gpsI Resolved · high auto-curated
H37Rv Rv2783c · MTBC0 mtbc0_002962 ·
752 aa · 3112754–3115012 (-) ·
RefSeq NP_217299.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | polyribonucleotide nucleotidyltransferase |
| Revised (this work) | Polyribonucleotide nucleotidyltransferase. Pfam: PNPase (PF03726.20), RNase_PH (PF01138.28), KH_1 (PF00013.36), S1 (PF00575.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI57
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Polyribonucleotide nucleotidyltransferase |
| EC (curated) |
EC 2.7.7.8
|
| Curated function | Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | pnp |
| eggNOG description | Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction |
| Orthologous group | COG1185 |
| EC number |
EC 2.7.7.8
|
| KEGG orthology |
K00962
|
| KEGG pathways |
map00230, map00240, map03018
|
| KEGG modules |
M00394
|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +1 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 | 0.152 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 4 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 |
|---|---|---|---|---|
PNPase | PF03726.20 | 3.5e-21 | 274–350 | Polyribonucleotide nucleotidyltransferase, RNA binding domain |
RNase_PH | PF01138.28 | 1.8e-21 | 355–487 | 3' exoribonuclease family, domain 1 |
KH_1 | PF00013.36 | 7.4e-11 | 598–655 | KH domain |
S1 | PF00575.30 | 1.6e-13 | 663–732 | S1 RNA binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pepR (zinc protease), high confidence from genomic context alone (score 941 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 985 | 957 | coexpression:866 experimental:676 textmining:679 |
Rv0702 rplD |
50S ribosomal protein L4 | 952 | 952 | coexpression:942 |
Rv2782c pepR |
zinc protease | 945 | 941 ctx | neighborhood:882 |
Rv0701 rplC |
50S ribosomal protein L3 | 954 | 932 | coexpression:931 |
Rv1297 rho |
transcription termination factor Rho | 967 | 928 | coexpression:916 textmining:568 |
Rv1643 rplT |
50S ribosomal protein L20 | 887 | 877 | coexpression:843 |
Rv0704 rplB |
50S ribosomal protein L2 | 876 | 876 | coexpression:860 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 875 | 859 | coexpression:823 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 904 | 856 | coexpression:852 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 907 | 850 | coexpression:848 textmining:413 |
Rv2444c rne |
ribonuclease E | 968 | 846 | experimental:826 textmining:807 |
Rv3458c rpsD |
30S ribosomal protein S4 | 867 | 846 | coexpression:843 |
Rv1158c hyp |
hypothetical protein | 861 | 843 | experimental:826 |
Rv2839c infB |
translation initiation factor IF-2 | 909 | 839 | coexpression:817 textmining:462 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 881 | 810 | coexpression:405 experimental:676 textmining:403 |
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: bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase
- MTBC0 PGAP product: polyribonucleotide nucleotidyltransferase
- Pfam (hmmscan --cut_ga): PNPase PF03726.20 (E=4e-21), RNase_PH PF01138.28 (E=2e-21), KH_1 PF00013.36 (E=7e-11), S1 PF00575.30 (E=2e-13)
- (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_217299.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNPase (PF03726.20), RNase_PH (PF01138.28), KH_1 (PF00013.36), S1 (PF00575.30)
- 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
COG1185 - Curated reference: UniProt P9WI57 (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 —
177 functional partner(s); context anchor
pepR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002962|Rv2783c|gpsI MSAAEIDEGVFETTATIDNGSFGTRTIRFETGRLALQAAGAVVAYLDDDNMLLSATTASKNPKEHFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPSFVDGLRNEIQIVVTILSLDPGDLYDVLAINAASASTQLGGLPFSGPIGGVRVALIDGTWVGFPTVDQIERAVFDMVVAGRIVEGDVAIMMVEAEATENVVELVEGGAQAPTESVVAAGLEAAKPFIAALCTAQQELADAAGKSGKPTVDFPVFPDYGEDVYYSVSSVATDELAAALTIGGKAERDQRIDEIKTQVVQRLADTYEGREKEVGAALRALTKKLVRQRILTDHFRIDGRGITDIRALSAEVAVVPRAHGSALFERGETQILGVTTLDMIKMAQQIDSLGPETSKRYMHHYNFPPFSTGETGRVGSPKRREIGHGALAERALVPVLPSVEEFPYAIRQVSEALGSNGSTSMGSVCASTLALLNAGVPLKAPVAGIAMGLVSDDIQVEGAVDGVVERRFVTLTDILGAEDAFGDMDFKVAGTKDFVTALQLDTKLDGIPSQVLAGALEQAKDARLTILEVMAEAIDRPDEMSPYAPRVTTIKVPVDKIGEVIGPKGKVINAITEETGAQISIEDDGTVFVGATDGPSAQAAIDKINAIANPQLPTVGERFLGTVVKTTDFGAFVSLLPGRDGLVHISKLGKGKRIAKVEDVVNVGDKLRVEIADIDKRGKISLILVADEDSTAAATDAATVTS