pheT Family assigned · medium auto-curated
H37Rv Rv1650 · MTBC0 mtbc0_001759 ·
831 aa · 1871779–1874274 (+) ·
RefSeq NP_216166.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phenylalanine--tRNA ligase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | phenylalanine--tRNA ligase subunit beta |
| Revised (this work) | Phenylalanine--tRNA ligase subunit beta. Pfam: tRNA_bind (PF01588.27), B3_4 (PF03483.23), B5 (PF03484.22), tRNA_synthFbeta (PF17759.7), FDX-ACB (PF03147.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFU1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phenylalanine--tRNA ligase beta subunit |
| EC (curated) |
EC 6.1.1.20
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | pheT |
| eggNOG description | Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily |
| Orthologous group | COG0072 |
| EC number |
EC 6.1.1.20
|
| KEGG orthology |
K01890
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (59) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006082, GO:0006139, GO:0006399, GO:0006412, GO:0006418, GO:0006432 +47 more
|
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 | 0.815 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 13 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 |
|---|---|---|---|---|
tRNA_bind | PF01588.27 | 2.1e-16 | 50–152 | Putative tRNA binding domain |
B3_4 | PF03483.23 | 2.2e-57 | 223–395 | B3/4 domain |
B5 | PF03484.22 | 2.7e-15 | 420–483 | tRNA synthetase B5 domain |
tRNA_synthFbeta | PF17759.7 | 8.2e-50 | 487–722 | Phenylalanyl tRNA synthetase beta chain CLM domain |
FDX-ACB | PF03147.20 | 6.6e-25 | 737–830 | Ferredoxin-fold anticodon binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pheS (phenylalanine--tRNA ligase subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1649 pheS |
phenylalanine--tRNA ligase subunit alpha | 999 | 1000 ctx | neighborhood:892 cooccurence:586 coexpression:998 experimental:999 database:963 textmining:965 |
Rv0041 leuS |
leucine--tRNA ligase | 994 | 970 | coexpression:965 textmining:825 |
Rv1536 ileS |
isoleucine--tRNA ligase | 980 | 958 | coexpression:916 textmining:554 |
Rv2890c rpsB |
30S ribosomal protein S2 | 978 | 957 | coexpression:907 textmining:509 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 960 | 914 | coexpression:894 textmining:558 |
Rv0723 rplO |
50S ribosomal protein L15 | 945 | 910 | coexpression:898 textmining:419 |
Rv1689 tyrS |
tyrosine--tRNA ligase | 956 | 907 ctx | neighborhood:544 coexpression:804 textmining:554 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 957 | 901 ctx | neighborhood:544 coexpression:731 textmining:591 |
Rv3396c guaA |
GMP synthase | 973 | 900 ctx | neighborhood:544 coexpression:790 textmining:745 |
Rv2614c thrS |
threonine--tRNA ligase | 956 | 877 ctx | neighborhood:544 coexpression:710 textmining:658 |
Rv0707 rpsC |
30S ribosomal protein S3 | 917 | 865 | coexpression:717 experimental:515 textmining:413 |
Rv2555c alaS |
alanine--tRNA ligase | 969 | 852 | coexpression:703 textmining:800 |
Rv2587c secD |
protein translocase subunit SecD | 933 | 843 | experimental:830 textmining:594 |
Rv0705 rpsS |
30S ribosomal protein S19 | 909 | 821 | coexpression:649 experimental:446 textmining:517 |
Rv0721 rpsE |
30S ribosomal protein S5 | 869 | 820 | coexpression:663 experimental:420 |
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: phenylalanine--tRNA ligase subunit beta
- MTBC0 PGAP product: phenylalanine--tRNA ligase subunit beta
- Pfam (hmmscan --cut_ga): tRNA_bind PF01588.27 (E=2e-16), B3_4 PF03483.23 (E=2e-57), B5 PF03484.22 (E=3e-15), tRNA_synthFbeta PF17759.7 (E=8e-50), FDX-ACB PF03147.20 (E=7e-25)
- (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_216166.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA_bind (PF01588.27), B3_4 (PF03483.23), B5 (PF03484.22), tRNA_synthFbeta (PF17759.7), FDX-ACB (PF03147.20)
- 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
COG0072 - Curated reference: UniProt P9WFU1 (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 —
363 functional partner(s); context anchor
pheS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001759|Rv1650|pheT MRLPYSWLREVVAVGASGWDVTPGELEQTLLRIGHEVEEVIPLGPVDGPVTVGRVADIEELTGYKKPIRACAVDIGDRQYREIICGATNFAVGDLVVVALPGATLPGGFTISARKAYGRNSDGMICSAAELNLGADHSGILVLPPGAAEPGADGAGVLGLDDVVFHLAITPDRGYCMSVRGLARELACAYDLDFVDPASNSRVPPLPIEGPAWPLTVQPETGVRRFALRPVIGIDPAAVSPWWLQRRLLLCGIRATCPAVDVTNYVMLELGHPMHAHDRNRISGTLGVRFARSGETAVTLDGIERKLDTADVLIVDDAATAAIGGVMGAASTEVRADSTDVLLEAAIWDPAAVSRTQRRLHLPSEAARRYERTVDPAISVAALDRCARLLADIAGGEVSPTLTDWRGDPPCDDWSPPPIRMGVDVPDRIAGVAYPQGTTARRLAQIGAVVTHDGDTLTVTPPSWRPDLRQPADLVEEVLRLEGLEVIPSVLPPAPAGRGLTAGQQRRRTIGRSLALSGYVEILPTPFLPAGVFDLWGLEADDSRRMTTRVLNPLEADRPQLATTLLPALLEALVRNVSRGLVDVALFAIAQVVQPTEQTRGVGLIPVDRRPTDDEIAMLDASLPRQPQHVAAVLAGLREPRGPWGPGRPVEAADAFEAVRIIARASRVDVTLRPAQYLPWHPGRCAQVFVGESSVGHAGQLHPAVIERSGLPKGTCAVELNLDAIPCSAPLPAPRVSPYPAVFQDVSLVVAADIPAQAVADAVRAGAGDLLEDIALFDVFTGPQIGEHRKSLTFALRFRAPDRTLTEDDASAARDAAVQSAAERVGAVLRG