sufB Resolved · high auto-curated
H37Rv Rv1461 · MTBC0 mtbc0_001563 ·
846 aa · 1656794–1659334 (+) ·
RefSeq NP_215977.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | intein-containing Fe-S cluster assembly protein SufB |
| Revised (this work) | Intein-containing Fe-S cluster assembly protein SufB. Pfam: SufBD_N (PF19295.6), SUFBD_core (PF01458.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFP7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Iron-sulfur cluster assembly SufBD family protein Rv1461 [Cleaved into: Endonuclease PI-MtuHIIP |
| EC (curated) |
EC 3.1.-.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | sufB |
| eggNOG description | assembly protein SufB |
| Orthologous group | COG0719 |
| KEGG orthology |
K09014
|
| Gene Ontology (30) |
GO:0003674, GO:0003824, GO:0004518, GO:0004519, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139, GO:0006725, GO:0006807 +18 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 | 0.182 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 12 synonymous, 7 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 |
|---|---|---|---|---|
SufBD_N | PF19295.6 | 1.3e-07 | 159–221 | SufBD protein N-terminal region |
SUFBD_core | PF01458.24 | 7.5e-78 | 609–817 | SUF system FeS cluster assembly, SufBD core domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sufC (ABC transporter ATP-binding protein), high confidence from genomic context alone (score 999 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1463 sufC |
ABC transporter ATP-binding protein | 999 | 999 ctx | neighborhood:791 cooccurence:774 coexpression:937 experimental:788 |
Rv1464 csd |
cysteine desulfurase | 990 | 990 ctx | neighborhood:781 cooccurence:773 coexpression:782 |
Rv1465 |
nitrogen fixation related protein | 987 | 986 ctx | neighborhood:791 cooccurence:751 coexpression:755 |
Rv1462 sufD hyp |
hypothetical protein | 967 | 968 ctx | neighborhood:781 coexpression:801 |
Rv1466 hyp |
hypothetical protein | 951 | 946 ctx | neighborhood:797 cooccurence:724 |
Rv3778c |
aminotransferase | 888 | 881 ctx | cooccurence:618 coexpression:647 |
Rv1460 sufR |
transcriptional regulator | 830 | 823 ctx | neighborhood:783 |
Rv3700c egtE |
pyridoxal-phosphate-dependent protein EgtE | 761 | 746 | coexpression:648 |
Rv2204c hyp |
hypothetical protein | 648 | 602 | coexpression:419 |
Rv1459c mptB |
alpha-(1->6)-mannopyranosyltransferase | 575 | 572 ctx | neighborhood:569 |
Rv3284 hyp |
hypothetical protein | 475 | 450 | |
Rv1457c |
antibiotic ABC transporter permease | 425 | 417 ctx | neighborhood:415 |
Rv1458c |
antibiotic ABC transporter ATP-binding protein | 403 | 403 ctx | neighborhood:403 |
Rv3052c nrdI |
NrdI protein | 403 | 400 | |
Rv0005 gyrB |
DNA gyrase subunit B | 452 | 144 |
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: hypothetical protein
- MTBC0 PGAP product: intein-containing Fe-S cluster assembly protein SufB
- Pfam (hmmscan --cut_ga): SufBD_N PF19295.6 (E=1e-07), SUFBD_core PF01458.24 (E=8e-78)
- (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_215977.1)
- Domains: Pfam-A via hmmscan --cut_ga — SufBD_N (PF19295.6), SUFBD_core (PF01458.24)
- 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
COG0719 - Curated reference: UniProt P9WFP7 (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 —
16 functional partner(s); context anchor
sufC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001563|Rv1461|sufB MTLTPEASKSVAQPPTQAPLTQEEAIASLGRYGYGWADSDVAGANAQRGLSEAVVRDISAKKNEPDWMLQSRLKALRIFDRKPIPKWGSNLDGIDFDNIKYFVRSTEKQAASWDDLPEDIRNTYDRLGIPEAEKQRLVAGVAAQYESEVVYHQIREDLEAQGVIFLDTDTGLREHPDIFKEYFGTVIPAGDNKFSALNTAVWSGGSFIYVPPGVHVDIPLQAYFRINTENMGQFERTLIIADEGSYVHYVEGCLPAGELITTADGDLRPIESIRVGDFVTGHDGRPHRVTAVQVRDLDGELFTFTPMSPANAFSVTAEHPLLAIPRDEVRVMRKERNGWKAEVNSTKLRSAEPRWIAAKDVAEGDFLIYPKPKPIPHRTVLPLEFARLAGYYLAEGHACLTNGCESLIFSFHSDEFEYVEDVRQACKSLYEKSGSVLIEEHKHSARVTVYTKAGYAAMRDNVGIGSSNKKLSDLLMRQDETFLRELVDAYVNGDGNVTRRNGAVWKRVHTTSRLWAFQLQSILARLGHYATVELRRPGGPGVIMGRNVVRKDIYQVQWTEGGRGPKQARDCGDYFAVPIKKRAVREAHEPVYNLDVENPDSYLAYGFAVHNCTAPIYKSDSLHSAVVEIIVKPHARVRYTTIQNWSNNVYNLVTKRARAEAGATMEWIDGNIGSKVTMKYPAVWMTGEHAKGEVLSVAFAGEDQHQDTGAKMLHLAPNTSSNIVSKSVARGGGRTSYRGLVQVNKGAHGSRSSVKCDALLVDTVSRSDTYPYVDIREDDVTMGHEATVSKVSENQLFYLMSRGLTEDEAMAMVVRGFVEPIAKELPMEYALELNRLIELQMEGAVG