Rv2229c Family assigned · medium auto-curated
H37Rv Rv2229c · MTBC0 mtbc0_002368 ·
245 aa · 2528893–2529630 (-) ·
RefSeq NP_216745.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | zinc ribbon domain-containing protein |
| Revised (this work) | Zinc ribbon domain-containing protein. Pfam: CT398_CC (PF24481.3), Zn_ribbon_9 (PF02591.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLH3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2229c |
UniProt still lists this protein as Uncharacterized protein Rv2229c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Zn-ribbon protein, possibly nucleic acid-binding |
| Orthologous group | COG1579 |
| KEGG orthology |
K07164
|
| Gene Ontology (10) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.676 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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 |
|---|---|---|---|---|
CT398_CC | PF24481.3 | 1.0e-57 | 14–192 | CT398-like coiled coil hairpin domain |
Zn_ribbon_9 | PF02591.21 | 1.9e-11 | 203–237 | C4-type zinc ribbon domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2228c (multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase), high confidence from genomic context alone (score 968 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) |
|---|---|---|---|---|
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 996 | 968 ctx | neighborhood:882 coexpression:742 textmining:886 |
Rv2230c |
GTP cyclohydrolase | 994 | 923 ctx | neighborhood:882 textmining:929 |
Rv2231c cobC |
aminotransferase | 984 | 888 ctx | neighborhood:882 textmining:870 |
Rv2235 |
transmembrane protein | 842 | 842 ctx | neighborhood:746 |
Rv2234 ptpA |
protein-tyrosine-phosphatase | 754 | 754 ctx | neighborhood:746 |
Rv2232 ptkA |
protein tyrosine kinase transcriptional regulator PtkA | 747 | 748 ctx | neighborhood:746 |
Rv2231A vapC16 |
ribonuclease VapC16 | 658 | 658 ctx | neighborhood:658 |
Rv2169c |
transmembrane protein | 564 | 564 ctx | cooccurence:564 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 600 | 537 ctx | cooccurence:534 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 514 | 514 ctx | cooccurence:508 |
Rv2256c hyp |
hypothetical protein | 511 | 512 ctx | cooccurence:510 |
Rv3015c hyp |
hypothetical protein | 494 | 494 ctx | cooccurence:487 |
Rv1342c hyp |
hypothetical protein | 490 | 491 ctx | cooccurence:489 |
Rv2242 hyp |
hypothetical protein | 472 | 473 ctx | cooccurence:464 |
Rv3256c hyp |
hypothetical protein | 462 | 462 ctx | cooccurence:441 |
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: zinc ribbon domain-containing protein
- Pfam (hmmscan --cut_ga): CT398_CC PF24481.3 (E=1e-57), Zn_ribbon_9 PF02591.21 (E=2e-11)
- (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_216745.1)
- Domains: Pfam-A via hmmscan --cut_ga — CT398_CC (PF24481.3), Zn_ribbon_9 (PF02591.21)
- 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
COG1579 - Curated reference: UniProt P9WLH3 (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 —
24 functional partner(s); context anchor
Rv2228c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002368|Rv2229c| MKAGVAQQRSLLELAKLDAELTRIAHRATHLPQRAAYQQVQAEHNAANDRMAALRIAAEDLDGQVSRFESEIDAVRKRGDRDRSLLTSGATDAKQLADLQHELDSLQRRQASLEDALLEVLERREELQAQQTAESRALQALRADLAAAQQALDEALAEIDQARHQHSSQRDMLTATLDPELAGLYERQRAGGGPGAGRLQGHRCGACRIEIGRGELAQISAAAEDEVVRCPECGAILLRLEGFEE