xerD Resolved · high auto-curated
H37Rv Rv1701 · MTBC0 mtbc0_001809 ·
311 aa · 1938217–1939152 (+) ·
RefSeq NP_216217.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tyrosine recombinase XerD |
|---|---|
| MTBC0 PGAP re-annotation | site-specific tyrosine recombinase XerD |
| Revised (this work) | Site-specific tyrosine recombinase XerD. 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 |
P9WF33
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Tyrosine recombinase XerD |
| 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. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| Preferred name | xerD |
| eggNOG description | Tyrosine recombinase XerD |
| Orthologous group | COG4974 |
| KEGG orthology |
K03733, K04763
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.262 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 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 | 8.8e-21 | 8–98 | Phage integrase, N-terminal SAM-like domain |
Phage_integrase | PF00589.28 | 8.9e-46 | 121–294 | Phage integrase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1700 (NUDIX hydrolase), high confidence from genomic context alone (score 976 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1700 |
NUDIX hydrolase | 996 | 976 ctx | neighborhood:882 coexpression:801 textmining:870 |
Rv1699 pyrG |
CTP synthase | 990 | 932 ctx | neighborhood:882 coexpression:449 textmining:860 |
Rv1697 steA hyp |
hypothetical protein | 766 | 767 ctx | neighborhood:731 |
Rv1698 mctB |
copper transporter MctB | 761 | 761 ctx | neighborhood:754 |
Rv1694 tlyA |
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | 646 | 646 ctx | neighborhood:625 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 641 | 641 ctx | neighborhood:625 |
Rv2748c ftsK |
DNA translocase FtsK | 717 | 602 ctx | cooccurence:596 |
Rv2584c apt |
adenine phosphoribosyltransferase | 527 | 527 | coexpression:462 |
Rv1696 recN |
DNA repair protein RecN | 546 | 517 ctx | neighborhood:503 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 496 | 497 | coexpression:435 |
Rv3917c parB |
chromosome partitioning protein ParB | 517 | 491 ctx | cooccurence:481 |
Rv3242c hyp |
hypothetical protein | 469 | 469 | coexpression:467 |
Rv1423 whiA |
transcriptional regulator WhiA | 448 | 448 | coexpression:448 |
Rv3226c hyp |
hypothetical protein | 454 | 434 | coexpression:434 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 420 | 420 | coexpression:420 |
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 XerD
- MTBC0 PGAP product: site-specific tyrosine recombinase XerD
- Pfam (hmmscan --cut_ga): Phage_int_SAM_1 PF02899.24 (E=9e-21), Phage_integrase PF00589.28 (E=9e-46)
- (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_216217.1)
- 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 P9WF33 (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 —
22 functional partner(s); context anchor
Rv1700 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001809|Rv1701|xerD MKTLALQLQGYLDHLTIERGVAANTLSSYRRDLRRYSKHLEERGITDLAKVGEHDVSEFLVALRRGDPDSGTAALSAVSAARALIAVRGLHRFAAAEGLAELDVARAVRPPTPSRRLPKSLTIDEVLSLLEGAGGDKPSDGPLTLRNRAVLELLYSTGARISEAVGLDLDDIDTHARSVLLRGKGGKQRLVPVGRPAVHALDAYLVRGRPDLARRGRGTAAIFLNARGGRLSRQSAWQVLQDAAERAGITAGVSPHMLRHSFATHLLEGGADVRVVQELLGHASVTTTQIYTLVTVHALREVWAGAHPRAR