devS Resolved · high auto-curated
H37Rv Rv3132c · MTBC0 mtbc0_003329 ·
578 aa · 3518894–3520630 (-) ·
RefSeq NP_217648.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | two component sensor histidine kinase DevS |
|---|---|
| MTBC0 PGAP re-annotation | two-component system sensor histidine kinase DevS |
| Revised (this work) | Two-component system sensor histidine kinase DevS. Pfam: GAF_2 (PF13185.13), GAF (PF01590.33), GAF_3 (PF13492.13), HisKA_3 (PF07730.20), HATPase_c (PF02518.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGK3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Oxygen sensor histidine kinase response regulator DevS/DosS |
| EC (curated) |
EC 2.7.13.3
|
| Curated function | Member of the two-component regulatory system DevR/DevS (DosR/DosS) involved in onset of the dormancy response. Regulates an approximately 48-member regulon. Required for full induction of the DevR (DosR) regulon; acts later than DosT to positively regulate expression of the DevR regulon during adaptation to anaerobiosis. Characterized as an oxygen sensor; O(2) acts as a switch, with O(2)-bound Fe(2+) protein inactive in autophosphorylation. Has also been suggested to act as a redox sensor, or perhaps as a dual oxygen/redox sensor. Autophosphorylates under anaerobic but not aerobic conditions,. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | devS |
| eggNOG description | the two-component regulatory system DevR DevS (DosR DosS) involved in onset of the dormancy response. May act as a |
| Orthologous group | COG2203 |
| EC number |
EC 2.7.13.3
|
| KEGG orthology |
K07682
|
| KEGG pathways |
map02020
|
| KEGG modules |
M00482
|
| Gene Ontology (71) |
GO:0000166, GO:0000287, GO:0003674, GO:0003824, GO:0004672, GO:0005488, GO:0005524, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006464 +59 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 | 0.722 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 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 |
|---|---|---|---|---|
GAF_2 | PF13185.13 | 4.2e-16 | 62–200 | GAF domain |
GAF | PF01590.33 | 4.1e-16 | 63–200 | GAF domain |
GAF_3 | PF13492.13 | 1.7e-07 | 320–368 | GAF domain |
HisKA_3 | PF07730.20 | 5.9e-13 | 387–447 | Histidine kinase |
HATPase_c | PF02518.32 | 2.9e-12 | 491–576 | Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: devR (two component transcriptional regulator DevR), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3133c devR |
two component transcriptional regulator DevR | 999 | 1000 ctx | neighborhood:882 cooccurence:769 coexpression:895 experimental:544 database:900 textmining:963 |
Rv3134c |
universal stress protein | 989 | 946 ctx | neighborhood:744 coexpression:730 textmining:809 |
Rv0569 hyp |
hypothetical protein | 904 | 870 | coexpression:803 |
Rv2005c |
universal stress protein | 850 | 838 | coexpression:833 |
Rv1736c narX |
nitrate reductase-like protein NarX | 871 | 819 | coexpression:799 |
Rv2624c |
universal stress protein | 845 | 814 | coexpression:744 |
Rv2004c hyp |
hypothetical protein | 822 | 811 | coexpression:805 |
Rv2028c |
universal stress protein | 888 | 809 | coexpression:748 textmining:440 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 827 | 807 | coexpression:806 |
Rv2629 hyp |
hypothetical protein | 797 | 797 | coexpression:797 |
Rv1997 ctpF |
cation transporter ATPase F | 829 | 795 | coexpression:793 |
Rv0844c narL |
nitrate/nitrite response transcriptional regulator NarL | 877 | 792 ctx | cooccurence:612 textmining:437 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 840 | 781 | coexpression:774 |
Rv0571c hyp |
hypothetical protein | 772 | 772 | coexpression:759 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 782 | 756 | 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: two component sensor histidine kinase DevS
- MTBC0 PGAP product: two-component system sensor histidine kinase DevS
- Pfam (hmmscan --cut_ga): GAF_2 PF13185.13 (E=4e-16), GAF PF01590.33 (E=4e-16), GAF_3 PF13492.13 (E=2e-07), HisKA_3 PF07730.20 (E=6e-13), HATPase_c PF02518.32 (E=3e-12)
- (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_217648.1)
- Domains: Pfam-A via hmmscan --cut_ga — GAF_2 (PF13185.13), GAF (PF01590.33), GAF_3 (PF13492.13), HisKA_3 (PF07730.20), HATPase_c (PF02518.32)
- 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
COG2203 - Curated reference: UniProt P9WGK3 (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 —
58 functional partner(s); context anchor
devR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003329|Rv3132c|devS MTTGGLVDENDGAAMRPLRHTLSQLRLHELLVEVQDRVEQIVEGRDRLDGLVEAMLVVTAGLDLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIGLLIEDPKPLRLDDVSAHPASIGFPPYHPPMRTFLGVPVRVRDESFGTLYLTDKTNGQPFSDDDEVLVQALAAAAGIAVANARLYQQAKARQSWIEATRDIATELLSGTEPATVFRLVAAEALKLTAADAALVAVPVDEDMPAADVGELLVIETVGSAVASTVGRTIPVAGAVLREVFVNGIPRRVDRVDLEGLDELADAGPALLLPLRARGTVAGVVVVLSQGGPGAFTDEQLEMMAAFADQAALAWQLATSQRRMRELDVLTDRDRIARDLHDHVIQRLFAIGLALQGAVPHERNPEVQQRLSDVVDDLQDVIQEIRTTIYDLHGASQGITRLRQRIDAAVAQFADSGLRTSVQFVGPLSVVDSALADQAEAVVREAVSNAVRHAKASTLTVRVKVDDDLCIEVTDNGRGLPDEFTGSGLTNLRQRAEQAGGEFTLASVPGASGTVLRWSAPLSQ