sufD Resolved · high auto-curated
H37Rv Rv1462 · MTBC0 mtbc0_001564 ·
397 aa · 1659331–1660524 (+) ·
RefSeq NP_215978.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | Fe-S cluster assembly protein SufD |
| Revised (this work) | Fe-S cluster assembly protein SufD. Pfam: 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 |
P9WFP5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Iron-sulfur cluster assembly SufBD family protein Rv1462 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | sufD |
| eggNOG description | FeS assembly protein SufD |
| Orthologous group | COG0719 |
| KEGG orthology |
K09015
|
| Gene Ontology (16) |
GO:0008150, GO:0009605, GO:0009607, GO:0040007, GO:0043207, GO:0044403, GO:0044419, GO:0050896, GO:0051701, GO:0051704, GO:0051707, GO:0052173 +4 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 | 0.239 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 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 |
|---|---|---|---|---|
SUFBD_core | PF01458.24 | 2.2e-69 | 127–360 | 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 1000 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 | 1000 ctx | neighborhood:882 cooccurence:774 coexpression:956 experimental:788 textmining:948 |
Rv1465 |
nitrogen fixation related protein | 999 | 998 ctx | neighborhood:881 cooccurence:706 coexpression:939 textmining:885 |
Rv1464 csd |
cysteine desulfurase | 999 | 998 ctx | neighborhood:882 cooccurence:771 coexpression:941 textmining:817 |
Rv1466 hyp |
hypothetical protein | 972 | 969 ctx | neighborhood:881 cooccurence:723 |
Rv1461 sufB hyp |
hypothetical protein | 967 | 968 ctx | neighborhood:781 coexpression:801 |
Rv1460 sufR |
transcriptional regulator | 909 | 906 ctx | neighborhood:882 |
Rv3778c |
aminotransferase | 893 | 887 ctx | cooccurence:622 coexpression:648 |
Rv1459c mptB |
alpha-(1->6)-mannopyranosyltransferase | 777 | 776 ctx | neighborhood:773 |
Rv3700c egtE |
pyridoxal-phosphate-dependent protein EgtE | 953 | 758 | coexpression:648 textmining:815 |
Rv1457c |
antibiotic ABC transporter permease | 718 | 714 ctx | neighborhood:712 |
Rv1458c |
antibiotic ABC transporter ATP-binding protein | 712 | 712 ctx | neighborhood:712 |
Rv2204c hyp |
hypothetical protein | 649 | 603 | coexpression:420 |
Rv1456c |
antibiotic ABC transporter permease | 601 | 601 ctx | neighborhood:600 |
Rv3284 hyp |
hypothetical protein | 538 | 515 | |
Rv2383c mbtB |
phenyloxazoline synthase | 417 | 150 |
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: Fe-S cluster assembly protein SufD
- Pfam (hmmscan --cut_ga): SUFBD_core PF01458.24 (E=2e-69)
- (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_215978.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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 P9WFP5 (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 —
15 functional partner(s); context anchor
sufC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001564|Rv1462|sufD MTAPGLTAAVEGIAHNKGELFASFDVDAFEVPHGRDEIWRFTPLRRLRGLHDGSARATGSATITVSERPGVYTQTVRRGDPRLGEGGVPTDRVAAQAFSSFNSATLVTVERDTQVVEPVGITVTGPGEGAVAYGHLQVRIEELGEAVVVIDHRGGGTYADNVEFVVDDAARLTAVWIADWADDTVHLSAHHARIGKDAVLRHVTVMLGGDVVRMSAGVRFCGAGGDAELLGLYFADDGQHLESRLLVDHAHPDCKSNVLYKGALQGDPASSLPDAHTVWVGDVLIRAQATGTDTFEVNRNLVLTDGARADSVPNLEIETGEIVGAGHASATGRFDDEQLFYLRSRGIPEAQARRLVVRGFFGEIIAKIAVPEVRERLTAAIEHELEITESTEKTTVS