Rv1465 Family assigned · medium auto-curated
H37Rv Rv1465 · MTBC0 mtbc0_001567 ·
162 aa · 1662573–1663061 (+) ·
RefSeq NP_215981.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitrogen fixation related protein |
|---|---|
| MTBC0 PGAP re-annotation | SUF system NifU family Fe-S cluster assembly protein |
| Revised (this work) | SUF system NifU family Fe-S cluster assembly protein. Pfam: NifU_N (PF01592.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53156
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible nitrogen fixation related protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | iscU |
| eggNOG description | SUF system FeS assembly protein |
| Orthologous group | COG0822 |
| KEGG orthology |
K04488
|
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 | 0.164 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 |
|---|---|---|---|---|
NifU_N | PF01592.22 | 3.9e-38 | 9–131 | NifU-like N terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: csd (cysteine desulfurase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1464 csd |
cysteine desulfurase | 999 | 1000 ctx | neighborhood:881 cooccurence:767 coexpression:955 experimental:785 textmining:824 |
Rv1463 sufC |
ABC transporter ATP-binding protein | 999 | 999 ctx | neighborhood:881 cooccurence:748 coexpression:966 textmining:872 |
Rv1462 sufD hyp |
hypothetical protein | 999 | 998 ctx | neighborhood:881 cooccurence:706 coexpression:939 textmining:885 |
Rv3025c iscS |
cysteine desulfurase | 998 | 998 | coexpression:857 experimental:928 database:844 |
Rv1466 hyp |
hypothetical protein | 996 | 997 ctx | neighborhood:882 cooccurence:574 coexpression:944 |
Rv1461 sufB hyp |
hypothetical protein | 987 | 986 ctx | neighborhood:791 cooccurence:751 coexpression:755 |
Rv3778c |
aminotransferase | 972 | 969 ctx | cooccurence:544 coexpression:692 experimental:785 |
Rv3700c egtE |
pyridoxal-phosphate-dependent protein EgtE | 968 | 952 | coexpression:692 experimental:785 |
Rv1460 sufR |
transcriptional regulator | 919 | 894 ctx | neighborhood:881 |
Rv1937 |
oxygenase | 870 | 856 | experimental:414 database:621 |
Rv2776c |
oxidoreductase | 872 | 853 | database:621 |
Rv3554 fdxB |
electron transfer protein FdxB | 885 | 851 | database:621 |
Rv3230c |
stearoyl-CoA 9-desaturase electron transfer protein | 869 | 850 | database:621 |
Rv3571 kshB |
3-ketosteroid-9-alpha-hydroxylase reductase subunit | 868 | 849 | database:621 |
Rv2204c hyp |
hypothetical protein | 859 | 817 | coexpression:802 |
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: nitrogen fixation related protein
- MTBC0 PGAP product: SUF system NifU family Fe-S cluster assembly protein
- Pfam (hmmscan --cut_ga): NifU_N PF01592.22 (E=4e-38)
- (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_215981.1)
- Domains: Pfam-A via hmmscan --cut_ga — NifU_N (PF01592.22)
- 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
COG0822 - Curated reference: UniProt O53156 (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)
- 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
csd - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001567|Rv1465| MTLRLEQIYQDVILDHYKHPQHRGLREPFGAQVYHVNPICGDEVTLRVALSEDGTRVTDVSYDGQGCSISQAATSVLTEQVIGQRVPRALNIVDAFTEMVSSRGTVPGDEDVLGDGVAFAGVAKYPARVKCALLGWMAFKDALAQASEAFEEVTDERNQRTG