hemL Resolved · high auto-curated
H37Rv Rv0524 · MTBC0 mtbc0_000552 ·
462 aa · 618292–619680 (+) ·
RefSeq NP_215038.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamate-1-semialdehyde 2,1-aminomutase |
|---|---|
| MTBC0 PGAP re-annotation | glutamate-1-semialdehyde 2%2C1-aminomutase |
| Revised (this work) | Glutamate-1-semialdehyde 2%2C1-aminomutase. Pfam: Aminotran_3 (PF00202.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMN9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamate-1-semialdehyde 2,1-aminomutase |
| EC (curated) |
EC 5.4.3.8
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | hemL |
| eggNOG description | Aminotransferase |
| Orthologous group | COG0001 |
| EC number |
EC 5.4.3.8
|
| KEGG orthology |
K01845
|
| KEGG pathways |
map00860, map01100, map01110, map01120
|
| KEGG modules |
M00121
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, 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 | 0.16 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 16 synonymous, 7 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 |
|---|---|---|---|---|
Aminotran_3 | PF00202.28 | 1.5e-87 | 46–449 | Aminotransferase class-III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hemB (delta-aminolevulinic acid dehydratase), high confidence from genomic context alone (score 992 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0512 hemB |
delta-aminolevulinic acid dehydratase | 997 | 992 ctx | cooccurence:772 coexpression:622 database:900 textmining:689 |
Rv0509 hemA |
glutamyl-tRNA reductase | 996 | 988 ctx | cooccurence:771 database:900 textmining:706 |
Rv0525 hyp |
hypothetical protein | 980 | 980 ctx | neighborhood:882 coexpression:838 |
Rv0526 |
thioredoxin | 991 | 974 ctx | neighborhood:865 coexpression:816 textmining:675 |
Rv0527 ccdA |
cytochrome C-type biogenesis protein CcdA | 970 | 915 ctx | neighborhood:865 textmining:661 |
Rv0510 hemC |
porphobilinogen deaminase | 955 | 915 ctx | cooccurence:769 coexpression:564 textmining:502 |
Rv0529 ccsA |
cytochrome C-type biogenesis protein CcsA | 935 | 909 ctx | neighborhood:820 coexpression:412 |
Rv0528 |
transmembrane protein | 872 | 855 ctx | neighborhood:820 |
Rv2383c mbtB |
phenyloxazoline synthase | 866 | 784 ctx | neighborhood:544 experimental:417 textmining:408 |
Rv3266c rmlD |
dTDP-4-dehydrorhamnose reductase | 745 | 746 | coexpression:733 |
Rv3709c ask |
aspartokinase | 733 | 718 | coexpression:717 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 821 | 706 ctx | cooccurence:560 textmining:418 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 824 | 671 ctx | cooccurence:556 textmining:489 |
Rv2947c pks15 |
polyketide synthase | 669 | 654 ctx | fusion:643 |
Rv2678c hemE |
uroporphyrinogen decarboxylase | 886 | 624 ctx | cooccurence:421 textmining:709 |
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: glutamate-1-semialdehyde 2,1-aminomutase
- MTBC0 PGAP product: glutamate-1-semialdehyde 2%2C1-aminomutase
- Pfam (hmmscan --cut_ga): Aminotran_3 PF00202.28 (E=2e-87)
- (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_215038.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_3 (PF00202.28)
- 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
COG0001 - Curated reference: UniProt P9WMN9 (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 —
64 functional partner(s); context anchor
hemB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000552|Rv0524|hemL MGSTEQATSRVRGAARTSAQLFEAACSVIPGGVNSPVRAFTAVGGTPRFITEAHGCWLIDADGNRYVDLVCSWGPMILGHAHPAVVEAVAKAAARGLSFGAPTPAETQLAGEIIGRVAPVERIRLVNSGTEATMSAVRLARGFTGRAKIVKFSGCYHGHVDALLADAGSGVATLGLCDDPQRPASPRSQSSRGLPSSPGVTGAAAADTIVLPYNDIDAVQQTFARFGEQIAAVITEASPGNMGVVPPGPGFNAALRAITAEHGALLILDEVMTGFRVSRSGWYGIDPVPADLFAFGKVMSGGMPAAAFGGRAEVMQRLAPLGPVYQAGTLSGNPVAVAAGLATLRAADDAVYTALDANADRLAGLLSEALTDAVVPHQISRAGNMLSVFFGETPVTDFASARASQTWRYPAFFHAMLDAGVYPPCSAFEAWFVSAALDDAAFGRIANALPAAARAAAQERPA