Rv3555c Family assigned · medium auto-curated
H37Rv Rv3555c · MTBC0 mtbc0_003772 ·
289 aa · 4018507–4019376 (-) ·
RefSeq NP_218072.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF559 domain-containing protein |
| Revised (this work) | DUF559 domain-containing protein. Pfam: AbiEi_1 (PF09407.17), DUF559 (PF04480.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96837
TrEMBL · unreviewed
· Predicted
|
|---|---|
| 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 |
S Function unknown
|
|---|---|
| eggNOG description | Protein conserved in bacteria |
| Orthologous group | COG2852 |
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 | 2.182 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 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 |
|---|---|---|---|---|
AbiEi_1 | PF09407.17 | 7.7e-06 | 63–174 | AbiEi antitoxin C-terminal domain |
DUF559 | PF04480.19 | 2.6e-04 | 217–271 | Protein of unknown function (DUF559) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadA6 (acetyl-CoA acetyltransferase FadA), medium confidence from genomic context alone (score 597 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) |
|---|---|---|---|---|
Rv3297 nei |
endonuclease VIII | 820 | 820 | coexpression:817 |
Rv3296 lhr |
ATP-dependent helicase | 800 | 800 | coexpression:799 |
Rv3202c adnA |
ATP-dependent DNA helicase | 744 | 745 | coexpression:730 |
Rv2191 hyp |
hypothetical protein | 730 | 731 | coexpression:730 |
Rv3556c fadA6 |
acetyl-CoA acetyltransferase FadA | 597 | 597 ctx | neighborhood:580 |
Rv0804 hyp |
hypothetical protein | 558 | 558 ctx | cooccurence:558 |
Rv3859c gltB |
glutamate synthase large subunit | 522 | 522 | coexpression:515 |
Rv3586 disA |
DNA integrity scanning protein DisA | 512 | 512 | coexpression:441 |
Rv3557c kstR2 |
HTH-type transcriptional regulator KstR2 | 485 | 485 ctx | neighborhood:480 |
Rv2735c hyp |
hypothetical protein | 483 | 484 | coexpression:409 |
Rv2345 |
transmembrane protein | 481 | 481 ctx | cooccurence:481 |
Rv0767c |
HTH-type transcriptional regulator | 437 | 437 ctx | cooccurence:437 |
Rv3585 radA |
DNA repair protein RadA | 432 | 432 | coexpression:431 |
Rv0083 |
oxidoreductase | 807 | 63 | textmining:803 |
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: DUF559 domain-containing protein
- Pfam (hmmscan --cut_ga): AbiEi_1 PF09407.17 (E=8e-06), DUF559 PF04480.19 (E=3e-04)
- (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_218072.1)
- Domains: Pfam-A via hmmscan --cut_ga — AbiEi_1 (PF09407.17), DUF559 (PF04480.19)
- 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
COG2852 - Curated reference: UniProt P96837 (TrEMBL, unreviewed; Predicted)
- 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 —
14 functional partner(s); context anchor
fadA6 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003772|Rv3555c| MDELPWPVLGSEVLAAKAIPERAMRQLYEPVYPGVYAPAGVELTARQRAHAAWLWSRRRAVVAGNSAAALLGAKWVNPALDAELVHANRKPPPRIVVHTDRLAPHETVAVDGVAVTTPARTAFDIGRRTPSRLQAVQRLDALANSTDVKVADVQAVIAEHTGARGLVRLRAVLPLIDGGAESPQETWTRLVLIDAGLPKPQTQIRVFDDYGDFVARIDLGYEQLRVGVEYDGPQHWTDPAQRARDIERSTALLDLGWTIIRVTSELLRYRRGTFVGRVDAAMRAAGWRP