mfd Resolved · high auto-curated
H37Rv Rv1020 · MTBC0 mtbc0_001096 ·
1234 aa · 1146304–1150008 (+) ·
RefSeq NP_215536.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcription-repair coupling factor |
|---|---|
| MTBC0 PGAP re-annotation | transcription-repair coupling factor |
| Revised (this work) | Transcription-repair coupling factor. Pfam: UvrB_inter (PF17757.7), CarD_TRCF_RID (PF02559.23), DEAD (PF00270.36), ResIII (PF04851.22), Helicase_C (PF00271.38), TRCF (PF03461.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMQ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcription-repair-coupling factor |
| EC (curated) |
EC 3.6.4.-
|
| Curated function | Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | mfd |
| eggNOG description | Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site |
| Orthologous group | COG1197 |
| KEGG orthology |
K03723
|
| KEGG pathways |
map03420
|
| Gene Ontology (11) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0044424, GO:0044444, 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 | 0.184 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 20 synonymous, 10 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 |
|---|---|---|---|---|
UvrB_inter | PF17757.7 | 3.2e-21 | 154–236 | UvrB interaction domain |
CarD_TRCF_RID | PF02559.23 | 1.3e-17 | 518–583 | CarD-like/TRCF RID domain |
DEAD | PF00270.36 | 3.3e-23 | 653–812 | DEAD/DEAH box helicase |
ResIII | PF04851.22 | 1.1e-05 | 653–806 | Type III restriction enzyme, res subunit |
Helicase_C | PF00271.38 | 3.9e-16 | 850–954 | Helicase conserved C-terminal domain |
TRCF | PF03461.21 | 3.0e-20 | 1060–1136 | TRCF domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mazG (nucleoside triphosphate pyrophosphohydrolase), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 963 | 949 | experimental:949 |
Rv1638 uvrA |
excinuclease ABC subunit UvrA | 975 | 918 | experimental:912 textmining:716 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 956 | 915 | experimental:915 textmining:509 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 913 | 904 | experimental:865 |
Rv1021 mazG |
nucleoside triphosphate pyrophosphohydrolase | 958 | 887 ctx | neighborhood:881 textmining:645 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 896 | 866 | experimental:865 |
Rv1024 |
membrane protein | 776 | 776 ctx | neighborhood:505 cooccurence:545 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 775 | 742 | coexpression:644 |
Rv3105c prfB |
peptide chain release factor PrfB | 773 | 739 | coexpression:690 |
Rv3625c mesJ |
tRNA(Ile)-lysidine synthase | 690 | 673 | coexpression:588 |
Rv1022 lpqU |
lipoprotein LpqU | 669 | 656 ctx | neighborhood:654 |
Rv1019 |
transcriptional regulator | 951 | 630 ctx | neighborhood:625 textmining:875 |
Rv1025 hyp |
hypothetical protein | 620 | 620 ctx | neighborhood:610 |
Rv3909 hyp |
hypothetical protein | 618 | 618 ctx | cooccurence:616 |
Rv1026 ppx2 hyp |
hypothetical protein | 615 | 616 ctx | neighborhood:610 |
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: transcription-repair coupling factor
- MTBC0 PGAP product: transcription-repair coupling factor
- Pfam (hmmscan --cut_ga): UvrB_inter PF17757.7 (E=3e-21), CarD_TRCF_RID PF02559.23 (E=1e-17), DEAD PF00270.36 (E=3e-23), ResIII PF04851.22 (E=1e-05), Helicase_C PF00271.38 (E=4e-16), TRCF PF03461.21 (E=3e-20)
- (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_215536.1)
- Domains: Pfam-A via hmmscan --cut_ga — UvrB_inter (PF17757.7), CarD_TRCF_RID (PF02559.23), DEAD (PF00270.36), ResIII (PF04851.22), Helicase_C (PF00271.38), TRCF (PF03461.21)
- 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
COG1197 - Curated reference: UniProt P9WMQ5 (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 —
60 functional partner(s); context anchor
mazG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001096|Rv1020|mfd MTAPGPACSDTPIAGLVELALSAPTFQQLMQRAGGRPDELTLIAPASARLLVASALARQGPLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLAHPDDAQLGPPLGVVVTSVRSLLQPMTPQLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACRELLLSEDVRARAAQLAARHPAAESTVTGSASDMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEASWSVAALGTAENQAPVDVEQLGGSGFVELDQVRAAAARTGHPWWTLSQLSDESAIELDVRAAPSARGHQRDIDEIFAMLRAHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAKRGGGAKNTDKLYVPMDSLDQLSRYVGGQAPALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTAASAATVRLSPLTLPDSAQVRLKRMYPGAHYRATTATVQVPIPRAGGLGAPRIRDVELVQMVADLITALAGKPRQHIGITNPSPPGEDGRGRNTTIKERQP