recF Resolved · high auto-curated
H37Rv Rv0003 · MTBC0 mtbc0_000003 ·
385 aa · 3280–4437 (+) ·
RefSeq NP_214517.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA replication/repair protein RecF |
|---|---|
| MTBC0 PGAP re-annotation | DNA replication/repair protein RecF |
| Revised (this work) | DNA replication/repair protein RecF. Pfam: SMC_N (PF02463.26), AAA_23 (PF13476.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHI9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA replication and repair protein RecF |
| Curated function | The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recF |
| eggNOG description | it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP |
| Orthologous group | COG1195 |
| KEGG orthology |
K03629
|
| KEGG pathways |
map03440
|
| Gene Ontology (46) |
GO:0000731, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006139, GO:0006259, GO:0006281, GO:0006302, GO:0006725 +34 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 | 0.466 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 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 |
|---|---|---|---|---|
SMC_N | PF02463.26 | 6.4e-17 | 2–353 | RecF/RecN/SMC N terminal domain |
AAA_23 | PF13476.13 | 1.4e-08 | 6–74 | AAA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dnaN (DNA polymerase III subunit beta), high confidence from genomic context alone (score 945 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0002 dnaN |
DNA polymerase III subunit beta | 992 | 945 ctx | neighborhood:855 coexpression:481 textmining:863 |
Rv0004 hyp |
hypothetical protein | 931 | 903 ctx | neighborhood:881 |
Rv0005 gyrB |
DNA gyrase subunit B | 975 | 900 ctx | neighborhood:727 coexpression:650 textmining:769 |
Rv0001 dnaA |
chromosomal replication initiator protein DnaA | 958 | 712 | coexpression:520 textmining:862 |
Rv0007 |
membrane protein | 649 | 616 ctx | neighborhood:612 |
Rv2147c sepF |
cell division protein SepF | 685 | 573 ctx | cooccurence:553 |
Rv0006 gyrA |
DNA gyrase subunit A | 861 | 548 ctx | neighborhood:525 textmining:707 |
Rv2116 lppK |
lipoprotein LppK | 555 | 496 | coexpression:467 |
Rv2838c rbfA |
ribosome-binding factor RbfA | 490 | 471 | coexpression:455 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 484 | 463 | |
Rv1122 gnd2 |
6-phosphogluconate dehydrogenase (decarboxylating) | 590 | 461 ctx | neighborhood:458 |
Rv3715c recR |
recombination protein RecR | 852 | 459 | textmining:738 |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 503 | 456 ctx | cooccurence:455 |
Rv1020 mfd |
transcription-repair coupling factor | 485 | 453 | |
Rv3423c alr |
alanine racemase | 471 | 424 ctx | cooccurence:422 |
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: DNA replication/repair protein RecF
- MTBC0 PGAP product: DNA replication/repair protein RecF
- Pfam (hmmscan --cut_ga): SMC_N PF02463.26 (E=6e-17), AAA_23 PF13476.13 (E=1e-08)
- (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_214517.1)
- Domains: Pfam-A via hmmscan --cut_ga — SMC_N (PF02463.26), AAA_23 (PF13476.13)
- 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
COG1195 - Curated reference: UniProt P9WHI9 (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 —
50 functional partner(s); context anchor
dnaN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000003|Rv0003|recF MYVRHLGLRDFRSWACVDLELHPGRTVFVGPNGYGKTNLIEALWYSTTLGSHRVSADLPLIRVGTDRAVISTIVVNDGRECAVDLEIATGRVNKARLNRSSVRSTRDVVGVLRAVLFAPEDLGLVRGDPADRRRYLDDLAIVRRPAIAAVRAEYERVLRQRTALLKSVPGARYRGDRGVFDTLEVWDSRLAEHGAELVAARIDLVNQLAPEVKKAYQLLAPESRSASIGYRASMDVTGPSEQSDTDRQLLAARLLAALAARRDAELERGVCLVGPHRDDLILRLGDQPAKGFASHGEAWSLAVALRLAAYQLLRVDGGEPVLLLDDVFAELDVMRRRALATAAESAEQVLVTAAVLEDIPAGWDARRVHIDVRADDTGSMSVVLP