nusB Resolved · high auto-curated

H37Rv Rv2533c · MTBC0 mtbc0_002699 · 156 aa · 2881144–2881614 MTBC0 (-) · 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).
Functional category (TubercuList)	information pathways

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

In the literature (TB corpus sweep) 6 publications

6 TB publications mention this gene. 6 publication(s) discuss this gene (6 in a M. tuberculosis context).

Most recent 5 of 6.
Publication	Date
Evolutionary comparison of ribosomal operon antitermination function. doi:10.1128/JB.00760-08	2008
Crystal structures of the antitermination factor NusB from Thermotoga maritima and implications for RNA binding. doi:10.1042/BJ20040889	2004
Spectroscopic and thermodynamic characterization of the transcription antitermination factor NusE and its interaction with NusB from Mycobacterium tuberculosis. doi:10.1021/bi0018279	2001
The crystal structure of NusB from Mycobacterium tuberculosis. doi:10.1038/75876	2000
The structure of the transcriptional antiterminator NusB from Escherichia coli. doi:10.1038/75869	2000

This layer CITES the literature and adds context; it does not change the verdict or the function stated elsewhere in this fiche. This distinguishes a gene that is dark because nobody has looked from one that is dark despite having been studied. Source: PubMed (whole): H37Rv locus tag + GENE NAME + ortholog identifiers (Mb…, MMAR_…, MSMEG_…, ML…, MAB_…), under a mycobacterial context filter; hits verified against the abstract text. Species-context counts distinguish M. tuberculosis literature from literature on other mycobacteria. phase76/phase77, 2026-07-13.

Genomic-neighbour overlap (structural caveat) co-directional · 0 % of gene

Neighbour	Rv2532c (Rv2532c, - strand)
Overlap	1 bp, 0 % of this gene's length

co-directional overlap: ordinary (e.g. shared stop/start codons in an operon), not the Rv2438A-type artefact P20.1, derived from GFF3 gene coordinates, 2026-08-03.

CRISPRi vulnerability

Vulnerability index -4.82 (95% CI -6.29 to -3.39). A more negative index = more vulnerable to knockdown (better drug-target quality); indicative threshold VI ≤ -6 = highly vulnerable.

Quantitative CRISPRi knockdown, graded (finer than binary Tn-seq essentiality). Source: CRISPRi vulnerability index (Bosch 2021, pebble.rockefeller.edu).

Legacy record & comparison (Mycobrowser)

Mycobrowser function	Involved in the transcription termination process. Interacts with RPSJ\|NUSE\|Rv0700.

The legacy Mycobrowser record is shown for verification. Mycobrowser is no longer maintained; its EC numbers predate recent nomenclature revisions, so a class change usually reflects re-numbering, not a conflict.

Orthologues (reciprocal best hits across mycobacteria)

M. bovis	`Mb2562c` · 99.4% identity
M. leprae	`ML0523` · 75.7% identity
M. marinum	`MMAR_2182` · 80.5% identity
M. smegmatis	`MSMEG_3036` · 79.9% identity
M. orygis	`RJtmp_002622` · 99.4% identity
M. abscessus	`MAB_2836c` · 73.9% identity

Reciprocal-best-hit orthologues (DIAMOND) against the Mycobrowser reference proteomes. A missing species is informative: e.g. a gene absent from M. leprae was likely lost in its reductive genome evolution. Locus tags link to Mycobrowser.

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.

Outgroup conservation (beyond the MTBC) Bacteria

M. canettii dN/dS (deep-divergence selection)	inf (low power) · 1 consensus substitution(s) low power (1 canettii-consensus substitution(s)); present in M. canettii but dN/dS not reliable
Genus-wide presence (~53 non-MTBC Mycobacterium)	present in 53/53 (100%) · mean identity 81.6% · 4/4 closest MTBAP relatives conserved across the genus (present in 53/53 non-MTBC Mycobacterium genomes, incl. distant relatives) — an ancient core gene predating the genus radiation
Phylostratum (deepest detected homolog)	MTBC-specific → Mycobacterium → Mycobacteriaceae → Corynebacteriales → Actinomycetia → Bacteria detected in 13/13 non-Mycobacterium reference genomes (down to Bacteria) · mean identity 48.9% detected down to outside the phylum (Proteobacteria/Firmicutes controls) — a universally conserved, ancient bacterial gene

Two orthogonal outgroup signals. M. canettii (the immediate outgroup) gives a deep-divergence dN/dS (a low value confirms a constrained, real gene; shown as confident only at ≥8 substitutions, else flagged low-power). Genus-wide presence/absence (tblastn vs assembled non-MTBC genomes) places the gene on the ancient-core ↔ MTBC-specific axis: a gene absent even from the closest MTBAP relatives is a candidate MTBC-specific innovation (possible host-adaptation factor, to confirm by synteny). The phylostratum extends that axis outside the genus (tblastn vs 13 reference genomes spanning Mycobacteriaceae → Corynebacteriales → Actinomycetia → outside the phylum): it is the deepest clade in which a homolog is still detected, i.e. a proxy for gene age. Read it with the null model in mind: a shallow (young) stratum can also reflect homology-detection failure for short or fast-evolving ORFs, so it is a descriptive axis, not a proof of novelty.

