xerC Resolved · high auto-curated
H37Rv Rv2894c · MTBC0 mtbc0_003076 ·
298 aa · 3224223–3225119 (-) ·
RefSeq NP_217410.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tyrosine recombinase XerC |
|---|---|
| MTBC0 PGAP re-annotation | tyrosine recombinase XerC |
| Revised (this work) | Tyrosine recombinase XerC. Pfam: Phage_int_SAM_1 (PF02899.24), Phage_integrase (PF00589.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WF35
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Tyrosine recombinase XerC |
| Curated function | Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | xerC |
| eggNOG description | Belongs to the 'phage' integrase family. XerC subfamily |
| Orthologous group | COG4974 |
| KEGG orthology |
K03733, K04763
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 0.202 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 3 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 |
|---|---|---|---|---|
Phage_int_SAM_1 | PF02899.24 | 2.7e-23 | 5–87 | Phage integrase, N-terminal SAM-like domain |
Phage_integrase | PF00589.28 | 1.5e-50 | 109–284 | Phage integrase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2646 (integrase), high confidence from genomic context alone (score 798 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3242c hyp |
hypothetical protein | 902 | 902 | coexpression:902 |
Rv2584c apt |
adenine phosphoribosyltransferase | 853 | 853 | coexpression:853 |
Rv2646 |
integrase | 798 | 798 ctx | cooccurence:773 |
Rv2895c viuB |
mycobactin utilization protein ViuB | 780 | 780 ctx | neighborhood:779 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 774 | 774 | coexpression:766 |
Rv1423 whiA |
transcriptional regulator WhiA | 772 | 772 | coexpression:767 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 780 | 770 | coexpression:731 |
Rv1435c hyp |
hypothetical protein | 780 | 770 | coexpression:770 |
Rv3226c hyp |
hypothetical protein | 775 | 767 | coexpression:767 |
Rv0063 |
oxidoreductase | 746 | 746 | coexpression:746 |
Rv2154c ftsW |
lipid II flippase FtsW | 753 | 743 | coexpression:735 |
Rv3717 hyp |
hypothetical protein | 739 | 739 | coexpression:731 |
Rv3209 hyp |
hypothetical protein | 729 | 729 | coexpression:729 |
Rv2896c dprA hyp |
hypothetical protein | 672 | 652 ctx | neighborhood:578 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 646 | 646 | coexpression:646 |
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: tyrosine recombinase XerC
- MTBC0 PGAP product: tyrosine recombinase XerC
- Pfam (hmmscan --cut_ga): Phage_int_SAM_1 PF02899.24 (E=3e-23), Phage_integrase PF00589.28 (E=1e-50)
- (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_217410.1)
- Domains: Pfam-A via hmmscan --cut_ga — Phage_int_SAM_1 (PF02899.24), Phage_integrase (PF00589.28)
- 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
COG4974 - Curated reference: UniProt P9WF35 (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 —
44 functional partner(s); context anchor
Rv2646 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003076|Rv2894c|xerC MQAILDEFDEYLALQCGRSVHTRRAYLGDLRSLFAFLADRGSSLDALTLSVLRSWLAATAGAGAARTTLARRTSAVKAFTAWAVRRGLLAGDPAARLQVPKARRTLPAVLRQDQALRAMAAAESGAEQGDPLALRDRLIVELLYATGIRVSELCGLDVDDIDTGHRLVRVLGKGNKQRTVPFGQPAADALHAWLVDGRRALVTAESGHALLLGARGRRLDVRQARTAVHQTVAAVDGAPDMGPHGLRHSAATHLLEGGADLRVVQELLGHSSLATTQLYTHVAVARLRAVHERAHPRA