cydD Family assigned · medium auto-curated
H37Rv Rv1621c · MTBC0 - ·
527 aa · 1821690–1823273 (-) ·
RefSeq NP_216137.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydD |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydD. Pfam: ABC_membrane (PF00664.29), ABC_tran (PF00005.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O06138
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable 'component linked with the assembly of cytochrome' transport transmembrane ATP-binding protein ABC transporter CydD |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | cydD |
| eggNOG description | ABC transporter |
| Orthologous group | COG4988 |
| KEGG orthology |
K16013
|
| KEGG pathways |
map02010
|
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 | 0.249 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 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 |
|---|---|---|---|---|
ABC_membrane | PF00664.29 | 5.7e-14 | 12–257 | ABC transporter transmembrane region |
ABC_tran | PF00005.34 | 1.9e-27 | 333–477 | ABC transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cydC (cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydC), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1620c cydC |
cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydC | 999 | 1000 ctx | neighborhood:882 coexpression:976 database:900 textmining:760 |
Rv1622c cydB |
cytochrome D ubiquinol oxidase subunit II CydB | 999 | 996 ctx | neighborhood:782 cooccurence:745 coexpression:942 textmining:948 |
Rv1623c cydA |
cytochrome D ubiquinol oxidase subunit I CydA | 999 | 991 ctx | neighborhood:731 cooccurence:746 coexpression:877 textmining:918 |
Rv1624c |
membrane protein | 691 | 691 ctx | neighborhood:688 |
Rv1625c cya |
adenylate cyclase | 420 | 421 ctx | neighborhood:412 |
Rv2952 |
phthiotriol/phenolphthiotriol dimycocerosates methyltransferase | 569 | 319 | |
Rv1161 narG |
nitrate reductase subunit alpha | 492 | 290 | |
Rv0553 menC |
muconate cycloisomerase | 425 | 54 | textmining:418 |
Rv3086 adhD |
alcohol dehydrogenase D | 437 | 47 | textmining:434 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydD
- Pfam (hmmscan --cut_ga): ABC_membrane PF00664.29 (E=6e-14), ABC_tran PF00005.34 (E=2e-27)
- (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_216137.1)
- Domains: Pfam-A via hmmscan --cut_ga — ABC_membrane (PF00664.29), ABC_tran (PF00005.34)
- 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
COG4988 - Curated reference: UniProt O06138 (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 —
9 functional partner(s); context anchor
cydC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1621c|cydD MACGVGISGCAIGSAIVLASIVAGVIDPANPGMAGLRRWLGPLSILLVLWGLRASIQWLQARLAQRGASAVIADLSGQVLTAVTARRPSQLAAQRDAAAVLITRGLDGLRPYFTGYLPTLLLAAILTPATVAVIGLYDLKSMAIVVITLPLIPIFMVLIGLATTNPSAAALAAMTAVQARLLDLIAGIPTLRALGRASGPEQRIAELSADHRRSAMATLRIAFLSALVLELLATLGVALVAVGIGLRLVFGEMSLTAGLTVLLLAPEVYWPLRRVGVQFHAAADGRTAADKAFALLGESPSPTPGRRTVTARGGVIRLERLSVRGRDGRAPYDLTADIEPGRVTVLTGRNGAGKSTTLQAIAGLTAPSSGRITVAGVDVTNLAPAAWWRQLSWLPQRPVLVPGTVRHNLVLLGPVDDLERACAAAGFDAVLDELPRGLDTVLGRGGVGLSLGQRQRLGLARALGSPAAVLLLDEPTAHLDARTEQHVLGAIVERARAGATVLVVAHRQQVAAAGDRVVEVNSDGFRR