Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   U9J37_RS13850 Genome accession   NZ_OY808997
Coordinates   2972725..2974413 (-) Length   562 a.a.
NCBI ID   WP_043887354.1    Uniprot ID   -
Organism   Vibrio sp. 16 isolate VDT1     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2967725..2979413
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  U9J37_RS13820 (VDT1_2815) rplS 2968291..2968644 (+) 354 WP_005476458.1 50S ribosomal protein L19 -
  U9J37_RS13825 (VDT1_2816) yacG 2968930..2969124 (-) 195 WP_038191328.1 DNA gyrase inhibitor YacG -
  U9J37_RS13830 (VDT1_2817) zapD 2969176..2969916 (-) 741 WP_005476491.1 cell division protein ZapD -
  U9J37_RS13835 (VDT1_2818) coaE 2969951..2970559 (-) 609 WP_322413840.1 dephospho-CoA kinase -
  U9J37_RS13840 (VDT1_2819) pilD 2970561..2971430 (-) 870 WP_039477926.1 prepilin peptidase Machinery gene
  U9J37_RS13845 (VDT1_2820) pilC 2971486..2972712 (-) 1227 WP_005475684.1 type II secretion system F family protein Machinery gene
  U9J37_RS13850 (VDT1_2821) pilB 2972725..2974413 (-) 1689 WP_043887354.1 type IV-A pilus assembly ATPase PilB Machinery gene
  U9J37_RS13855 (VDT1_2822) pilA 2974413..2974814 (-) 402 WP_005475654.1 type IV pilin protein Machinery gene
  U9J37_RS13860 (VDT1_2823) nadC 2975071..2975958 (-) 888 WP_005475682.1 carboxylating nicotinate-nucleotide diphosphorylase -
  U9J37_RS13865 (VDT1_2824) ampD 2976100..2976654 (+) 555 WP_005475679.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  U9J37_RS13870 (VDT1_2825) fldB 2976708..2977229 (-) 522 WP_005475668.1 flavodoxin FldB -
  U9J37_RS13875 (VDT1_2826) xerD 2977393..2978289 (+) 897 WP_005475659.1 site-specific tyrosine recombinase XerD -
  U9J37_RS13880 (VDT1_2827) - 2978318..2979061 (+) 744 WP_043887353.1 thioredoxin fold domain-containing protein -

Sequence

Protein


Download         Length: 562 a.a.        Molecular weight: 61840.77 Da        Isoelectric Point: 5.3752

>NTDB_id=1161999 U9J37_RS13850 WP_043887354.1 2972725..2974413(-) (pilB) [Vibrio sp. 16 isolate VDT1]
MLTNLPAILRQARLLDAAQEASVIEHCQASGQSVPEALLTLNLIEHQQLTEQLAHIFGLPKVEIDQFDYAAMCQKLGLRE
LITHHQALPLYESAQQLTIAITDPTNLELEDEFRFATGRQIELVLADIKALHSAIRKLYGRTIETGLSAKKELNEQDLEQ
LVDVSDDEIGTIEDLSLDTAPVSRYINQILLDAVRKGASDIHFEPYEDSYRVRLRCDGILVEIQQPAHHLSRRLAARLKI
LSKLDIAERRLPQDGRIKLKIGTNTAIDMRVSTLPTLWGEKIVLRLLDSSEASLNIDALGYNDTQKQQYLNALRRPQGLI
LMTGPTGSGKTVSLYTGLKLLNTAEVNIATAEDPVEINLSGINQVQVQPQIGFGFAQALRAFLRQDPDIVMVGEIRDIET
AGIAVKAAQTGHLVLSTLHTNSAAESVARLSNMGVEPFNIASSLSLIIAQRLARRLCSHCKIAYQVDHTQAIGLDLTLGE
TLYRASSDGCSECNNGYVGRVGIYEVMSFTPTLSQAIAQGSSIQSLEQLARSEGMATLKESGLEKLRLGITSVSELQRVL
YL

