sufC Resolved · high auto-curated
H37Rv Rv1463 · MTBC0 mtbc0_001565 ·
266 aa · 1660521–1661321 (+) ·
RefSeq NP_215979.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ABC transporter ATP-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | Fe-S cluster assembly ATPase SufC |
| Revised (this work) | Fe-S cluster assembly ATPase SufC. Pfam: ABC_tran (PF00005.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53154
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved ATP-binding protein ABC transporter |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | sufC |
| eggNOG description | FeS assembly ATPase SufC |
| Orthologous group | COG0396 |
| KEGG orthology |
K09013
|
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 | 0.417 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 | 7.4e-23 | 26–177 | ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: csd (cysteine desulfurase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1462 sufD hyp |
hypothetical protein | 999 | 1000 ctx | neighborhood:882 cooccurence:774 coexpression:956 experimental:788 textmining:948 |
Rv1464 csd |
cysteine desulfurase | 999 | 999 ctx | neighborhood:882 cooccurence:774 coexpression:955 textmining:692 |
Rv1465 |
nitrogen fixation related protein | 999 | 999 ctx | neighborhood:881 cooccurence:748 coexpression:966 textmining:872 |
Rv1461 sufB hyp |
hypothetical protein | 999 | 999 ctx | neighborhood:791 cooccurence:774 coexpression:937 experimental:788 |
Rv1466 hyp |
hypothetical protein | 982 | 980 ctx | neighborhood:881 cooccurence:741 coexpression:415 |
Rv3778c |
aminotransferase | 913 | 905 ctx | cooccurence:679 coexpression:694 |
Rv1460 sufR |
transcriptional regulator | 891 | 891 ctx | neighborhood:882 |
Rv1459c mptB |
alpha-(1->6)-mannopyranosyltransferase | 774 | 774 ctx | neighborhood:773 |
Rv3700c egtE |
pyridoxal-phosphate-dependent protein EgtE | 957 | 773 | coexpression:693 textmining:822 |
Rv1457c |
antibiotic ABC transporter permease | 730 | 714 ctx | neighborhood:712 |
Rv1458c |
antibiotic ABC transporter ATP-binding protein | 724 | 712 ctx | neighborhood:712 |
Rv2204c hyp |
hypothetical protein | 689 | 652 | coexpression:407 |
Rv3284 hyp |
hypothetical protein | 641 | 627 | coexpression:421 |
Rv1456c |
antibiotic ABC transporter permease | 601 | 601 ctx | neighborhood:600 |
Rv0638 secE1 |
preprotein translocase SecE | 406 | 407 | coexpression:407 |
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: Fe-S cluster assembly ATPase SufC
- Pfam (hmmscan --cut_ga): ABC_tran PF00005.34 (E=7e-23)
- (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_215979.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_tran (PF00005.34)
- 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
COG0396 - Curated reference: UniProt O53154 (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
csd - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001565|Rv1463|sufC MTILEIKDLHVSVENPAEADHEIPILRGVDLTVKSGETHALMGPNGSGKSTLSYAIAGHPKYHVTSGTITLDGADVLAMSIDERARAGLFLAMQYPVEVPGVSMSNFLRSAATAIRGEPPKLRHWVKEVKAAMAALDIDPAFAERSVNEGFSGGEKKRHEILQLELLKPKIAILDETDSGLDVDALRVVSEGVNRYAESQHGGILLITHYTRILRYIHPEYVHVFVGGRIVESGGSELADELDQNGYVRFSPASGRYPHQPAPTGA