Rv2204c Resolved · high auto-curated
H37Rv Rv2204c · MTBC0 mtbc0_002340 ·
118 aa · 2495088–2495444 (-) ·
RefSeq NP_216720.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | iron-sulfur cluster assembly accessory protein |
| Revised (this work) | Iron-sulfur cluster assembly accessory protein. Pfam: Fe-S_biosyn (PF01521.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMN5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein Rv2204c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | iscA |
| eggNOG description | Belongs to the HesB IscA family |
| Orthologous group | COG0316 |
| KEGG orthology |
K13628
|
| Gene Ontology (43) |
GO:0003674, GO:0005488, GO:0005506, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006790, GO:0006807, GO:0008150 +31 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
Fe-S_biosyn | PF01521.27 | 3.9e-19 | 16–115 | Iron-sulphur cluster biosynthesis |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2206 (transmembrane protein), high confidence from genomic context alone (score 703 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) |
|---|---|---|---|---|
Rv1465 |
nitrogen fixation related protein | 859 | 817 | coexpression:802 |
Rv2205c hyp |
hypothetical protein | 774 | 774 ctx | neighborhood:773 |
Rv3025c iscS |
cysteine desulfurase | 814 | 758 | coexpression:691 |
Rv3053c nrdH |
glutaredoxin electron transport protein NrdH | 757 | 737 | coexpression:728 |
Rv2206 |
transmembrane protein | 703 | 703 ctx | neighborhood:701 |
Rv2207 cobT |
nicotinate-nucleotide-dimethylbenzimidazol phosphoribosyltransferase | 667 | 668 ctx | neighborhood:663 |
Rv2208 cobS |
adenosylcobinamide-GDP ribazoletransferase | 675 | 664 ctx | neighborhood:663 |
Rv1463 sufC |
ABC transporter ATP-binding protein | 689 | 652 | coexpression:407 |
Rv1299 prfA |
peptide chain release factor PrfA | 650 | 621 | database:617 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 656 | 604 ctx | cooccurence:598 |
Rv1462 sufD hyp |
hypothetical protein | 649 | 603 | coexpression:420 |
Rv1461 sufB hyp |
hypothetical protein | 648 | 602 | coexpression:419 |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 631 | 583 | database:557 |
Rv0811c hyp |
hypothetical protein | 679 | 581 | experimental:412 |
Rv0352 dnaJ1 |
chaperone protein DnaJ | 619 | 569 | database:557 |
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: iron-sulfur cluster assembly accessory protein
- Pfam (hmmscan --cut_ga): Fe-S_biosyn PF01521.27 (E=4e-19)
- (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_216720.1)
- Domains: Pfam-A via hmmscan --cut_ga — Fe-S_biosyn (PF01521.27)
- 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
COG0316 - Curated reference: UniProt P9WMN5 (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 —
45 functional partner(s); context anchor
Rv2206 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002340|Rv2204c| MTVQNEPSAKTHGVILTEAAAAKAKSLLDQEGRDDLALRIAVQPGGCAGLRYNLFFDDRTLDGDQTAEFGGVRLIVDRMSAPYVEGASIDFVDTIEKQGFTIDNPNATGSCACGDSFN