xseB Family assigned · medium auto-curated
H37Rv Rv1107c · MTBC0 mtbc0_001189 ·
85 aa · 1242406–1242663 (-) ·
RefSeq NP_215623.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | exodeoxyribonuclease VII small subunit |
|---|---|
| MTBC0 PGAP re-annotation | exodeoxyribonuclease VII small subunit |
| Revised (this work) | Exodeoxyribonuclease VII small subunit. Pfam: Exonuc_VII_S (PF02609.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WF29
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Exodeoxyribonuclease 7 small 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 | xseB |
| eggNOG description | Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides |
| Orthologous group | COG1722 |
| EC number |
EC 3.1.11.6
|
| KEGG orthology |
K03602
|
| KEGG pathways |
map03430
|
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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Exonuc_VII_S | PF02609.22 | 2.9e-16 | 24–74 | Exonuclease VII small subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: xseA (exodeoxyribonuclease VII large subunit), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1108c xseA |
exodeoxyribonuclease VII large 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 | 888 | 884 ctx | neighborhood:882 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 808 | 788 ctx | neighborhood:782 |
Rv0510 hemC |
porphobilinogen deaminase | 678 | 678 | coexpression:678 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 637 | 637 ctx | cooccurence:636 |
Rv2699c hyp |
hypothetical protein | 587 | 587 ctx | cooccurence:587 |
Rv3195 hyp |
hypothetical protein | 576 | 577 ctx | cooccurence:574 |
Rv0807 hyp |
hypothetical protein | 569 | 569 ctx | cooccurence:565 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 669 | 568 ctx | cooccurence:530 |
Rv1830 |
HTH-type transcriptional regulator | 567 | 567 ctx | cooccurence:557 |
Rv2588c yajC |
membrane protein secretion factor YajC | 572 | 531 | coexpression:443 |
Rv1423 whiA |
transcriptional regulator WhiA | 529 | 529 ctx | cooccurence:525 |
Rv1540 |
RNA pseudouridine synthase | 542 | 523 | coexpression:414 |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 552 | 516 | coexpression: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 small subunit
- MTBC0 PGAP product: exodeoxyribonuclease VII small subunit
- Pfam (hmmscan --cut_ga): Exonuc_VII_S PF02609.22 (E=3e-16)
- (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_215623.1)
- Domains: Pfam-A via hmmscan --cut_ga — Exonuc_VII_S (PF02609.22)
- 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
COG1722 - Curated reference: UniProt P9WF29 (SwissProt, reviewed; Evidence at protein level)
- 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
xseA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001189|Rv1107c|xseB MVCDPNGDDTGRTHATVPVSQLGYEACRDELMEVVRLLEQGGLDLDASLRLWERGEQLAKRCEEHLAGARQRVSDVLAGDEAQNG