recA Resolved · high auto-curated
H37Rv Rv2737c · MTBC0 mtbc0_002911 ·
790 aa · 3071467–3073839 (-) ·
RefSeq NP_217253.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | recombinase A |
|---|---|
| MTBC0 PGAP re-annotation | intein-containing recombinase RecA |
| Revised (this work) | Intein-containing recombinase RecA. Pfam: RecA_N (PF00154.28), Rad51 (PF08423.18), Intein_splicing (PF14890.12), LAGLIDADG_3 (PF14528.12), RecA_C (PF21096.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHJ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein RecA |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage.; FUNCTION: PI-MtuI is an endonuclease. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recA |
| eggNOG description | Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage |
| Orthologous group | COG0468 |
| KEGG orthology |
K03553
|
| KEGG pathways |
map03440
|
| KEGG modules |
M00729
|
| Gene Ontology (89) |
GO:0000150, GO:0000166, GO:0000287, GO:0000725, GO:0003674, GO:0003676, GO:0003677, GO:0003697, GO:0003824, GO:0004518, GO:0004519, GO:0004520 +77 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 | 0.253 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 12 synonymous, 9 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 |
|---|---|---|---|---|
RecA_N | PF00154.28 | 3.0e-131 | 9–252 | RecA N-terminal domain |
Rad51 | PF08423.18 | 2.5e-06 | 35–259 | Rad51 |
Intein_splicing | PF14890.12 | 6.2e-10 | 268–691 | Intein splicing domain |
LAGLIDADG_3 | PF14528.12 | 2.6e-12 | 464–554 | LAGLIDADG-like domain |
RecA_C | PF21096.3 | 7.0e-25 | 713–769 | RecA C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recX (regulatory protein RecX), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2736c recX |
regulatory protein RecX | 999 | 998 ctx | neighborhood:881 coexpression:984 textmining:865 |
Rv1629 polA |
DNA polymerase I | 996 | 987 | coexpression:460 experimental:898 database:585 textmining:750 |
Rv2720 lexA |
repressor LexA | 998 | 977 | coexpression:855 experimental:829 textmining:958 |
Rv3585 radA |
DNA repair protein RadA | 979 | 939 | coexpression:926 textmining:686 |
Rv2090 |
5'-3' exonuclease | 952 | 926 ctx | cooccurence:537 experimental:455 database:585 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 935 | 860 | coexpression:434 experimental:436 database:564 textmining:561 |
Rv2116 lppK |
lipoprotein LppK | 898 | 859 | coexpression:430 experimental:436 database:564 |
Rv1277 hyp |
hypothetical protein | 908 | 853 | experimental:449 database:635 textmining:406 |
Rv2101 helZ |
helicase HelZ | 944 | 852 | experimental:841 textmining:638 |
Rv3646c topA |
DNA topoisomerase I | 954 | 844 | experimental:446 database:635 textmining:720 |
Rv2735c hyp |
hypothetical protein | 901 | 841 ctx | neighborhood:801 textmining:403 |
Rv1278 hyp |
hypothetical protein | 859 | 816 | experimental:421 database:635 |
Rv3394c hyp |
hypothetical protein | 826 | 808 | experimental:439 database:523 |
Rv2529 hyp |
hypothetical protein | 851 | 806 | experimental:528 database:594 |
Rv1537 dinX |
DNA polymerase IV | 967 | 800 | experimental:439 database:523 textmining:845 |
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: recombinase A
- MTBC0 PGAP product: intein-containing recombinase RecA
- Pfam (hmmscan --cut_ga): RecA_N PF00154.28 (E=3e-131), Rad51 PF08423.18 (E=3e-06), Intein_splicing PF14890.12 (E=6e-10), LAGLIDADG_3 PF14528.12 (E=3e-12), RecA_C PF21096.3 (E=7e-25)
- (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_217253.1)
- Domains: Pfam-A via hmmscan --cut_ga — RecA_N (PF00154.28), Rad51 (PF08423.18), Intein_splicing (PF14890.12), LAGLIDADG_3 (PF14528.12), RecA_C (PF21096.3)
- 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
COG0468 - Curated reference: UniProt P9WHJ3 (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 —
296 functional partner(s); context anchor
recX - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002911|Rv2737c|recA MTQTPDREKALELAVAQIEKSYGKGSVMRLGDEARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFINQLRDKIGVMFGSPETTTGGKALKFYASVRMDVRRVETLKDGTNAVGNRTRVKVVKNKCLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAQPRRFDGFGDSAPIPADHARLLGYLIGDGRDGWVGGKTPINFINVQRALIDDVTRIAATLGCAAHPQGRISLAIAHRPGERNGVADLCQQAGIYGKLAWEKTIPNWFFEPDIAADIVGNLLFGLFESDGWVSREQTGALRVGYTTTSEQLAHQIHWLLLRFGVGSTVRDYDPTQKRPSIVNGRRIQSKRQVFEVRISGMDNVTAFAESVPMWGPRGAALIQAIPEATQGRRRGSQATYLAAEMTDAVLNYLDERGVTAQEAAAMIGVASGDPRGGMKQVLGASRLRRDRVQALADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEELHTLVAEGVVVHNCSPPFKQAEFDILYGKGISREGSLIDMGVDQGLIRKSGAWFTYEGEQLGQGKENARNFLVENADVADEIEKKIKEKLGIGAVVTDDPSNDGVLPAPVDF