Rv3678c Family assigned · medium auto-curated
H37Rv Rv3678c · MTBC0 mtbc0_003897 ·
151 aa · 4141889–4142344 (-) ·
RefSeq NP_218195.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | RidA family protein |
| Revised (this work) | RidA family protein. Pfam: YjgF_endoribonc (PF14588.12), Ribonuc_L-PSP (PF01042.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YGW9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | yabJ |
| eggNOG description | endoribonuclease L-PSP |
| Orthologous group | COG0251 |
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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
YjgF_endoribonc | PF14588.12 | 3.6e-21 | 5–149 | YjgF/chorismate_mutase-like, putative endoribonuclease |
Ribonuc_L-PSP | PF01042.27 | 7.0e-22 | 19–149 | Endoribonuclease L-PSP |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3677c (beta lactamase), high confidence from genomic context alone (score 891 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3677c |
beta lactamase | 891 | 891 ctx | neighborhood:882 |
Rv3678A hyp |
hypothetical protein | 875 | 875 ctx | neighborhood:867 |
Rv3679 |
anion transporter ATPase | 781 | 781 ctx | neighborhood:774 |
Rv3680 |
anion transporter ATPase | 777 | 777 ctx | neighborhood:774 |
Rv0684 fusA1 |
elongation factor G | 700 | 689 | database:629 |
Rv0120c fusA2 |
elongation factor G | 692 | 681 | database:629 |
Rv1340 rphA |
ribonuclease PH | 579 | 560 | experimental:434 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 490 | 491 | |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 488 | 488 | coexpression:419 |
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: hypothetical protein
- MTBC0 PGAP product: RidA family protein
- Pfam (hmmscan --cut_ga): YjgF_endoribonc PF14588.12 (E=4e-21), Ribonuc_L-PSP PF01042.27 (E=7e-22)
- (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_218195.1)
- Domains: Pfam-A via hmmscan --cut_ga — YjgF_endoribonc (PF14588.12), Ribonuc_L-PSP (PF01042.27)
- 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
COG0251 - Curated reference: UniProt I6YGW9 (TrEMBL, unreviewed; Evidence at protein level)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
9 functional partner(s); context anchor
Rv3677c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003897|Rv3678c| MSAKARLGQLGVTLPQVAAPLAAYVPAVRTGNLVYTAGQLPLEAGKLVRTGKLGADVNPEEGKTLARICALNALAAVDSLVDLDAVTRVVKVVGFVASAPGFHGQPSVINGASDLLAEVFGDSGAHARSAVGVSELPLDAPVEVELIVEVG