gcvH Resolved · high auto-curated
H37Rv Rv1826 · MTBC0 mtbc0_001940 ·
134 aa · 2090040–2090444 (+) ·
RefSeq NP_216342.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycine cleavage system protein H |
|---|---|
| MTBC0 PGAP re-annotation | glycine cleavage system protein GcvH |
| Revised (this work) | Glycine cleavage system protein GcvH. Pfam: GCV_H (PF01597.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN55
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycine cleavage system H protein |
| Curated function | The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gcvH |
| eggNOG description | The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein |
| Orthologous group | COG0509 |
| KEGG orthology |
K02437
|
| KEGG pathways |
map00260, map00630, map01100, map01110, map01130, map01200
|
| KEGG modules |
M00532
|
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 | 1.028 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
GCV_H | PF01597.26 | 3.1e-39 | 8–131 | Glycine cleavage H-protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gcvB (glycine dehydrogenase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1832 gcvB |
glycine dehydrogenase | 999 | 1000 ctx | cooccurence:711 coexpression:999 database:984 textmining:625 |
Rv2211c gcvT |
aminomethyltransferase | 999 | 1000 ctx | cooccurence:774 coexpression:859 experimental:790 database:984 textmining:625 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 983 | 976 | database:961 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 965 | 952 | coexpression:656 database:844 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 963 | 950 | coexpression:458 database:900 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 963 | 950 | coexpression:461 database:900 |
Rv2218 lipA |
lipoyl synthase | 939 | 921 | database:844 |
Rv2217 lipB |
octanoyltransferase | 954 | 891 | database:844 textmining:596 |
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta | 871 | 853 | database:844 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 855 | 849 | database:844 |
Rv2220 glnA1 |
glutamine synthetase | 849 | 840 | database:800 |
Rv1825 hyp |
hypothetical protein | 835 | 835 ctx | neighborhood:826 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 823 | 823 | database:800 |
Rv0685 tuf |
elongation factor Tu | 820 | 820 ctx | fusion:805 |
Rv1824 hyp |
hypothetical protein | 819 | 820 ctx | neighborhood:810 |
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: glycine cleavage system protein H
- MTBC0 PGAP product: glycine cleavage system protein GcvH
- Pfam (hmmscan --cut_ga): GCV_H PF01597.26 (E=3e-39)
- (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_216342.1)
- Domains: Pfam-A via hmmscan --cut_ga — GCV_H (PF01597.26)
- 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
COG0509 - Curated reference: UniProt P9WN55 (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 —
80 functional partner(s); context anchor
gcvB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001940|Rv1826|gcvH MSDIPSDLHYTAEHEWIRRSGDDTVRVGITDYAQSALGDVVFVQLPVIGTAVTAGETFGEVESTKSVSDLYAPISGKVSAVNSDLDGTPQLVNSDPYGAGWLLDIQVDSSDVAALESALTTLLDAEAYRGTLTE