cinA Resolved · high auto-curated
H37Rv Rv1901 · MTBC0 mtbc0_002016 ·
430 aa · 2165772–2167064 (+) ·
RefSeq NP_216417.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | competence damage-inducible protein CinA |
|---|---|
| MTBC0 PGAP re-annotation | competence/damage-inducible protein A |
| Revised (this work) | Competence/damage-inducible protein A. Pfam: MoCF_biosynth (PF00994.30), CinA (PF02464.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPE3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | CinA-like protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | cinA |
| eggNOG description | Belongs to the CinA family |
| Orthologous group | COG1058 |
| EC number |
EC 3.5.1.42
|
| KEGG orthology |
K03742, K03743
|
| KEGG pathways |
map00760
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 0.647 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (194) · clonal |
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 |
|---|---|---|---|---|
MoCF_biosynth | PF00994.30 | 4.0e-35 | 8–178 | Probable molybdopterin binding domain |
CinA | PF02464.24 | 6.9e-54 | 275–423 | Competence-damaged protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fmu (16S rRNA m5C967 methyltransferase), high confidence from genomic context alone (score 717 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 978 | 935 | database:900 textmining:687 |
Rv1330c pncB1 |
nicotinic acid phosphoribosyltransferase PncB1 | 977 | 919 | database:900 textmining:729 |
Rv0573c pncB2 |
nicotinic acid phosphoribosyltransferase PncB2 | 960 | 919 | database:900 textmining:532 |
Rv0212c nadR |
transcriptional regulator NadR | 948 | 913 | database:900 textmining:436 |
Rv1596 nadC |
nicotinate-nucleotide pyrophosphatase | 971 | 912 | database:900 textmining:694 |
Rv3199c nudC |
NADH pyrophosphatase | 955 | 906 | database:900 textmining:547 |
Rv2746c pgsA3 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 880 | 843 | coexpression:733 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 823 | 769 | coexpression:736 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 823 | 769 | coexpression:736 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 717 | 717 ctx | neighborhood:544 coexpression:405 |
Rv1900c lipJ |
lignin peroxidase LipJ | 692 | 693 ctx | neighborhood:686 |
Rv2737c recA |
recombinase A | 811 | 595 | textmining:554 |
Rv1899c lppD |
lipoprotein LppD | 592 | 593 ctx | neighborhood:580 |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 592 | 578 ctx | neighborhood:544 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 566 | 566 ctx | neighborhood:544 |
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: competence damage-inducible protein CinA
- MTBC0 PGAP product: competence/damage-inducible protein A
- Pfam (hmmscan --cut_ga): MoCF_biosynth PF00994.30 (E=4e-35), CinA PF02464.24 (E=7e-54)
- (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_216417.1)
- Domains: Pfam-A via hmmscan --cut_ga — MoCF_biosynth (PF00994.30), CinA (PF02464.24)
- 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
COG1058 - Curated reference: UniProt P9WPE3 (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 —
103 functional partner(s); context anchor
fmu - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002016|Rv1901|cinA MAVSARAGIVITGTEVLTGRVQDRNGPWIADRLLELGVELAHITICGDRPADIEAQLRFMAEQGVDLIVTSGGLGPTADDMTVEVVARYCGRELVLDDELENRIANILKKLMGRNPAIEPANFDSIRAANRKQAMIPAGSQVIDPVGTAPGLVVPGRPAVMVLPGPPRELQPIWSKAIQTAPVQDAIAGRTTYRQETIRIFGLPESSLADTLRDAEAAIPGFDLVEITTCLRRGEIEMVTRFEPNAAQVYTQLARLLRDRHGHQVYSEDGASVDELVAKLLTGRRIATAESCTAGLLAARLTDRPGSSKYVAGAVVAYSNEAKAQLLGVDPALIEAHGAVSEPVAQAMAAGALQGFGADTATAITGIAGPSGGTPEKPVGTVCFTVLLDDGRTTTRTVRLPGNRSDIRERSTTVAMHLLRRTLSGIPGSP