Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   VR487_RS02480 Genome accession   NZ_CP143431
Coordinates   534569..536278 (-) Length   569 a.a.
NCBI ID   WP_330147971.1    Uniprot ID   -
Organism   Shewanella oncorhynchi strain B     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 529569..541278
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  VR487_RS02450 (VR487_02450) mutT 530023..530415 (-) 393 WP_198573100.1 8-oxo-dGTP diphosphatase MutT -
  VR487_RS02455 (VR487_02455) yacG 530495..530704 (-) 210 WP_006083355.1 DNA gyrase inhibitor YacG -
  VR487_RS02460 (VR487_02460) zapD 530778..531512 (-) 735 WP_198573099.1 cell division protein ZapD -
  VR487_RS02465 (VR487_02465) coaE 531505..532122 (-) 618 WP_263257122.1 dephospho-CoA kinase -
  VR487_RS02470 (VR487_02470) pilD 532288..533214 (-) 927 WP_263257120.1 prepilin peptidase Machinery gene
  VR487_RS02475 (VR487_02475) pilC 533247..534515 (-) 1269 WP_263257118.1 type II secretion system F family protein Machinery gene
  VR487_RS02480 (VR487_02480) pilB 534569..536278 (-) 1710 WP_330147971.1 type IV-A pilus assembly ATPase PilB Machinery gene
  VR487_RS02485 (VR487_02485) - 536350..536784 (-) 435 WP_306683490.1 pilin -
  VR487_RS02490 (VR487_02490) nadC 537532..538413 (-) 882 WP_105250404.1 carboxylating nicotinate-nucleotide diphosphorylase -
  VR487_RS02495 (VR487_02495) ampD 538672..539220 (+) 549 WP_263169631.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  VR487_RS02500 (VR487_02500) ampE 539317..540168 (+) 852 WP_168825821.1 beta-lactamase regulator AmpE -
  VR487_RS02505 (VR487_02505) pdhR 540486..541238 (+) 753 WP_105250401.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -

Sequence

Protein


Download         Length: 569 a.a.        Molecular weight: 62735.19 Da        Isoelectric Point: 6.1659

>NTDB_id=929031 VR487_RS02480 WP_330147971.1 534569..536278(-) (pilB) [Shewanella oncorhynchi strain B]
MPTTGLHLGLSTLFIRKGLLNEEQMANAITKSRQNKQALVSTLVQSKLVSARAIAELCYEEYGTPLLDLNEFDLASIPED
FLNKKLIEKHRCLPLFKRGNRLYIGTSDPTNIAALEDFQFSAGLHAEAILVEEDKLAKALEKILEEDISGLDLGGMDEAA
LASIEITDTDRRNEESAGEASDDAPIVIYINKILTDAIRKGASDLHFEPYEKRYRIRFRIDGILHEVSEPPISLAGRLSA
RLKVMSKLDIAERRVPQDGRIKMKLSRTKSIDFRVSTLPTLWGEKIVMRILDSSSAQLGIEKLGYEPDQEKLYLEMLAKP
QGMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINLKAGLTFASALRSFLRQDPDVVMVGEIR
DLETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLINMGVPGYNIASSVNLIIAQRLARRLCPECKQAEIIPEHELLRLGF
AQAQITQGFTTFKPVGCEHCSGGYKGRVGIYEVMKMSDEIARTIMEGGNSLQIASQAKAQGMRDLRQSGLLKVIHGVTSI
AEVNRVTSF

