cydB Family assigned · medium auto-curated
H37Rv Rv1622c · MTBC0 mtbc0_001729 ·
346 aa · 1835324–1836364 (-) ·
RefSeq NP_216138.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome D ubiquinol oxidase subunit II CydB |
|---|---|
| MTBC0 PGAP re-annotation | cytochrome d ubiquinol oxidase subunit II |
| Revised (this work) | Cytochrome d ubiquinol oxidase subunit II. Pfam: Cyt_bd_oxida_II (PF02322.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06139
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable integral membrane cytochrome D ubiquinol oxidase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | cydB |
| eggNOG description | cytochrome D ubiquinol oxidase subunit II |
| Orthologous group | COG1294 |
| EC number |
EC 1.10.3.14
|
| KEGG orthology |
K00426
|
| KEGG pathways |
map00190, map01100, map02020
|
| KEGG modules |
M00153
|
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 | 0.302 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 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 |
|---|---|---|---|---|
Cyt_bd_oxida_II | PF02322.21 | 2.7e-97 | 3–326 | Cytochrome bd terminal oxidase subunit II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cydA (cytochrome D ubiquinol oxidase subunit I CydA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1623c cydA |
cytochrome D ubiquinol oxidase subunit I CydA | 999 | 1000 ctx | neighborhood:841 cooccurence:774 coexpression:976 experimental:999 database:540 textmining:966 |
Rv1621c cydD |
cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydD | 999 | 996 ctx | neighborhood:782 cooccurence:745 coexpression:942 textmining:948 |
Rv1620c cydC |
cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydC | 998 | 987 ctx | neighborhood:782 cooccurence:530 coexpression:884 textmining:887 |
Rv1624c |
membrane protein | 761 | 761 ctx | neighborhood:743 |
Rv0558 menH |
demethylmenaquinone methyltransferase | 457 | 457 | |
Rv1625c cya |
adenylate cyclase | 455 | 455 ctx | neighborhood:447 |
Rv1854c ndh |
NADH dehydrogenase | 485 | 275 | |
Rv0392c ndhA |
NADH dehydrogenase NdhA | 441 | 269 | |
Rv1304 atpB |
ATP synthase subunit A | 538 | 216 | textmining:435 |
Rv1456c |
antibiotic ABC transporter permease | 424 | 212 | |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 402 | 182 | |
Rv1307 atpH |
ATP synthase subunit b/delta | 468 | 98 | textmining:435 |
Rv1163 narJ |
nitrate reductase subunit delta | 426 | 93 | |
Rv1161 narG |
nitrate reductase subunit alpha | 536 | 91 | textmining:511 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 467 | 91 | textmining:438 |
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: cytochrome D ubiquinol oxidase subunit II CydB
- MTBC0 PGAP product: cytochrome d ubiquinol oxidase subunit II
- Pfam (hmmscan --cut_ga): Cyt_bd_oxida_II PF02322.21 (E=3e-97)
- (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_216138.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cyt_bd_oxida_II (PF02322.21)
- 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
COG1294 - Curated reference: UniProt O06139 (TrEMBL, unreviewed; 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 —
29 functional partner(s); context anchor
cydA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001729|Rv1622c|cydB MVLQELWFGVIAALFLGFFILEGFDFGVGMLMAPFAHVGMGDPETHRRTALNTIGPVWDGNEVWLITAGAAIFAAFPGWYATVFSALYLPLLAILFGMILRAVAIEWRGKIDDPKWRTGADFGIAAGSWLPALLWGVAFAILVRGLPVDANGHVALSIPDVLNAYTLLGGLATAGLFSLYGAVFIALKTSGPIRDDAYRFAVWLSLPVAGLVAGFGLWTQLAYGKDWTWLVLAVAGCAQAAATVLVWRRVSDGWAFMCTLIVVAAVVVLLFGALYPNLVPSTLNPQWSLTIHNASSTPYTLKIMTWVTAFFAPLTVAYQTWTYWVFRQRISAERIPPPTGLARRAP