xseA Family assigned · medium auto-curated
H37Rv Rv1108c · MTBC0 mtbc0_001190 ·
415 aa · 1242653–1243900 (-) ·
RefSeq NP_215624.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | exodeoxyribonuclease VII large subunit |
|---|---|
| MTBC0 PGAP re-annotation | exodeoxyribonuclease VII large subunit |
| Revised (this work) | Exodeoxyribonuclease VII large subunit. Pfam: tRNA_anti_2 (PF13742.13), Exonuc_VII_L (PF02601.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WF31
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Exodeoxyribonuclease 7 large subunit |
| EC (curated) |
EC 3.1.11.6
|
| Curated function | Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | xseA |
| eggNOG description | Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides |
| Orthologous group | COG1570 |
| EC number |
EC 3.1.11.6
|
| KEGG orthology |
K03601
|
| KEGG pathways |
map03430
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.315 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 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 |
|---|---|---|---|---|
tRNA_anti_2 | PF13742.13 | 3.2e-14 | 12–105 | OB-fold nucleic acid binding domain |
Exonuc_VII_L | PF02601.21 | 9.3e-62 | 128–342 | Exonuclease VII, large subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: xseB (exodeoxyribonuclease VII small subunit), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1107c xseB |
exodeoxyribonuclease VII small subunit | 999 | 999 ctx | neighborhood:882 coexpression:890 experimental:474 database:900 textmining:622 |
Rv1109c hyp |
hypothetical protein | 886 | 886 ctx | neighborhood:882 |
Rv1106c |
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase | 883 | 883 ctx | neighborhood:882 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 788 | 787 ctx | neighborhood:782 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 671 | 671 | coexpression:590 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 605 | 587 | coexpression:587 |
Rv1709 scpA |
segregation and condensation protein ScpA | 462 | 463 | |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 462 | 462 | |
Rv2883c pyrH |
uridylate kinase | 453 | 454 | coexpression:423 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 446 | 446 | |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 455 | 424 | coexpression:405 |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 453 | 422 | coexpression:403 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 452 | 421 | coexpression:402 |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 452 | 421 | coexpression:402 |
Rv0989c grcC2 |
polyprenyl-diphosphate synthase GrcC | 449 | 417 |
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: exodeoxyribonuclease VII large subunit
- MTBC0 PGAP product: exodeoxyribonuclease VII large subunit
- Pfam (hmmscan --cut_ga): tRNA_anti_2 PF13742.13 (E=3e-14), Exonuc_VII_L PF02601.21 (E=9e-62)
- (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_215624.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA_anti_2 (PF13742.13), Exonuc_VII_L (PF02601.21)
- 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
COG1570 - Curated reference: UniProt P9WF31 (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 —
51 functional partner(s); context anchor
xseB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001190|Rv1108c|xseA MTQNSAENPFPVRAVAIRVAGWIDKLGAVWVEGQLAQITMRPDAKTVFMVLRDPAADMSLTVTCSRDLVLSAPVKLAEGVQVVVCGKPSFYTGRGTFSLRLSEIRAVGIGELLARIDRLRRLLDAEGLFDPRLKRPIPYLPNMIGLITGRASAAERDVTTVASARWPAARFAVRNVAVQGPNAVGQIVEALRELDRDPDVDVIVLARGGGSVEDLLPFSDETLCRAIAACRTPVVSAVGHEPDNPLCDLVVDLRAATPTDAAKKVVPDTAAEQRLIDDLRRRSAQALRNWVSREQRAVAQLRSRPVLADPMTMVSVRAEEVHRARSTLRRNLTLMVAAETERIGHLAARLATLGPAATLARGYAIVQTVAQTGPEGGSEPQVLRSVHDAPEGTKLRVRVADGALAAVSEGQTNGL