carD Resolved · high auto-curated
H37Rv Rv3583c · MTBC0 mtbc0_003802 ·
162 aa · 4048733–4049221 (-) ·
RefSeq NP_218100.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | RNA polymerase-binding transcription factor CarD |
|---|---|
| MTBC0 PGAP re-annotation | RNA polymerase-binding transcription factor CarD |
| Revised (this work) | RNA polymerase-binding transcription factor CarD. Pfam: CarD_TRCF_RID (PF02559.23), CarD_C (PF21095.4). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJG3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | RNA polymerase-binding transcription factor CarD |
| Curated function | Controls rRNA transcription by binding to the RNA polymerase (RNAP). Required for replication and persistence during infection of mice. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | carD |
| eggNOG description | transcription factor CarD |
| Orthologous group | COG1329 |
| KEGG orthology |
K07736
|
| Gene Ontology (20) |
GO:0006950, GO:0007154, GO:0008150, GO:0009267, GO:0009405, GO:0009605, GO:0009987, GO:0009991, GO:0015968, GO:0031667, GO:0031668, GO:0031669 +8 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 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 |
|---|---|---|---|---|
CarD_TRCF_RID | PF02559.23 | 2.9e-16 | 3–60 | CarD-like/TRCF RID domain |
CarD_C | PF21095.4 | 1.3e-37 | 69–155 | CarD, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ispD (2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 999 | 999 | experimental:999 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 982 | 979 | experimental:974 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 990 | 975 | experimental:974 textmining:617 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 976 | 974 | experimental:960 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 974 | 973 | experimental:971 |
Rv3197A whiB7 |
transcriptional regulator WhiB7 | 898 | 898 | experimental:898 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 992 | 897 | experimental:895 textmining:930 |
Rv3582c ispD |
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 955 | 887 ctx | neighborhood:865 textmining:622 |
Rv3581c ispF |
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 877 | 871 ctx | neighborhood:865 |
Rv1872c lldD2 |
L-lactate dehydrogenase | 820 | 820 | coexpression:820 |
Rv1871c hyp |
hypothetical protein | 800 | 800 | coexpression:800 |
Rv3579c rlmB |
23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB | 789 | 790 ctx | neighborhood:788 |
Rv3580c cysS1 |
cysteine--tRNA ligase | 788 | 789 ctx | neighborhood:788 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 802 | 781 | experimental:765 |
Rv1398c vapB10 |
antitoxin VapB10 | 740 | 740 | coexpression:740 |
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: RNA polymerase-binding transcription factor CarD
- MTBC0 PGAP product: RNA polymerase-binding transcription factor CarD
- Pfam (hmmscan --cut_ga): CarD_TRCF_RID PF02559.23 (E=3e-16), CarD_C PF21095.4 (E=1e-37)
- (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_218100.1)
- Domains: Pfam-A via hmmscan --cut_ga — CarD_TRCF_RID (PF02559.23), CarD_C (PF21095.4)
- 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
COG1329 - Curated reference: UniProt P9WJG3 (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 —
25 functional partner(s); context anchor
ispD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003802|Rv3583c|carD MIFKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVGVRDVVGQEGLDKVFQVLRAPHTEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQERGLSAGEKRMLAKARQILVGELALAESTDDAKAETILDEVLAAAS