nusB Resolved · high auto-curated
H37Rv Rv2533c · MTBC0 mtbc0_002699 ·
156 aa · 2881144–2881614 (-) ·
RefSeq NP_217049.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | N utilization substance protein B |
|---|---|
| MTBC0 PGAP re-annotation | transcription antitermination factor NusB |
| Revised (this work) | Transcription antitermination factor NusB. Pfam: NusB (PF01029.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIV1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcription antitermination protein NusB |
| Curated function | Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | nusB |
| eggNOG description | Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons |
| Orthologous group | COG0781 |
| KEGG orthology |
K03625
|
| 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
NusB | PF01029.24 | 1.1e-32 | 11–139 | NusB family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: efp (elongation factor P), high confidence from genomic context alone (score 910 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2532c hyp |
hypothetical protein | 968 | 969 ctx | neighborhood:882 coexpression:744 |
Rv2534c efp |
elongation factor P | 957 | 910 ctx | neighborhood:882 textmining:540 |
Rv2535c pepQ |
cytoplasmic peptidase PepQ | 911 | 888 ctx | neighborhood:882 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 892 | 835 | experimental:822 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 900 | 815 | experimental:652 textmining:482 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 745 | 711 | coexpression:416 experimental:446 |
Rv3404c hyp |
hypothetical protein | 710 | 683 | coexpression:650 |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 773 | 680 | coexpression:662 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 708 | 680 | coexpression:647 |
Rv2531c |
amino acid decarboxylase | 687 | 668 ctx | neighborhood:652 |
Rv2536 |
transmembrane protein | 650 | 650 ctx | neighborhood:646 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 652 | 610 | experimental:446 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 961 | 600 | experimental:420 textmining:908 |
Rv1630 rpsA |
30S ribosomal protein S1 | 598 | 583 | coexpression:432 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 602 | 577 | experimental:446 |
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: N utilization substance protein B
- MTBC0 PGAP product: transcription antitermination factor NusB
- Pfam (hmmscan --cut_ga): NusB PF01029.24 (E=1e-32)
- (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_217049.1)
- Domains: Pfam-A via hmmscan --cut_ga — NusB (PF01029.24)
- 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
COG0781 - Curated reference: UniProt P9WIV1 (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 —
77 functional partner(s); context anchor
efp - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002699|Rv2533c|nusB MSDRKPVRGRHQARKRAVDLLFEAEVRGISAAEVVDTRAALAEAKPDIARLHPYTAAVARGVSEHAAHIDDLITAHLRGWTLDRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAKELSTDDSPGFVNGVLGQVMLVTPQLRAAAQAVRGGA