Nucleotide


Download         Length: 1710 bp        

>NTDB_id=929031 VR487_RS02480 WP_330147971.1 534569..536278(-) (pilB) [Shewanella oncorhynchi strain B]
ATGCCCACAACTGGCCTTCATTTAGGTTTATCGACCCTGTTTATTCGTAAGGGCCTGCTTAATGAAGAGCAGATGGCTAA
TGCCATCACAAAATCCCGCCAAAATAAGCAAGCGTTAGTCAGTACTTTAGTACAAAGTAAACTGGTTTCAGCACGTGCTA
TTGCAGAGCTTTGCTATGAGGAATATGGCACGCCACTACTCGACCTCAATGAGTTTGATCTTGCTTCCATTCCTGAGGAC
TTCCTCAACAAAAAACTGATTGAAAAGCACCGCTGCTTACCGCTGTTTAAACGGGGAAATCGCCTCTATATAGGCACATC
CGACCCGACCAATATTGCCGCCCTCGAAGATTTCCAATTTAGTGCAGGCCTGCACGCCGAAGCGATTCTAGTTGAAGAAG
ATAAATTGGCTAAAGCGCTAGAAAAAATCCTCGAAGAAGACATCAGCGGCCTAGATTTAGGCGGCATGGATGAAGCGGCA
CTGGCGAGCATTGAAATTACCGACACTGACAGACGTAATGAAGAGTCCGCAGGCGAGGCCAGCGATGATGCACCTATTGT
TATCTATATCAATAAAATTCTAACCGATGCCATTCGTAAAGGAGCCTCGGATTTACACTTTGAACCCTATGAGAAGCGCT
ACCGCATTCGTTTTCGCATCGACGGTATTTTACACGAAGTCTCTGAACCCCCTATAAGCCTTGCAGGTCGTTTATCAGCG
CGCCTAAAAGTAATGTCGAAACTTGATATTGCCGAACGCCGCGTGCCGCAAGACGGCCGAATCAAGATGAAACTTTCCCG
CACTAAGTCCATCGACTTTCGGGTAAGTACCCTGCCGACCCTGTGGGGTGAAAAAATTGTAATGCGGATCTTGGATTCAT
CCTCCGCACAACTGGGCATTGAAAAGCTCGGCTACGAGCCTGACCAAGAAAAACTTTACCTTGAGATGTTGGCAAAACCC
CAAGGGATGATTTTAGTTACCGGCCCTACAGGCTCAGGTAAAACCGTCTCCCTCTATACAGGATTAAATATTCTCAATAC
TGAAGAGCGTAATATTTCTACTGCCGAAGATCCGGTAGAAATAAACCTTGAGGGCGTAAACCAAGTTCACATTAACTTAA
AAGCCGGTCTCACTTTCGCCTCTGCTTTACGCTCATTCCTGCGCCAAGACCCCGATGTGGTGATGGTGGGCGAAATTCGC
GATCTTGAAACCGCCGAGATAGCCATTAAAGCGGCACAAACAGGCCACTTAGTATTATCGACCTTACACACGAACTCGGC
CGCAGAAACCTTGACTCGTTTAATTAATATGGGCGTGCCTGGTTATAACATCGCCAGCTCAGTTAACCTGATTATTGCAC
AGCGTTTAGCGCGTCGACTTTGCCCCGAATGTAAGCAGGCTGAAATCATCCCCGAGCACGAACTATTACGTTTAGGTTTT
GCCCAAGCACAAATTACACAAGGTTTTACCACCTTTAAACCTGTGGGCTGCGAGCATTGCTCCGGCGGCTACAAAGGCCG
GGTTGGTATTTACGAAGTGATGAAGATGTCCGATGAGATAGCGCGTACTATCATGGAAGGCGGTAACTCCTTACAAATCG
CCTCCCAAGCTAAAGCGCAAGGGATGCGTGATTTACGTCAGTCAGGATTATTAAAAGTAATTCATGGTGTTACTAGCATC
GCAGAAGTCAATCGCGTAACGAGTTTTTAA

Domains

Predicted by InterproScan.

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

(43-144)

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

59.537

98.594

0.587
  pilB Acinetobacter baumannii D1279779

59.266

95.782

0.568
  pilB Legionella pneumophila strain ERS1305867

56.05

98.77

0.554
  pilB Vibrio cholerae strain A1552

53.249

97.364

0.518
  pilB Vibrio parahaemolyticus RIMD 2210633

51.67

100

0.517
  pilB Vibrio campbellii strain DS40M4

51.327

99.297

0.51
  pilF Neisseria gonorrhoeae MS11

48.233

99.473

0.48
  pilF Thermus thermophilus HB27

38.869

99.473

0.387
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.71

98.067

0.38