Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   RA178_RS19845 Genome accession   NZ_CP132914
Coordinates   4482006..4483715 (+) Length   569 a.a.
NCBI ID   WP_306683491.1    Uniprot ID   A0AA50Q587
Organism   Shewanella oncorhynchi strain Z-P2     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 4477006..4488715
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RA178_RS19820 (RA178_19815) pdhR 4477076..4477828 (-) 753 WP_105250401.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  RA178_RS19825 (RA178_19820) ampE 4478115..4478966 (-) 852 WP_306683485.1 beta-lactamase regulator AmpE -
  RA178_RS19830 (RA178_19825) ampD 4479048..4479611 (-) 564 WP_306683487.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  RA178_RS19835 (RA178_19830) nadC 4479869..4480750 (+) 882 WP_306683489.1 carboxylating nicotinate-nucleotide diphosphorylase -
  RA178_RS19840 (RA178_19835) - 4481500..4481934 (+) 435 WP_306683490.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  RA178_RS19845 (RA178_19840) pilB 4482006..4483715 (+) 1710 WP_306683491.1 type IV-A pilus assembly ATPase PilB Machinery gene
  RA178_RS19850 (RA178_19845) pilC 4483769..4485037 (+) 1269 WP_113940789.1 type II secretion system F family protein Machinery gene
  RA178_RS19855 (RA178_19850) pilD 4485070..4485996 (+) 927 WP_306683493.1 A24 family peptidase Machinery gene
  RA178_RS19860 (RA178_19855) coaE 4486158..4486775 (+) 618 WP_263223082.1 dephospho-CoA kinase -
  RA178_RS19865 (RA178_19860) zapD 4486768..4487502 (+) 735 WP_173247868.1 cell division protein ZapD -
  RA178_RS19870 (RA178_19865) yacG 4487576..4487785 (+) 210 WP_219251915.1 DNA gyrase inhibitor YacG -
  RA178_RS19875 (RA178_19870) mutT 4487864..4488256 (+) 393 WP_131523409.1 8-oxo-dGTP diphosphatase MutT -

Sequence

Protein


Download         Length: 569 a.a.        Molecular weight: 62847.36 Da        Isoelectric Point: 6.3067

>NTDB_id=870709 RA178_RS19845 WP_306683491.1 4482006..4483715(+) (pilB) [Shewanella oncorhynchi strain Z-P2]
MPTTGLHLGLSTLFIRKGLLNEEQMANAITKSRQNKQALVSTLVQSKLVSARAIAELCYEEYGTPLLDLNEFDLASIPED
FLNKKLIEKHRCLPLFKRGNRLYIGTSDPTNIAALEDFQFSAGLHAEAILVEEDKLAKALEKILEVDISGLDLGGMDEAA
LANIEITDTDRRNEELTGESSDDAPIVIYINKILTDAIRKGASDLHFEPYEKRYRIRFRIDGILHEVSEPPISLANRLSA
RLKVMSKLDIAERRVPQDGRIKMKLSRTKSIDFRVSTLPTLWGEKIVMRILDSSSAQLGIEKLGYEPDQEKLYLEMLAKP
QGMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINLKAGLTFASALRSFLRQDPDVVMVGEIR
DLETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLINMGVPGYNIASSVNLIIAQRLARRLCPECKQAEVIPEHELLRLGF
AQAQITQGFTTFKPVGCEHCSGGYKGRVGIYEVMKMSDEIARTIMEGGNSLQIASQAKAQGMRDLRQSGLLKVIHGVTSI
AEVNRVTSF