Essentiality (transposon mutagenesis) essential

DeJesus 2017 call	ES · essential
What the call means	essential: insertions absent across the whole ORF
TA sites (Himar1)	4 in the ORF — 4 in the essential state, 0 growth-defect, 0 non-essential, 0 growth-advantage. Saturation 0.000, mean read count 0. A region of the protein devoid of TA sites is invisible to this assay: nothing can be inferred about it, in either direction.
Caveat	Statistically thin call: only 4 TA (Himar1) sites in the whole ORF (atlas median 13; genes under 300 nt typically have very few). A DeJesus 2017 call built on so few independent observations is less robust than the same call on a longer gene, in either direction. Cross-check against the CRISPRi vulnerability index (independent of TA-site density) and, if this gene overlaps a neighbour (see Genomic-neighbour overlap section below), verify how many of its TA sites actually fall inside its own ORF. (P20.3)

Genome-wide Himar1 transposon essentiality in H37Rv (DeJesus 2017). An essential call (ES/ESD/GD) is strong, independent evidence that a "hypothetical" locus encodes a functional, selectively required gene — orthogonal to intra-species conservation.

Chemical-genetic target & druggability (PROSPECT) hypomorph tool strain

This gene is part of the PROSPECT collection of TetON transcriptional-knockdown (hypomorph) strains of essential M. tuberculosis genes, built as a sensitised background for chemical-genetic mechanism-of-action deconvolution. Being in the panel means the gene is an essential / vulnerable target for which a validated knockdown tool strain exists.

Hypomorph strain	Rv2533c-nusB_TetOn6.1 (TetON promoter 6)
Baseline knockdown fitness	2.357 median doublings (across 1 screen pool(s)) — fewer doublings = stronger growth defect on knockdown
Used in target deconvolution	no (Excluded - not in all screening waves)

Panel membership reflects essentiality/vulnerability and the availability of a genetic tool, not a specific molecular function; it never changes the verdict here. Source: Bond AN et al., Nat Commun 2025;16:9673 (doi:10.1038/s41467-025-64662-x); PROSPECT chemical-genetic platform.

Proteomics (mass spectrometry) detected

MS detection	detected in 13 of 16 independent MS datasets
Integrated abundance	175.0 ppm · rank 920/3519 (73.9th percentile)

Detection by mass spectrometry is direct, experimental evidence that the protein product exists — orthogonal to sequence conservation and to Tn-seq essentiality, and especially decisive for a "hypothetical" locus. Reproducible detection across several independent datasets (PaxDb) makes the existence claim robust; the integrated abundance places the protein in the proteome's dynamic range.

Physico-chemical properties (computed, ProtParam)

Length	156 aa
Molecular weight	16.8 kDa
Theoretical pI	6.29
GRAVY	-0.0 (hydrophilic)
Aliphatic index	107.0
Aromaticity	0.032
Instability index	23.1 (stable)

Computed from the ancestral MTBC0 sequence with the ExPASy ProtParam method (Biopython). Descriptive biophysical context: a positive GRAVY flags a hydrophobic (often membrane) protein, a high instability index (>40) predicts a short in-vitro half-life, an extreme pI hints at compartment or binding partner.

Domains (Pfam, hmmscan --cut_ga)

Pfam	Accession	i-Evalue	Residues	Description
`NusB`	PF01029.24	1.1e-32	11–139	NusB family

Experimental structures (Protein Data Bank) 1 solved

PDB	Method	Resolution	Coverage
`1eyv`	X-ray diffraction	1.6 Å	100%

Experimentally solved structures mapped from the UniProt accession via PDBe/SIFTS (1 total; up to 8 shown, ranked by sequence coverage then resolution). An experimental structure is direct proof of the folded product and the strongest structural evidence — superseding the predicted ESMFold/AlphaFold models below for any covered region.

