Rv3071 Family assigned · low auto-curated · to review
H37Rv Rv3071 · MTBC0 mtbc0_003264 ·
369 aa · 3455828–3456937 (+) ·
RefSeq NP_217587.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF190 domain-containing protein |
| Revised (this work) | DUF190 domain-containing protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
Curated reference (UniProt)
| UniProt |
P95087
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DUF190 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterized ACR, COG1993 |
| Orthologous group | COG1993 |
| KEGG orthology |
K09137
|
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 | 1.763 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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 |
|---|---|---|---|---|
DUF190 | PF02641.21 | 4.5e-21 | 248–343 | Uncharacterized ACR, COG1993 |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 89.1 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
2dcl-assembly1_C-2 |
1.00 | 0.78 | 1.4e-03 sig | 2dcl-assembly1_C-2 Structure of PH1503 protein from Pyrococcus Horikoshii OT3 |
1o51-assembly1_A |
1.00 | 0.80 | 6.1e-03 sig | 1o51-assembly1_A Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.50 A resolution |
5d4o-assembly1_A |
0.96 | 0.61 | 3.4e-02 | 5d4o-assembly1_A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound to ADP, AMP and bicarbonate. |
4iyq-assembly1_C |
0.89 | 0.64 | 1.6e-01 | 4iyq-assembly1_C Crystal structure of divalent ion tolerance protein CutA1 from Ehrlichia chaffeensis |
1nza-assembly1_A |
0.69 | 0.62 | 3.6e-01 | 1nza-assembly1_A Divalent cation tolerance protein (Cut A1) from thermus thermophilus HB8 |
4zk7-assembly1_M |
0.69 | 0.61 | 3.8e-01 | 4zk7-assembly1_M Crystal structure of rescued two-component self-assembling tetrahedral cage T33-31 |
4e98-assembly1_B |
0.63 | 0.62 | 4.8e-01 | 4e98-assembly1_B Crystal structure of possible CutA1 divalent ion tolerance protein from Cryptosporidium parvum Iowa II |
6nf8-assembly1_F |
0.63 | 0.56 | 2.4e-01 | 6nf8-assembly1_F Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit -Class I |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: crcB (fluoride ion transporter CrcB), high confidence from genomic context alone (score 926 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) |
|---|---|---|---|---|
Rv3069 crcB |
fluoride ion transporter CrcB | 936 | 926 ctx | neighborhood:881 cooccurence:402 |
Rv3070 crcB |
fluoride ion transporter CrcB | 925 | 914 ctx | neighborhood:881 |
Rv3413c rsdA |
anti-sigma-D factor RsdA | 689 | 689 ctx | cooccurence:689 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 654 | 654 ctx | neighborhood:636 |
Rv0210 hyp |
hypothetical protein | 642 | 642 ctx | cooccurence:611 |
Rv0441c hyp |
hypothetical protein | 622 | 623 ctx | cooccurence:622 |
Rv3338 |
Rv3338, (MTV016.38), len: 214 aa. Hypothetical protein, equivalent to C-termini of Q49926|ML0685 TPEA (putative hydrolase) from Mycobacteriu | 607 | 607 ctx | cooccurence:607 |
Rv2629 hyp |
hypothetical protein | 589 | 590 ctx | cooccurence:587 |
Rv0493c hyp |
hypothetical protein | 586 | 587 ctx | cooccurence:583 |
Rv0760c hyp |
hypothetical protein | 562 | 563 ctx | cooccurence:560 |
Rv1913 hyp |
hypothetical protein | 532 | 533 ctx | cooccurence:528 |
Rv2721c hyp |
hypothetical protein | 515 | 515 ctx | cooccurence:515 |
Rv2751 hyp |
hypothetical protein | 509 | 510 ctx | cooccurence:508 |
Rv2633c hyp |
hypothetical protein | 498 | 498 ctx | cooccurence:495 |
Rv0479c |
membrane protein | 492 | 493 ctx | cooccurence:490 |
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: DUF190 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF190 PF02641.21 (E=4e-21)
- Foldseek best: 2dcl-assembly1_C-2 Structure of PH1503 protein from Pyrococcus Horikoshii OT3 (prob 1.00, E=1e-03, TM=0.78)
- (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_217587.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF190 (PF02641.21)
- 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
COG1993 - Curated reference: UniProt P95087 (TrEMBL, unreviewed; 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)
- Model confidence: ESMFold per-residue pLDDT (mean 89.1, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
28 functional partner(s); context anchor
crcB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003264|Rv3071| MNEQCLKLTAYFGERQRAVGGAGRFLADAMLDLFGSHNVATSVMLRGTTSFGPKHEFRCDQSLSLSEDPPVTVAAVDIESKIRSLVDDVTAMTDRGLVTLERARLVTRHSGAEEFGDIDSRNGDAAKLTIYAGRQVRVAGAPAYYTICELLHRHGFAGATVLLGVDGTAHGRRRRARFFGRNVNVPLMIIAVGTPAQVAVAAMELTAALPNPLLTIERVRLCKRDGELFARPQQLPQTDDQGRTLWQKLMVHTAEATHHEGLPIHRALVHRLMQSETARGATALRGIWGFYGDHKPHGDKLFQLVRRVPVTTIIVDTPQAIARSFDIVDELTNWHGLVTSEMVPAAVSLTGSRDGTQKTGETPLARYDY