Nucleotide


Download         Length: 1710 bp        

>NTDB_id=870709 RA178_RS19845 WP_306683491.1 4482006..4483715(+) (pilB) [Shewanella oncorhynchi strain Z-P2]
ATGCCCACAACTGGCCTTCATTTAGGTTTATCGACCCTGTTTATTCGTAAGGGCCTGCTTAATGAAGAGCAGATGGCTAA
CGCCATCACAAAATCCCGCCAAAATAAGCAAGCGTTGGTCAGCACCTTAGTGCAAAGCAAACTAGTCTCAGCACGTGCTA
TTGCAGAGCTTTGCTATGAAGAATATGGCACGCCACTACTCGATCTTAATGAGTTTGATCTTGCTTCCATTCCTGAGGAC
TTCCTCAATAAAAAACTGATTGAGAAACACCGCTGCTTACCCCTGTTTAAACGTGGTAATCGCCTCTATATAGGGACATC
CGACCCGACCAATATCGCCGCCCTCGAAGATTTCCAATTTAGTGCAGGCCTCCACGCCGAAGCGATTCTGGTTGAAGAAG
ATAAATTGGCTAAAGCGCTAGAAAAAATCCTCGAAGTAGATATTAGTGGCCTAGATTTAGGCGGTATGGATGAAGCGGCT
CTAGCCAATATTGAAATAACGGATACCGACAGACGCAATGAAGAGTTAACAGGTGAGAGTAGCGATGATGCGCCTATTGT
TATCTATATCAATAAAATTTTAACCGACGCGATCCGCAAGGGTGCCTCGGATTTACACTTTGAACCCTATGAGAAGCGCT
ACCGCATTCGTTTTCGCATCGACGGTATTTTACACGAAGTCTCTGAACCACCTATTAGCCTTGCAAATCGTTTATCGGCG
CGATTAAAAGTAATGTCGAAACTTGATATCGCCGAACGCCGCGTGCCACAAGACGGCCGAATCAAGATGAAACTTTCCCG
CACTAAGTCCATCGACTTCCGAGTTAGTACCCTGCCGACCCTGTGGGGCGAAAAAATTGTGATGCGGATCTTAGATTCTT
CCTCCGCACAACTGGGCATTGAAAAACTTGGCTACGAGCCCGACCAAGAAAAACTTTACCTTGAGATGTTAGCAAAACCC
CAAGGGATGATTTTAGTGACCGGTCCTACTGGCTCAGGTAAAACCGTCTCCCTCTATACAGGGTTAAATATTCTTAATAC
CGAAGAGCGTAATATTTCTACCGCCGAAGATCCGGTAGAAATAAACCTTGAAGGTGTAAACCAAGTTCACATTAACTTAA
AAGCTGGTCTGACTTTCGCCTCCGCTTTACGTTCATTCCTGCGCCAAGACCCCGATGTAGTGATGGTGGGTGAAATTCGC
GATCTTGAAACCGCCGAAATTGCCATTAAAGCGGCACAAACGGGTCACTTAGTGTTATCGACCCTACACACTAATTCGGC
CGCTGAAACCTTGACTCGTTTAATCAATATGGGCGTGCCAGGTTATAACATCGCCAGCTCAGTTAACCTGATTATTGCCC
AGCGTTTGGCGCGTCGCCTCTGCCCCGAATGTAAGCAAGCTGAAGTCATCCCTGAGCATGAACTATTACGTTTAGGTTTT
GCCCAAGCACAAATTACCCAAGGTTTTACCACTTTTAAACCTGTGGGCTGCGAGCATTGCTCCGGCGGCTACAAAGGCCG
GGTTGGTATTTACGAAGTGATGAAGATGTCCGATGAAATAGCGCGTACTATTATGGAAGGTGGTAACTCCCTACAAATCG
CCTCCCAAGCTAAAGCGCAAGGGATGCGTGATTTACGTCAGTCAGGATTATTGAAAGTAATCCACGGTGTTACTAGCATC
GCAGAAGTCAATCGCGTAACGAGTTTTTAA

Domains

Predicted by InterproScan.

Type II secretion system (T2SS), protein E, N-terminal domain (MshEN)

(43-143)

Type II/IV secretion system protein (T2SSE)

(192-459)


Secondary structure

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



3D structure

Source ID Structure

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
  pilB Acinetobacter baylyi ADP1

59.358

98.594

0.585
  pilB Acinetobacter baumannii D1279779

59.266

95.782

0.568
  pilB Legionella pneumophila strain ERS1305867

56.406

98.77

0.557
  pilB Vibrio parahaemolyticus RIMD 2210633

52.021

100

0.52
  pilB Vibrio cholerae strain A1552

53.526

97.188

0.52
  pilB Vibrio campbellii strain DS40M4

51.59

99.473

0.513
  pilF Neisseria gonorrhoeae MS11

47.359

99.824

0.473
  pilF Thermus thermophilus HB27

39.223

99.473

0.39
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.393

98.418

0.378