gcvB Resolved · high auto-curated
H37Rv Rv1832 · MTBC0 mtbc0_001945 ·
941 aa · 2093909–2096734 (+) ·
RefSeq NP_216348.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycine dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | aminomethyl-transferring glycine dehydrogenase |
| Revised (this work) | Aminomethyl-transferring glycine dehydrogenase. Pfam: GDC-P (PF02347.23), GcvP2_C (PF21478.4). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN53
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable glycine dehydrogenase |
| EC (curated) |
EC 1.4.4.2
|
| Curated function | The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gcvP |
| eggNOG description | The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor |
| Orthologous group | COG0403 |
| EC number |
EC 1.4.4.2
|
| KEGG orthology |
K00281, K00283
|
| KEGG pathways |
map00260, map00630, map01100, map01110, map01130, map01200
|
| KEGG modules |
M00532
|
| Gene Ontology (10) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.174 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 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 |
|---|---|---|---|---|
GDC-P | PF02347.23 | 8.2e-186 | 9–438 | Glycine cleavage system P-protein |
GcvP2_C | PF21478.4 | 7.2e-55 | 762–883 | Glycine dehydrogenase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gcvH (glycine cleavage system protein H), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1826 gcvH |
glycine cleavage system protein H | 999 | 1000 ctx | cooccurence:711 coexpression:999 database:984 textmining:625 |
Rv2211c gcvT |
aminomethyltransferase | 999 | 1000 ctx | fusion:679 cooccurence:743 coexpression:999 database:900 textmining:625 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 996 | 992 | coexpression:911 database:900 textmining:511 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 995 | 992 | coexpression:910 database:900 textmining:477 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 978 | 958 | coexpression:952 textmining:497 |
Rv0772 purD |
phosphoribosylamine--glycine ligase | 975 | 955 | coexpression:954 textmining:478 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 942 | 920 | database:900 |
Rv1905c aao |
D-amino acid oxidase | 933 | 910 | database:900 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 899 | 900 | coexpression:453 database:800 |
Rv0951 sucC |
succinyl-CoA ligase subunit beta | 871 | 852 | coexpression:848 |
Rv3859c gltB |
glutamate synthase large subunit | 959 | 849 | database:800 textmining:745 |
Rv3339c icd1 |
isocitrate dehydrogenase | 855 | 840 | coexpression:840 |
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX | 833 | 833 ctx | neighborhood:544 coexpression:649 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 900 | 831 | coexpression:492 database:500 textmining:435 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 920 | 824 | database:800 textmining:567 |
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 dehydrogenase
- MTBC0 PGAP product: aminomethyl-transferring glycine dehydrogenase
- Pfam (hmmscan --cut_ga): GDC-P PF02347.23 (E=8e-186), GcvP2_C PF21478.4 (E=7e-55)
- (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_216348.1)
- Domains: Pfam-A via hmmscan --cut_ga — GDC-P (PF02347.23), GcvP2_C (PF21478.4)
- 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
COG0403 - Curated reference: UniProt P9WN53 (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 —
185 functional partner(s); context anchor
gcvH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001945|Rv1832|gcvB MSDHSTFADRHIGLDSQAVATMLAVIGVDSLDDLAVKAVPAGILDTLTDTGAAPGLDSLPPAASEAEALAELRALADANTVAVSMIGQGYYDTHTPPVLLRNIIENPAWYTAYTPYQPEISQGRLEALLNFQTLVTDLTGLEIANASMLDEGTAAAEAMTLMHRAARGPVKRVVVDADVFTQTAAVLATRAKPLGIEIVTADLRAGLPDGEFFGVIAQLPGASGRITDWSALVQQAHDRGALVAVGADLLALTLIAPPGEIGADVAFGTTQRFGVPMGFGGPHAGYLAVHAKHARQLPGRLVGVSVDSDGTPAYRLALQTREQHIRRDKATSNICTAQVLLAVLAAMYASYHGAGGLTAIARRVHAHAEAIAGALGDALVHDKYFDTVLARVPGRADEVLARAKANGINLWRVDADHVSVACDEATTDTHVAVVLDAFGVAAAAPAHADIATRTSEFLTHPAFTQYRTETSMMRYLRALADKDIALDRSMIPLGSCTMKLNAAAEMESITWPEFGRQHPFAPASDTAGLRQLVADLQSWLVLITGYDAVSLQPNAGSQGEYAGLLAIHEYHASRGEPHRDICLIPSSAHGTNAASAALAGMRVVVVDCHDNGDVDLDDLRAKVGEHAERLSALMITYPSTHGVYEHDIAEICAAVHDAGGQVYVDGANLNALVGLARPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPVAVRAHLAPFLPGHPFAPELPKGYPVSSAPYGSASILPITWAYIRMMGAEGLRAASLTAITSANYIARRLDEYYPVLYTGENGMVAHECILDLRGITKLTGITVDDVAKRLADYGFHAPTMSFPVAGTLMVEPTESESLAEVDAFCEAMIGIRAEIDKVGAGEWPVDDNPLRGAPHTAQCLLASDWDHPYTREQAAYPLGTAFRPKVWPAVRRIDGAYGDRNLVCSCPPVEAFA