Nucleotide


Download         Length: 1689 bp        

>NTDB_id=1161999 U9J37_RS13850 WP_043887354.1 2972725..2974413(-) (pilB) [Vibrio sp. 16 isolate VDT1]
GTGCTAACTAACCTCCCAGCTATCTTGCGCCAAGCCCGCCTTTTAGATGCGGCGCAAGAAGCGAGCGTTATCGAACATTG
TCAAGCCTCCGGCCAATCCGTGCCGGAGGCGTTGCTTACTCTCAACCTCATTGAACACCAGCAACTGACCGAGCAACTCG
CACACATTTTTGGCCTGCCGAAAGTAGAGATTGACCAATTTGACTACGCTGCGATGTGTCAAAAGTTAGGGCTGAGGGAA
CTCATCACCCACCACCAAGCCTTGCCACTATATGAAAGTGCTCAACAACTCACTATTGCCATTACCGATCCGACAAACCT
TGAACTAGAAGATGAGTTTCGCTTTGCGACAGGTCGGCAAATTGAGCTAGTTCTTGCCGATATAAAAGCGCTTCATAGTG
CAATTCGTAAACTCTATGGCCGAACAATAGAGACGGGATTATCGGCAAAAAAAGAGCTCAATGAACAAGATCTCGAACAG
CTGGTCGATGTTTCCGATGATGAAATCGGTACTATTGAAGATCTCAGTTTAGACACCGCTCCGGTGAGTCGTTACATCAA
TCAAATTCTGCTTGATGCAGTACGAAAAGGGGCATCCGACATTCACTTCGAGCCCTATGAAGATTCCTATCGCGTCAGGC
TTCGCTGTGACGGTATTTTGGTCGAAATCCAGCAACCTGCACATCATTTAAGTCGACGTTTAGCCGCCCGATTGAAAATT
CTCTCCAAACTCGACATCGCAGAACGGCGGCTTCCGCAAGATGGGCGTATTAAACTAAAAATCGGCACCAATACCGCAAT
TGATATGCGCGTTTCAACATTACCCACCTTGTGGGGAGAAAAAATCGTCCTCCGTTTGCTAGATAGCAGTGAGGCGAGTC
TTAACATTGATGCCCTCGGATATAATGACACACAAAAACAGCAATACCTGAATGCATTACGCCGCCCACAAGGGCTAATC
CTTATGACGGGACCAACGGGCAGTGGTAAAACCGTCTCACTCTATACCGGATTAAAACTATTAAACACAGCGGAAGTGAA
CATCGCGACAGCGGAAGATCCCGTAGAAATCAACCTCTCTGGTATCAACCAAGTCCAAGTCCAACCTCAAATTGGCTTTG
GTTTTGCGCAAGCCTTACGCGCGTTTCTCCGCCAAGACCCAGACATCGTCATGGTGGGTGAAATCCGAGATATTGAGACC
GCAGGGATTGCCGTTAAAGCCGCCCAAACTGGCCACCTCGTGCTCTCGACCTTACACACAAACTCTGCCGCGGAAAGTGT
CGCTAGACTCAGCAACATGGGCGTCGAGCCCTTTAATATCGCCTCTTCACTCAGTTTGATTATCGCCCAACGGCTTGCTC
GACGTTTGTGTAGTCATTGCAAAATCGCTTATCAAGTCGATCACACTCAAGCGATAGGACTCGACCTAACCCTAGGTGAA
ACTCTTTATCGTGCATCTAGCGATGGGTGTTCAGAATGTAATAACGGCTACGTAGGACGTGTTGGCATCTACGAAGTCAT
GTCCTTTACCCCTACCTTATCTCAAGCCATCGCGCAGGGCTCTTCAATCCAAAGCCTCGAGCAACTTGCTCGCAGTGAAG
GGATGGCGACATTAAAAGAATCTGGCTTAGAAAAGTTGCGTTTGGGCATTACCAGTGTCTCTGAGCTGCAACGCGTACTC
TACTTATAG

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(188-455)

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

(38-141)


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 Vibrio cholerae strain A1552

70.641

100

0.706
  pilB Vibrio parahaemolyticus RIMD 2210633

68.142

100

0.685
  pilB Vibrio campbellii strain DS40M4

67.318

100

0.674
  pilB Legionella pneumophila strain ERS1305867

48.649

98.754

0.48
  pilB Acinetobacter baumannii D1279779

51.064

91.993

0.47
  pilB Acinetobacter baylyi ADP1

49.901

90.214

0.45
  pilF Neisseria gonorrhoeae MS11

42.756

100

0.431
  pilB/pilB1 Synechocystis sp. PCC 6803

37.086

100

0.399
  pilB Haemophilus influenzae 86-028NP

40.727

93.06

0.379
  pilF Thermus thermophilus HB27

39.587

94.84

0.375
  pilB Haemophilus influenzae Rd KW20

42.062

86.299

0.363

Multiple sequence alignment