Detailed information    

insolico Bioinformatically predicted

Overview

Name   ruvB   Type   Machinery gene
Locus tag   IUD21_RS04685 Genome accession   NZ_CP064332
Coordinates   1110498..1111529 (+) Length   343 a.a.
NCBI ID   WP_004572899.1    Uniprot ID   Q87D00
Organism   Xylella fastidiosa subsp. fastidiosa strain Bakersfield-11     
Function   homologous recombination (predicted from homology)   
Homologous recombination

Genomic Context

Location: 1105498..1116529
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  IUD21_RS04660 (IUD21_04660) - 1105771..1106304 (+) 534 WP_228446171.1 DUF2726 domain-containing protein -
  IUD21_RS04665 (IUD21_04665) - 1106433..1107167 (+) 735 WP_004572895.1 YebC/PmpR family DNA-binding transcriptional regulator -
  IUD21_RS04670 (IUD21_04670) ruvC 1107287..1107808 (+) 522 WP_011097831.1 crossover junction endodeoxyribonuclease RuvC -
  IUD21_RS04675 (IUD21_04675) ruvA 1107894..1108478 (+) 585 WP_004572897.1 Holliday junction branch migration protein RuvA -
  IUD21_RS04680 (IUD21_04680) - 1108533..1110437 (+) 1905 WP_004572898.1 potassium transporter Kup -
  IUD21_RS04685 (IUD21_04685) ruvB 1110498..1111529 (+) 1032 WP_004572899.1 Holliday junction branch migration DNA helicase RuvB Machinery gene
  IUD21_RS04690 (IUD21_04690) ybgC 1111547..1111972 (+) 426 WP_004572900.1 tol-pal system-associated acyl-CoA thioesterase -
  IUD21_RS04695 (IUD21_04695) tolQ 1111996..1112769 (+) 774 WP_004572901.1 protein TolQ -
  IUD21_RS04700 (IUD21_04700) tolR 1112812..1113237 (+) 426 WP_014607736.1 protein TolR -
  IUD21_RS04705 (IUD21_04705) tolA 1113227..1114267 (+) 1041 WP_004572903.1 cell envelope integrity protein TolA -
  IUD21_RS04710 (IUD21_04710) tolB 1114610..1115929 (+) 1320 WP_011097833.1 Tol-Pal system beta propeller repeat protein TolB -

Sequence

Protein


Download         Length: 343 a.a.        Molecular weight: 38105.66 Da        Isoelectric Point: 4.8169

>NTDB_id=442789 IUD21_RS04685 WP_004572899.1 1110498..1111529(+) (ruvB) [Xylella fastidiosa subsp. fastidiosa strain Bakersfield-11]
MDRIIDSAATREDEAIEVSIRPKRLADYLGQQPVREQMDIYIQATKARAEALDHVLIFGPPGLGKTTLSHVIAYELGVKL
RVTSGPVIEKAGDLAALLTNLQPYDVLFIDEIHRLSPVVEEVLYPAMEDFQIDIMIGEGPAARSIKIDLPPFTLIGATTR
TGLLTAPLRDRFGIVQRLEFYSPEDLARIVRRSAGILNIDCTTEGAAEIAQRARGTPRIANRLLRRVRDYAEVKADGQIT
IEVAQAAMQMLKVDQGGFDELDRRLLHTIVEYFDGGPVGIESLAASLSEERGTLEDVVEPYLIQQGFLVRTARGRMATDK
AYQHLALQPRERVSAFTDPEDLF

Nucleotide


Download         Length: 1032 bp        

>NTDB_id=442789 IUD21_RS04685 WP_004572899.1 1110498..1111529(+) (ruvB) [Xylella fastidiosa subsp. fastidiosa strain Bakersfield-11]
ATGGATCGCATCATCGACAGCGCAGCCACCCGTGAGGATGAAGCGATTGAGGTCAGTATTCGTCCCAAGCGTTTGGCTGA
TTATCTCGGTCAACAACCTGTACGTGAGCAGATGGATATCTACATCCAAGCCACTAAGGCGCGTGCTGAGGCATTGGATC
ACGTACTCATTTTTGGTCCACCTGGATTGGGCAAGACCACCTTGAGCCATGTCATTGCTTACGAACTCGGGGTCAAGCTA
CGTGTGACTTCTGGTCCAGTGATCGAGAAAGCAGGAGATCTGGCCGCACTGCTTACCAATCTACAGCCTTACGATGTGCT
GTTTATTGATGAGATTCATCGGCTATCACCAGTGGTTGAGGAGGTGTTATATCCAGCAATGGAGGACTTCCAGATCGATA
TTATGATTGGCGAGGGGCCGGCTGCGCGGTCGATAAAGATCGACTTGCCACCTTTCACTCTCATAGGTGCTACTACTCGT
ACAGGTTTGCTGACTGCGCCGCTGCGCGACCGTTTTGGTATCGTCCAGCGTTTGGAGTTCTATAGTCCTGAGGATCTTGC
TAGGATCGTAAGACGCTCGGCAGGCATTCTCAATATCGACTGTACTACGGAGGGTGCAGCTGAGATTGCGCAACGTGCAC
GCGGTACGCCTCGCATTGCTAATCGTTTGTTGCGGCGGGTACGCGATTATGCCGAGGTTAAGGCGGATGGGCAGATTACA
ATTGAGGTGGCGCAAGCAGCGATGCAGATGCTCAAGGTTGATCAAGGAGGCTTTGATGAACTAGACCGACGCTTGCTTCA
CACCATCGTTGAGTATTTCGACGGCGGTCCTGTCGGAATCGAGTCACTCGCTGCCTCGTTGTCGGAGGAGCGTGGTACCC
TTGAGGATGTCGTTGAGCCTTACCTAATTCAACAAGGTTTCTTGGTACGTACTGCACGTGGACGTATGGCCACAGATAAG
GCCTACCAGCATCTCGCTCTGCAGCCTCGTGAGCGAGTTTCGGCTTTCACTGATCCAGAAGATTTGTTTTGA

Domains

Predicted by InterProScan.

RuvB C-terminal winged helix domain (WHD_RuvB)

(256-325)

Holliday junction DNA helicase RuvB P-loop domain (RuvB_N)

(20-178)

RuvB AAA lid domain (AAA_lid_4)

(181-254)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB Q87D00

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  ruvB Streptococcus pneumoniae TIGR4

56.627

96.793

0.548
  ruvB Streptococcus pneumoniae R6

56.627

96.793

0.548
  ruvB Streptococcus pneumoniae D39

56.627

96.793

0.548
  ruvB Bacillus subtilis subsp. subtilis str. 168

56.97

96.21

0.548
  ruvB Helicobacter pylori 26695

53.681

95.044

0.51
  ruvB Synechocystis sp. PCC 6803

52.469

94.461

0.496