sufR Family assigned · medium auto-curated
H37Rv Rv1460 · MTBC0 mtbc0_001562 ·
268 aa · 1655991–1656797 (+) ·
RefSeq NP_215976.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | suf operon transcriptional regulator SufR |
| Revised (this work) | Suf operon transcriptional regulator SufR. Pfam: HTH_20 (PF12840.14), HTH_24 (PF13412.13), HTH_5 (PF01022.27), HTH_11 (PF08279.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53151
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sufR |
| eggNOG description | regulatory protein |
| Orthologous group | COG2345 |
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 | 0.63 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (200) · clonal |
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 | 8.5e-09 | 43–84 | Helix-turn-helix domain |
HTH_24 | PF13412.13 | 1.8e-08 | 43–84 | Winged helix-turn-helix DNA-binding |
HTH_5 | PF01022.27 | 2.2e-06 | 43–84 | Bacterial regulatory protein, arsR family |
HTH_11 | PF08279.19 | 2.4e-06 | 44–84 | HTH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1465 (nitrogen fixation related protein), high confidence from genomic context alone (score 894 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1462 sufD hyp |
hypothetical protein | 909 | 906 ctx | neighborhood:882 |
Rv1465 |
nitrogen fixation related protein | 919 | 894 ctx | neighborhood:881 |
Rv1463 sufC |
ABC transporter ATP-binding protein | 891 | 891 ctx | neighborhood:882 |
Rv1464 csd |
cysteine desulfurase | 886 | 886 ctx | neighborhood:882 |
Rv1466 hyp |
hypothetical protein | 881 | 882 ctx | neighborhood:881 |
Rv3167c |
TetR family transcriptional regulator | 853 | 848 | coexpression:848 |
Rv2359 zur |
zinc uptake regulation protein | 847 | 847 | coexpression:842 |
Rv0212c nadR |
transcriptional regulator NadR | 827 | 828 | coexpression:827 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 825 | 826 | coexpression:800 |
Rv1461 sufB hyp |
hypothetical protein | 830 | 823 ctx | neighborhood:783 |
Rv1674c |
transcriptional regulator | 824 | 823 | coexpression:822 |
Rv1931c |
transcriptional regulator | 810 | 810 | coexpression:810 |
Rv1725c hyp |
hypothetical protein | 808 | 809 | coexpression:809 |
Rv3183 higA3 |
transcriptional regulator | 808 | 808 | coexpression:808 |
Rv1167c |
transcriptional regulator | 812 | 805 | coexpression:805 |
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: transcriptional regulator
- MTBC0 PGAP product: suf operon transcriptional regulator SufR
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=9e-09), HTH_24 PF13412.13 (E=2e-08), HTH_5 PF01022.27 (E=2e-06), HTH_11 PF08279.19 (E=2e-06)
- (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_215976.2)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_20 (PF12840.14), HTH_24 (PF13412.13), HTH_5 (PF01022.27), HTH_11 (PF08279.19)
- 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
COG2345 - Curated reference: UniProt O53151 (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 —
80 functional partner(s); context anchor
Rv1465 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001562|Rv1460|sufR MTSTTLPHRASLVDRSTEFCHTDVVKIPAVSTTVPAAVSDGHTRRAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAGDAEASAAAPWQQVGRGRPAKRYRLTAAGRAKLDHSYDDLASAAMRQLREIGGEEAVRTFARRRIDAILADVAPADGPDDAALEAAAERIATALSKAGYVATTTRVGGPIHGVQICQHHCPVSHVAEEFPELCETEQQAMAEVLGTHVQRLATIVNGDCACTTHVPLSPAPSPRPPATSTEGASR