whiA Family assigned · medium auto-curated
H37Rv Rv1423 · MTBC0 mtbc0_001523 ·
325 aa · 1607250–1608227 (+) ·
RefSeq NP_215939.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator WhiA |
|---|---|
| MTBC0 PGAP re-annotation | DNA-binding protein WhiA |
| Revised (this work) | DNA-binding protein WhiA. Pfam: WhiA_N (PF10298.15), LAGLIDADG_WhiA (PF14527.12), HTH_WhiA (PF02650.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WF45
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable cell division protein WhiA |
| Curated function | Involved in cell division and chromosome segregation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | whiA |
| eggNOG description | May be required for sporulation |
| Orthologous group | COG1481 |
| KEGG orthology |
K09762
|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0043937, GO:0044464, GO:0050789, GO:0050793, GO:0065007 +1 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 | 4.238 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 11 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 |
|---|---|---|---|---|
WhiA_N | PF10298.15 | 9.5e-23 | 18–102 | WhiA N-terminal LAGLIDADG-like domain |
LAGLIDADG_WhiA | PF14527.12 | 2.4e-25 | 125–216 | WhiA LAGLIDADG-like domain |
HTH_WhiA | PF02650.21 | 1.2e-21 | 219–301 | WhiA C-terminal HTH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uvrC (excinuclease ABC subunit UvrC), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1422 cuvA hyp |
hypothetical protein | 969 | 965 ctx | neighborhood:882 coexpression:673 |
Rv1421 rapZ hyp |
hypothetical protein | 948 | 941 ctx | neighborhood:882 coexpression:431 |
Rv1420 uvrC |
excinuclease ABC subunit UvrC | 883 | 883 ctx | neighborhood:882 |
Rv2894c xerC |
tyrosine recombinase XerC | 772 | 772 | coexpression:767 |
Rv2699c hyp |
hypothetical protein | 766 | 766 ctx | cooccurence:766 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 744 | 745 ctx | cooccurence:743 |
Rv1830 |
HTH-type transcriptional regulator | 754 | 719 ctx | cooccurence:716 |
Rv1417 |
membrane protein | 696 | 689 ctx | neighborhood:682 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 686 | 686 ctx | neighborhood:682 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 685 | 685 ctx | neighborhood:682 |
Rv2256c hyp |
hypothetical protein | 683 | 683 ctx | cooccurence:681 |
Rv1402 priA |
primosomal protein N' | 678 | 678 ctx | cooccurence:597 |
Rv2413c hyp |
hypothetical protein | 675 | 676 ctx | cooccurence:635 |
Rv1440 secG |
protein-export membrane protein SecG | 932 | 670 ctx | cooccurence:584 textmining:802 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 658 | 643 ctx | cooccurence:590 |
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 WhiA
- MTBC0 PGAP product: DNA-binding protein WhiA
- Pfam (hmmscan --cut_ga): WhiA_N PF10298.15 (E=1e-22), LAGLIDADG_WhiA PF14527.12 (E=2e-25), HTH_WhiA PF02650.21 (E=1e-21)
- (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_215939.1)
- Domains: Pfam-A via hmmscan --cut_ga — WhiA_N (PF10298.15), LAGLIDADG_WhiA (PF14527.12), HTH_WhiA (PF02650.21)
- 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
COG1481 - Curated reference: UniProt P9WF45 (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 —
102 functional partner(s); context anchor
uvrC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001523|Rv1423|whiA MTTDVKDELSRLVVKSVSARRAEVTSLLRFAGGLHIVGGRVVVEAELDLGSIARRLRKEIFELYGYTAVVHVLSASGIRKSTRYVLRVANDGEALARQTGLLDMRGRPVRGLPAQVVGGSIDDAEAAWRGAFLAHGSLTEPGRSSALEVSCPGPEAALALVGAARRLGVGAKAREVRGADRVVVRDGEAIGALLTRMGAQDTRLVWEERRLRREVRATANRLANFDDANLRRSARAAVAAAARVERALEILGDTVPEHLASAGKLRVEHRQASLEELGRLADPPMTKDAVAGRIRRLLSMADRKAKVDGIPDTESVVTPDLLEDA