Structural search (AlphaFold DB model, Foldseek vs PDB — genome-wide) pLDDT 92.7

PDB hit	prob	TM-score	E-value	Description
`1eyv-assembly1_A`	1.00	0.99	1.6e-16 sig	1eyv-assembly1_A THE CRYSTAL STRUCTURE OF NUSB FROM MYCOBACTERIUM TUBERCULOSIS
`3imq-assembly1_A`	1.00	0.86	5.5e-07 sig	3imq-assembly1_A Crystal structure of the NusB101-S10(delta loop) complex
`1tzw-assembly1_A`	1.00	0.81	1.7e-06 sig	1tzw-assembly1_A T. maritima NusB, P3121, Form 2
`3d3c-assembly3_C`	1.00	0.82	8.1e-06 sig	3d3c-assembly3_C Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
`4eya-assembly1_A`	1.00	0.82	3.1e-05 sig	4eya-assembly1_A Crystal Structure of a Plectonemic RNA Supercoil

Foldseek search of the AlphaFold DB model (mean pLDDT 92.7, gated at 70) against the PDB — a genome-wide extension of the ESMFold dark-gene search that also covers proteins beyond the single-sequence length limit. Confident structural neighbours (E < 0.01) shown.

Genomic context (neighbours & predicted operon) operon of 4

Upstream (5' on genome)	`Rv2532c` (- strand, -1 bp gap)
Downstream (3' on genome)	`efp` (- strand, 2 bp gap)
Predicted operon	`Rv2532c` · `nusB` · `efp` · `pepQ`

Neighbours from the H37Rv annotation (- strand). The operon is predicted by co-directional intergenic distance (same strand, gaps ≤50 bp) — a transcription-unit hypothesis, not a mapped TSS. For a "hypothetical", co-transcription with a characterised operon is a concrete functional lead (complements the STRING neighborhood channel below).

Functional interaction network (STRING v12, guilt-by-association)

Explore full network →

Node colour = verdict, dashed = hypothetical; edge colour = evidence (green experimental, orange genomic-context, grey co-expression), width ∝ score. Click a partner to open its page; "Explore full network" to walk the graph.

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 exp	30S ribosomal protein S10	892	835	experimental:822
`Rv2841c` nusA exp	transcription termination/antitermination protein NusA	900	815	experimental:652 textmining:482
`Rv1390` rpoZ exp	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 exp	DNA-directed RNA polymerase subunit beta	652	610	experimental:446
`Rv0639` nusG exp	transcription termination/antitermination protein NusG	961	600	experimental:420 textmining:908
`Rv1630` rpsA	30S ribosomal protein S1	598	583	coexpression:432
`Rv0668` rpoC exp	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 exp badge marks an experimentally-supported partner (measured interaction, experimental/database channel ≥400) as opposed to a purely predicted one — but note that the M. tuberculosis experimental interactome is dominated by a noisy bacterial-two-hybrid screen, so a strong measured link that contradicts the operon/localisation context is likely a false positive. 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)
Genome-wide structure: AlphaFold DB model (Jumper et al. 2021, doi:10.1038/s41586-021-03819-2; Varadi et al. 2024, doi:10.1093/nar/gkad1011) searched vs PDB with Foldseek (mean pLDDT 92.7)
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
Essentiality: genome-wide transposon mutagenesis in H37Rv — DeJesus et al. 2017 (mBio, doi:10.1128/mBio.02133-16, CC BY)
Proteomics: integrated mass-spectrometry abundance from PaxDb 5.0 (Huang et al. 2023, doi:10.1016/j.mcpro.2023.100640), taxon 83332 — weighted average of 16 datasets, incl. Schubert et al. 2013 (doi:10.1016/j.chom.2013.04.008) and Albrethsen et al. 2013 (doi:10.1074/mcp.M112.018846)
Functional category: TubercuList scheme (Cole et al. 1998, doi:10.1038/31159), via Mycobrowser (Kapopoulou et al. 2011, doi:10.1016/j.tube.2010.09.006)
Orthologues: reciprocal best hits (DIAMOND, Buchfink et al. 2021, doi:10.1038/s41592-021-01101-x) against Mycobrowser release 5 reference proteomes
Experimental structures: PDBe/SIFTS UniProt→PDB mapping (Dana et al. 2019, doi:10.1093/nar/gky1114)
Genomic context / operon: H37Rv annotation; operon predicted by co-directional intergenic distance (Salgado et al. 2000, doi:10.1073/pnas.030539397)
Physico-chemical properties: ExPASy ProtParam method via Biopython (Gasteiger et al. 2005), computed from the MTBC0 sequence
Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_002699|Rv2533c|nusB
MSDRKPVRGRHQARKRAVDLLFEAEVRGISAAEVVDTRAALAEAKPDIARLHPYTAAVARGVSEHAAHIDDLITAHLRGWTLDRLPAVDRAILRVSVWELLHAADVPEPVVVDEAVQLAKELSTDDSPGFVNGVLGQVMLVTPQLRAAAQAVRGGA

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Genomic neighbourhood (genome browser)