Rv3778c Family assigned · medium auto-curated
H37Rv Rv3778c · MTBC0 mtbc0_004006 ·
398 aa · 4247820–4249016 (-) ·
RefSeq NP_218295.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aminotransferase |
|---|---|
| MTBC0 PGAP re-annotation | cysteine desulfurase-like protein |
| Revised (this work) | Cysteine desulfurase-like protein. Pfam: Aminotran_5 (PF00266.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ67
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3778c |
| Curated function | Is essential for optimal growth. |
UniProt still lists this protein as Uncharacterized protein Rv3778c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | csd |
| eggNOG description | cysteine desulfurase family protein |
| Orthologous group | COG0520 |
| EC number |
EC 2.8.1.7
|
| KEGG orthology |
K04487
|
| KEGG pathways |
map00730, map01100, map04122
|
| 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 | 0.499 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Aminotran_5 | PF00266.26 | 1.4e-36 | 21–390 | Aminotransferase class-V |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1465 (nitrogen fixation related protein), high confidence from genomic context alone (score 969 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1465 |
nitrogen fixation related protein | 972 | 969 ctx | cooccurence:544 coexpression:692 experimental:785 |
Rv1463 sufC |
ABC transporter ATP-binding protein | 913 | 905 ctx | cooccurence:679 coexpression:694 |
Rv1462 sufD hyp |
hypothetical protein | 893 | 887 ctx | cooccurence:622 coexpression:648 |
Rv1461 sufB hyp |
hypothetical protein | 888 | 881 ctx | cooccurence:618 coexpression:647 |
Rv0888 spmT hyp |
hypothetical protein | 783 | 783 | experimental:780 |
Rv3783 rfbD |
O-antigen/lipopolysaccharide ABC transporter permease RfbD | 701 | 701 ctx | neighborhood:636 |
Rv3284 hyp |
hypothetical protein | 701 | 670 | experimental:490 |
Rv3780 bpa hyp |
hypothetical protein | 639 | 639 ctx | neighborhood:636 |
Rv3782 glfT1 |
galactofuranosyl transferase GlfT | 638 | 638 ctx | neighborhood:636 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 637 | 637 ctx | neighborhood:636 |
Rv3779 |
transmembrane protein | 615 | 615 ctx | neighborhood:615 |
Rv2360c hyp |
hypothetical protein | 516 | 516 ctx | cooccurence:516 |
Rv2520c |
membrane protein | 468 | 469 ctx | cooccurence:467 |
Rv2468c hyp |
hypothetical protein | 451 | 452 | |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 401 | 401 |
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: aminotransferase
- MTBC0 PGAP product: cysteine desulfurase-like protein
- Pfam (hmmscan --cut_ga): Aminotran_5 PF00266.26 (E=1e-36)
- (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_218295.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_5 (PF00266.26)
- 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
COG0520 - Curated reference: UniProt P9WQ67 (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 —
22 functional partner(s); context anchor
Rv1465 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004006|Rv3778c| MAYDVARVRGLHPSLGDGWVHFDAPAGMLIPDSVATTVSTAFRRSGASTVGAHPSARRSAAVLDAAREAVADLVNADPGGVVLGADRAVLLSLLAEASSSRAGLGYEVIVSRLDDEANIAPWLRAAHRYGAKVKWAEVDIETGELPTWQWESLISKSTRLVAVNSASGTLGGVTDLRAMTKLVHDVGALVVVDHSAAAPYRLLDIRETDADVVTVNAHAWGGPPIGAMVFRDPSVMNSFGSVSTNPYATGPARLEIGVHQFGLLAGVVASIEYLAALDESARGSRRERLAVSMQSADAYLNRVFDYLMVSLRSLPLVMLIGRPEAQIPVVSFAVHKVPADRVVQRLADNGILAIANTGSRVLDVLGVNDVGGAVTVGLAHYSTMAEVDQLVRALASLG