ramB Family assigned · medium auto-curated
H37Rv Rv0465c · MTBC0 mtbc0_000489 ·
474 aa · 558247–559671 (-) ·
RefSeq NP_214979.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | acetate metabolism transcriptional regulator RamB |
| Revised (this work) | Acetate metabolism transcriptional regulator RamB. Pfam: HTH_19 (PF12844.14), HTH_31 (PF13560.13), HTH_3 (PF01381.29), Peptidase_M78 (PF06114.20), ScfRs (PF09856.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMI1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator RamB |
| Curated function | Involved in the control of the glyoxylate cycle. RamB negatively controls the expression of icl expression during growth on acetate as the sole carbon source. Does not regulate the expression of other genes involved in acetate metabolism. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | ramB |
| eggNOG description | transcriptional |
| Orthologous group | COG1396 |
| KEGG orthology |
K07110
|
| Gene Ontology (37) |
GO:0001666, GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0006355, GO:0006950, GO:0008150, GO:0009628 +25 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 | 1.146 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 17 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 |
|---|---|---|---|---|
HTH_19 | PF12844.14 | 1.4e-10 | 7–62 | Helix-turn-helix domain |
HTH_31 | PF13560.13 | 1.4e-09 | 7–61 | Helix-turn-helix domain |
HTH_3 | PF01381.29 | 8.7e-13 | 10–63 | Helix-turn-helix |
Peptidase_M78 | PF06114.20 | 5.3e-27 | 188–310 | IrrE N-terminal-like domain |
ScfRs | PF09856.15 | 4.6e-70 | 311–469 | Short-chain fatty acyl coenzyme A regulator, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: icl1 (isocitrate lyase), medium confidence from genomic context alone (score 590 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0464c hyp |
hypothetical protein | 883 | 883 ctx | neighborhood:882 |
Rv0467 icl1 |
isocitrate lyase | 835 | 590 ctx | neighborhood:403 textmining:616 |
Rv0466 hyp |
hypothetical protein | 551 | 551 ctx | neighborhood:551 |
Rv1130 prpD |
2-methylcitrate dehydratase | 763 | 540 ctx | cooccurence:474 textmining:507 |
Rv0332 hyp |
hypothetical protein | 523 | 497 | experimental:434 |
Rv0366c hyp |
hypothetical protein | 476 | 448 | experimental:434 |
Rv3833 |
AraC family transcriptional regulator | 419 | 341 | |
Rv1915 aceAa |
isocitrate lyase AceAa | 498 | 317 | |
Rv1837c glcB |
malate synthase | 423 | 171 | |
Rv1994c cmtR |
HTH-type transcriptional regulator CmtR | 416 | 69 | textmining:400 |
Rv1776c |
transcriptional regulator | 462 | 55 | textmining:455 |
Rv3173c |
TetR/Acr family transcriptional regulator | 491 | 52 | textmining:486 |
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: HTH-type transcriptional regulator
- MTBC0 PGAP product: acetate metabolism transcriptional regulator RamB
- Pfam (hmmscan --cut_ga): HTH_19 PF12844.14 (E=1e-10), HTH_31 PF13560.13 (E=1e-09), HTH_3 PF01381.29 (E=9e-13), Peptidase_M78 PF06114.20 (E=5e-27), ScfRs PF09856.15 (E=5e-70)
- (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_214979.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_19 (PF12844.14), HTH_31 (PF13560.13), HTH_3 (PF01381.29), Peptidase_M78 (PF06114.20), ScfRs (PF09856.15)
- 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
COG1396 - Curated reference: UniProt P9WMI1 (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 —
12 functional partner(s); context anchor
icl1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000489|Rv0465c|ramB MSKTYVGSRVRQLRNERGFSQAALAQMLEISPSYLNQIEHDVRPLTVAVLLRITEVFGVDATFFASQDDTRLVAELREVTLDRDLDIAIDPHEVAEMVSAHPGLARAVVNLHRRYRITTAQLAAATEERFSDGSGRGSITMPHEEVRDYFYQRQNYLHALDTAAEDLTAQMRMHHGDLARELTRRLTEVHGVRINKRIDLGDTVLHRYDPATNTLEISSHLSPGQQVFKMAAELAYLEFGDLIDAMVTDGKFTSAESRTLARLGLANYFAAATVLPYRQFHDVAENFRYDVERLSAFYSVSYETIAHRLSTLQRPSMRGVPFTFVRVDRAGNMSKRQSATGFHFSSSGGTCPLWNVYETFANPGKILVQIAQMPDGRNYLWVARTVELRAARYGQPGKTFAIGLGCELRHAHRLVYSEGLDLSGDPNTAATPIGAGCRVCERDNCPQRAFPALGRALDLDEHRSTVSPYLVKQL