subI Family assigned · medium auto-curated
H37Rv Rv2400c · MTBC0 mtbc0_002555 ·
356 aa · 2720891–2721961 (-) ·
RefSeq NP_216916.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | sulfate ABC transporter substrate-binding lipoprotein SubI |
|---|---|
| MTBC0 PGAP re-annotation | sulfate ABC transporter substrate-binding protein |
| Revised (this work) | Sulfate ABC transporter substrate-binding protein. Pfam: SBP_bac_11 (PF13531.12), 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 |
P71744
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable sulfate-binding lipoprotein SubI |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | subI |
| eggNOG description | sulfate ABC transporter |
| Orthologous group | COG1613 |
| KEGG orthology |
K02048
|
| KEGG pathways |
map00920, map02010
|
| KEGG modules |
M00185
|
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 | 0.665 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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_11 | PF13531.12 | 4.6e-31 | 62–303 | Bacterial extracellular solute-binding protein |
SBP_bac_1 | PF01547.31 | 3.3e-12 | 68–295 | Bacterial extracellular solute-binding protein |
SBP_bac_8 | PF13416.12 | 3.4e-09 | 76–311 | Bacterial extracellular solute-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysA1 (sulfate ABC transporter ATP-binding protein CysA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2397c cysA1 |
sulfate ABC transporter ATP-binding protein CysA | 999 | 1000 ctx | neighborhood:865 cooccurence:771 coexpression:948 database:900 textmining:773 |
Rv2399c cysT |
sulfate ABC transporter permease CysT | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:963 database:900 textmining:741 |
Rv2398c cysW |
sulfate ABC transporter permease CysW | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:965 database:900 textmining:865 |
Rv1286 cysC |
adenylyl-sulfate kinase | 999 | 1000 | coexpression:998 database:900 textmining:765 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 982 | 966 | coexpression:657 database:900 textmining:496 |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 771 | 741 | coexpression:688 |
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 851 | 718 | coexpression:659 textmining:498 |
Rv2401 hyp |
hypothetical protein | 583 | 583 ctx | neighborhood:578 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 545 | 546 ctx | neighborhood:544 |
Rv2401A |
membrane protein | 545 | 545 ctx | neighborhood:544 |
Rv1858 modB |
molybdenum ABC transporter permease ModB | 553 | 536 ctx | cooccurence:516 |
Rv2391 sirA |
sulfite reductase | 538 | 470 | coexpression:440 |
Rv2064 cobG |
precorrin-3B synthase | 528 | 465 | coexpression:434 |
Rv2334 cysK1 |
O-acetylserine sulfhydrylase | 484 | 451 | coexpression:433 |
Rv1077 cbs |
cystathionine beta-synthase | 498 | 421 | coexpression:402 |
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: sulfate ABC transporter substrate-binding lipoprotein SubI
- MTBC0 PGAP product: sulfate ABC transporter substrate-binding protein
- Pfam (hmmscan --cut_ga): SBP_bac_11 PF13531.12 (E=5e-31), SBP_bac_1 PF01547.31 (E=3e-12), SBP_bac_8 PF13416.12 (E=3e-09)
- (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_216916.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBP_bac_11 (PF13531.12), 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
COG1613 - Curated reference: UniProt P71744 (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 —
24 functional partner(s); context anchor
cysA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002555|Rv2400c|subI MLSLTLSEASCIASASRWRHIIPAGVVCALIAGIGVGCHGGPSDVVGRAGPDRAHTSITLVAYAVPEPGWSAVIPAFNASEQGRGVQVITSYGASADQSRGVADGKPADLVNFSVEPDIARLVKAGKVDKDWDADATKGIPFGSVVTFVVRAGNPKNIRDWDDLLRPGIEVITPSPLSSGSAKWNLLAPYAAKSDGGRNNQAGIDFVNTLVNEHVKLRPGSGREATDVFVQGSGDVLISYENEAIATERAGKPVQHVTPPQTFKIENPLAVVATSTHLGAATAFRNFQYTVQAQKLWAQAGFRPVDPAVAADFADLFPVPAKLWTIADLGGWGSVDPQLFDKATGSITKIYLRATG