smtB Family assigned · medium auto-curated
H37Rv Rv2358 · MTBC0 mtbc0_002510 ·
135 aa · 2665439–2665846 (+) ·
RefSeq NP_216874.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator SmtB |
|---|---|
| MTBC0 PGAP re-annotation | metalloregulator ArsR/SmtB family transcription factor |
| Revised (this work) | Metalloregulator ArsR/SmtB family transcription factor. Pfam: HTH_20 (PF12840.14), HTH_5 (PF01022.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMI5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional repressor SmtB |
| Curated function | Transcriptional regulator involved in zinc homeostasis. Represses the expression of the smtB-zur operon in the absence of zinc. Could act as the metal sensor that controls the expression of zur in response to zinc availability. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | smtB |
| eggNOG description | transcriptional |
| Orthologous group | COG0640 |
| KEGG orthology |
K22298
|
| Gene Ontology (32) |
GO:0001067, GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0006355, GO:0008150, GO:0009889, GO:0010035, GO:0010038, GO:0010043, GO:0010468 +20 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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_20 | PF12840.14 | 2.4e-06 | 55–103 | Helix-turn-helix domain |
HTH_5 | PF01022.27 | 5.0e-15 | 58–102 | Bacterial regulatory protein, arsR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: zur (zinc uptake regulation protein), high confidence from genomic context alone (score 907 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2359 zur |
zinc uptake regulation protein | 965 | 907 ctx | neighborhood:882 textmining:639 |
Rv2642 |
ArsR family transcriptional regulator | 565 | 566 ctx | cooccurence:564 |
Rv2357c glyS |
glycine--tRNA ligase | 565 | 565 ctx | neighborhood:565 |
Rv1994c cmtR |
HTH-type transcriptional regulator CmtR | 797 | 433 ctx | cooccurence:429 textmining:658 |
Rv0081 |
HTH-type transcriptional regulator | 664 | 432 ctx | cooccurence:432 textmining:433 |
Rv1674c |
transcriptional regulator | 501 | 309 | |
Rv3270 ctpC |
manganese/zinc-exporting P-type ATPase | 406 | 293 | |
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase | 408 | 260 | |
Rv3744 nmtR |
HTH-type transcriptional regulator NmtR | 408 | 234 | |
Rv2788 sirR |
transcriptional repressor SirR | 455 | 226 | |
Rv2711 ideR |
iron-dependent repressor and activator IdeR | 413 | 209 | |
Rv2641 cadI |
cadmium inducible protein CadI | 658 | 84 | textmining:643 |
Rv2025c |
cation efflux system protein | 719 | 78 | textmining:708 |
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 SmtB
- MTBC0 PGAP product: metalloregulator ArsR/SmtB family transcription factor
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=2e-06), HTH_5 PF01022.27 (E=5e-15)
- (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_216874.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_20 (PF12840.14), HTH_5 (PF01022.27)
- 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
COG0640 - Curated reference: UniProt P9WMI5 (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 —
13 functional partner(s); context anchor
zur - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002510|Rv2358|smtB MVTSPSTPTAAHEDVGADEVGGHQHPADRFAECPTFPAPPPREILDAAGELLRALAAPVRIAIVLQLRESQRCVHELVDALHVPQPLVSQHLKILKAAGVVTGERSGREVLYRLADHHLAHIVLDAVAHAGEDAI