glnB Family assigned · medium auto-curated
H37Rv Rv2919c · MTBC0 mtbc0_003101 ·
112 aa · 3251567–3251905 (-) ·
RefSeq NP_217435.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrogen regulatory protein P-II |
|---|---|
| MTBC0 PGAP re-annotation | nitrogen regulatory protein P-II |
| Revised (this work) | Nitrogen regulatory protein P-II. Pfam: P-II (PF00543.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN31
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nitrogen regulatory protein P-II |
| Curated function | In nitrogen-limiting conditions, when the ratio of Gln to 2-ketoglutarate decreases, P-II is uridylylated to P-II-UMP. P-II-UMP allows the deadenylation of glutamine synthetase (GS), thus activating the enzyme. Conversely, in nitrogen excess P-II is deuridylated and promotes the adenylation of GS. P-II indirectly controls the transcription of the GS gene (glnA). P-II prevents NR-II-catalyzed conversion of NR-I to NR-I-phosphate, the transcriptional activator of glnA. When P-II is uridylylated to P-II-UMP, these events are reversed (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | glnB |
| eggNOG description | nitrogen regulatory protein P-II |
| Orthologous group | COG0347 |
| KEGG orthology |
K04751
|
| KEGG pathways |
map02020
|
| Gene Ontology (34) |
GO:0000166, GO:0003674, GO:0005488, GO:0005524, GO:0005575, GO:0005623, GO:0005886, GO:0008144, GO:0008150, GO:0016020, GO:0017076, GO:0030554 +22 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 | 0.648 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
P-II | PF00543.28 | 7.7e-32 | 1–106 | Nitrogen regulatory protein P-II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: amt (ammonium transporter integral membrane protein), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2920c amt |
ammonium transporter integral membrane protein | 999 | 1000 ctx | neighborhood:881 fusion:899 cooccurence:632 coexpression:859 experimental:911 textmining:634 |
Rv2918c glnD |
bifunctional uridylyltransferase/uridylyl-removing enzyme | 999 | 996 ctx | neighborhood:805 cooccurence:617 experimental:468 database:900 textmining:955 |
Rv1654 argB |
acetylglutamate kinase | 952 | 938 | experimental:928 |
Rv3529c hyp |
hypothetical protein | 807 | 789 | experimental:787 |
Rv2267c stf3 hyp |
hypothetical protein | 806 | 788 | experimental:787 |
Rv1691 hyp |
hypothetical protein | 805 | 787 | experimental:787 |
Rv2387 hyp |
hypothetical protein | 718 | 679 | experimental:652 |
Rv3859c gltB |
glutamate synthase large subunit | 884 | 566 ctx | neighborhood:544 textmining:745 |
Rv2921c ftsY |
signal recognition particle receptor FtsY | 553 | 512 ctx | neighborhood:510 |
Rv2922c smc |
chromosome partition protein Smc | 486 | 460 ctx | neighborhood:460 |
Rv2220 glnA1 |
glutamine synthetase | 958 | 457 | textmining:927 |
Rv2922A acyP |
acylphosphatase | 457 | 457 ctx | neighborhood:457 |
Rv1475c acn |
iron-regulated aconitate hydratase | 462 | 428 | |
Rv2923c hyp |
hypothetical protein | 413 | 414 ctx | neighborhood:412 |
Rv2924c fpg |
formamidopyrimidine-DNA glycosylase | 420 | 398 |
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: nitrogen regulatory protein P-II
- MTBC0 PGAP product: nitrogen regulatory protein P-II
- Pfam (hmmscan --cut_ga): P-II PF00543.28 (E=8e-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_217435.1)
- Domains: Pfam-A via hmmscan --cut_ga — P-II (PF00543.28)
- 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
COG0347 - Curated reference: UniProt P9WN31 (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 —
26 functional partner(s); context anchor
amt - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003101|Rv2919c|glnB MKLITAIVKPFTLDDVKTSLEDAGVLGMTVSEIQGYGRQKGHTEVYRGAEYSVDFVPKVRIEVVVDDSIVDKVVDSIVRAARTGKIGDGKVWVSPVDTIVRVRTGERGHDAL