nusA Resolved · high auto-curated
H37Rv Rv2841c · MTBC0 mtbc0_003020 ·
347 aa · 3169051–3170094 (-) ·
RefSeq NP_217357.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcription termination/antitermination protein NusA |
|---|---|
| MTBC0 PGAP re-annotation | transcription termination factor NusA |
| Revised (this work) | Transcription termination factor NusA. Pfam: NusA_N (PF08529.17), KH_NusA_1st (PF13184.13), KH_NusA_2nd (PF26594.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIV3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcription termination/antitermination protein NusA |
| Curated function | Participates in both transcription termination and antitermination. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | nusA |
| eggNOG description | Participates in both transcription termination and antitermination |
| Orthologous group | COG0195 |
| KEGG orthology |
K02600
|
| Gene Ontology (43) |
GO:0003674, GO:0003676, GO:0003723, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006355 +31 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 | 0.697 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
NusA_N | PF08529.17 | 6.3e-09 | 6–61 | NusA N-terminal domain |
KH_NusA_1st | PF13184.13 | 2.5e-30 | 183–260 | NusA-like first KH domain |
KH_NusA_2nd | PF26594.2 | 6.8e-24 | 264–324 | NusA-like second KH domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rimP (ribosome maturation factor RimP), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2842c rimP |
ribosome maturation factor RimP | 994 | 994 ctx | neighborhood:881 coexpression:953 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 993 | 990 ctx | cooccurence:479 coexpression:755 experimental:927 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 991 | 990 | coexpression:819 experimental:928 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 988 | 986 ctx | cooccurence:442 coexpression:681 experimental:919 |
Rv0640 rplK |
50S ribosomal protein L11 | 983 | 983 | coexpression:842 experimental:892 |
Rv0683 rpsG |
30S ribosomal protein S7 | 972 | 970 | coexpression:858 experimental:778 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 978 | 968 | coexpression:803 experimental:790 |
Rv2840c hyp |
hypothetical protein | 960 | 960 ctx | neighborhood:760 coexpression:840 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 964 | 954 ctx | cooccurence:418 coexpression:784 experimental:652 |
Rv3458c rpsD |
30S ribosomal protein S4 | 950 | 948 | coexpression:757 experimental:793 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 981 | 944 | coexpression:413 experimental:882 textmining:675 |
Rv2839c infB |
translation initiation factor IF-2 | 955 | 942 ctx | neighborhood:492 coexpression:861 |
Rv2890c rpsB |
30S ribosomal protein S2 | 942 | 931 | coexpression:839 experimental:474 |
Rv0707 rpsC |
30S ribosomal protein S3 | 931 | 929 | coexpression:844 experimental:503 |
Rv0715 rplX |
50S ribosomal protein L24 | 922 | 922 | coexpression:854 experimental:488 |
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 termination/antitermination protein NusA
- MTBC0 PGAP product: transcription termination factor NusA
- Pfam (hmmscan --cut_ga): NusA_N PF08529.17 (E=6e-09), KH_NusA_1st PF13184.13 (E=2e-30), KH_NusA_2nd PF26594.2 (E=7e-24)
- (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_217357.1)
- Domains: Pfam-A via hmmscan --cut_ga — NusA_N (PF08529.17), KH_NusA_1st (PF13184.13), KH_NusA_2nd (PF26594.2)
- 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
COG0195 - Curated reference: UniProt P9WIV3 (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 —
176 functional partner(s); context anchor
rimP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003020|Rv2841c|nusA MNIDMAALHAIEVDRGISVNELLETIKSALLTAYRHTQGHQTDARIEIDRKTGVVRVIARETDEAGNLISEWDDTPEGFGRIAATTARQVMLQRFRDAENERTYGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPGESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLVRKLFSLEVPEIADGSVEIVAVAREAGHRSKIAVRSNVAGLNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDDPARFVANALSPAKVVSVSVIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAPPPPPGQPEPGVSRGMAHDR