | database:900 |
Rv1280c oppA |
oligopeptide ABC transporter substrate-binding lipoprotein OppA | 913 | 913 | database:900 |
Rv2587c secD |
protein translocase subunit SecD | 884 | 885 ctx | neighborhood:881 |
Rv2586c secF |
protein translocase subunit SecF | 885 | 884 ctx | neighborhood:881 |
Rv2588c yajC |
membrane protein secretion factor YajC | 800 | 800 ctx | neighborhood:768 |
Rv2584c apt |
adenine phosphoribosyltransferase | 774 | 774 ctx | neighborhood:771 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 759 | 748 ctx | neighborhood:746 |
Rv1275 lprC |
lipoprotein LprC | 766 | 745 ctx | cooccurence:743 |
Rv1274 lprB |
lipoprotein LprB | 760 | 739 ctx | cooccurence:737 |
Rv3668c |
protease | 698 | 685 ctx | cooccurence:675 |
Rv3244c lpqB |
lipoprotein LpqB | 691 | 680 ctx | cooccurence:672 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 669 | 669 | coexpression:647 |
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: lipoprotein
- MTBC0 PGAP product: ABC transporter substrate-binding protein
- Pfam (hmmscan --cut_ga): SBP_bac_5 PF00496.28 (E=1e-17)
- (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_217101.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBP_bac_5 (PF00496.28)
- 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
COG0747 - Curated reference: UniProt P9WL77 (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 —
62 functional partner(s); context anchor
secD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002752|Rv2585c| MAPRRRRHTRIAGLRVVGTATLVAATTLTACSGSAAAQIDYVVDGALVTYNTNTVIGAASAGAQAFARTLTGFGYHGPDGQVVADRDFGTVSVVEGSPLILDYQISDDAVYSDGRPVTCDDLVLAWAAQSGRFPGFDAATQAGYVDIANIECTAGQKKARVSFIPDRSVVDHSQLFTATSLMPSHVIADQLHIDVTAALLSNNVSAVEQIARLWNSTWDLKPGRSHDEVRSRFPSSGPYKIESVLDDGAVVLVANDRWWGTKAITKRITVWPQGADIQDRVNNRSVDVVDVAAGSSGSLVTPDSYQRTDYPSAGIEQLIFAPQGSLAQSRTRRALALCVPRDAIARDAGVPIANSRLSPATDDALTDADGAAEARQFGRVDPAAARDALGGTPLTVRIGYGRPNARLAATIGTIADACAPAGITVSDVTVDTPGPQALRDGKIDVLLASTGGATGSGSSGSSAMDAYDLHSGNGNNLSGYANAQIDGIISALAVSADPAERARLLAEAAPVLWDEMPTLPLYRQQRTLLMSTKMYAVSRNPTRWGAGWNMDRWALAR