Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   GLA29479_RS08890 Genome accession   NZ_CP013141
Coordinates   2207391..2209118 (+) Length   575 a.a.
NCBI ID   WP_057971375.1    Uniprot ID   -
Organism   Lysobacter antibioticus strain ATCC 29479     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
Genomic island 2197337..2207255 2207391..2209118 flank 136


Gene organization within MGE regions


Location: 2197337..2209118
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GLA29479_RS25740 (GLA29479_2006) - 2197337..2197753 (+) 417 WP_057916958.1 pilin -
  GLA29479_RS08845 (GLA29479_2007) - 2197809..2199737 (+) 1929 WP_057916957.1 hypothetical protein -
  GLA29479_RS08850 - 2199745..2200917 (+) 1173 WP_057919928.1 DegT/DnrJ/EryC1/StrS family aminotransferase -
  GLA29479_RS08855 (GLA29479_2009) - 2201101..2201925 (+) 825 WP_248842822.1 hypothetical protein -
  GLA29479_RS08860 - 2201912..2202661 (+) 750 WP_057971370.1 class I SAM-dependent methyltransferase -
  GLA29479_RS23615 - 2202658..2203722 (+) 1065 WP_169795633.1 NAD(P)-binding domain-containing protein -
  GLA29479_RS23620 (GLA29479_2012) - 2203693..2204553 (-) 861 WP_082638434.1 GNAT family N-acetyltransferase -
  GLA29479_RS08875 (GLA29479_2014) - 2204546..2205697 (-) 1152 WP_057971373.1 glycosyltransferase -
  GLA29479_RS23625 (GLA29479_2015) - 2205694..2206398 (-) 705 WP_082638436.1 class I SAM-dependent methyltransferase -
  GLA29479_RS08885 (GLA29479_2016) - 2206395..2207255 (-) 861 WP_057916950.1 glycosyltransferase family 2 protein -
  GLA29479_RS08890 (GLA29479_2017) pilB 2207391..2209118 (+) 1728 WP_057971375.1 type IV-A pilus assembly ATPase PilB Machinery gene

Sequence

Protein


Download         Length: 575 a.a.        Molecular weight: 62543.85 Da        Isoelectric Point: 6.2692

>NTDB_id=160284 GLA29479_RS08890 WP_057971375.1 2207391..2209118(+) (pilB) [Lysobacter antibioticus strain ATCC 29479]
MSSVATANLVGITGIARRLVLDGALDEVKAREAMAAATAERKPLATYLAEHRLATSAQLAAANSIEFGVPLFDPSSLDPS
QSAVRAISEELIRKHSALPLFKRGNKLFIGLADPTNTAALDEIKFQTNAAVEAILVDDELIRRTLDRWLENSDALANAVG
DSDGLDTLEIGKDDDLSTTSDSGIDAKGDDTPVVKFINKVLVDAIRRGASDIHFEPYETDYRVRLRIDGLLKQVAKVPNK
LHSRIAARLKVMAQLDIAEKRVPQDGRIKLNLSKTKQIDFRMSTLPTLFGEKIVLRILDGSAAKLGIEKLGYEDYQKELF
INAVAKPYGMVLVTGPTGSGKTVSLYTALNILNDEQRNISTVEDPVEIRVPGINQVQMNVKRGMTFAAALRSFLRQDPDV
IMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGVAPYNITSSVTLVIAQRLARRLHDCKREVHLPEHA
LLAEGFTAEEIASGFKLYEPAGCPDCTEGYKGRTGIYQVMPMTDEIQAIVLEGGNAMQIAAAAIKSGVNDLRRSALIKVM
NGVTGLAEINRVTKD

Nucleotide


Download         Length: 1728 bp        

>NTDB_id=160284 GLA29479_RS08890 WP_057971375.1 2207391..2209118(+) (pilB) [Lysobacter antibioticus strain ATCC 29479]
ATGTCCAGCGTCGCAACCGCCAACTTGGTGGGTATCACCGGCATTGCCCGGCGTTTGGTTTTGGATGGAGCTTTGGACGA
GGTCAAGGCGCGCGAAGCCATGGCCGCGGCCACCGCCGAGCGCAAGCCACTGGCTACCTACCTCGCCGAACATCGCCTGG
CCACCTCCGCCCAACTGGCCGCCGCCAACTCGATCGAATTCGGCGTGCCGCTGTTCGACCCGAGCTCGCTGGACCCCAGC
CAGTCTGCGGTCCGGGCGATCAGCGAGGAACTGATCCGCAAACACAGCGCGCTGCCGTTGTTCAAACGCGGCAACAAGCT
GTTCATCGGCTTGGCCGATCCGACCAATACCGCCGCCCTGGACGAGATCAAGTTCCAGACCAATGCCGCGGTCGAAGCCA
TCCTGGTCGACGACGAGCTGATCCGGCGGACCCTGGACCGCTGGCTGGAGAACTCCGACGCCCTCGCCAACGCAGTCGGC
GATAGCGACGGCCTCGACACCCTGGAGATCGGCAAGGACGACGATCTCAGCACGACAAGCGACAGTGGCATCGACGCCAA
GGGCGACGATACCCCGGTCGTAAAGTTCATCAACAAGGTTCTGGTCGACGCCATCCGCCGCGGCGCCTCGGACATCCACT
TCGAACCTTACGAGACCGATTATCGGGTGCGCCTGCGCATCGACGGCCTGCTCAAGCAGGTCGCCAAGGTCCCGAACAAG
CTGCACTCGCGCATCGCCGCGCGCCTGAAGGTCATGGCGCAGCTCGACATCGCCGAGAAGCGCGTGCCGCAGGACGGCCG
CATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGCATGAGCACCTTGCCGACCCTGTTCGGCGAGAAGATCG
TGTTGCGTATCCTCGATGGCAGCGCGGCGAAGCTCGGTATCGAAAAGCTCGGCTACGAGGATTACCAGAAGGAATTGTTC
ATCAATGCCGTGGCCAAGCCCTACGGTATGGTGCTCGTGACCGGTCCGACCGGCTCGGGCAAGACGGTCTCGCTGTACAC
CGCCTTGAACATCCTTAACGACGAGCAGCGCAACATCTCCACGGTCGAAGACCCGGTCGAAATCCGCGTACCCGGCATCA
ACCAGGTGCAGATGAACGTCAAACGCGGCATGACCTTCGCCGCGGCGCTGCGCAGCTTCCTGCGTCAGGATCCGGACGTG
ATCATGGTCGGCGAAATCCGCGACCTCGAAACCGCCGAGATCGCGATCAAGGCCGCCCAGACCGGCCACATGGTGCTGTC
GACCCTGCACACCAACGATGCGCCGCAGACCATCGCCCGCCTGATGAACATGGGCGTCGCGCCCTACAACATCACTTCCT
CGGTGACCCTGGTCATCGCCCAGCGCCTCGCCCGCCGTCTGCATGACTGCAAGCGCGAGGTGCATCTGCCCGAACACGCT
CTGCTCGCCGAAGGCTTCACCGCGGAAGAGATCGCGTCCGGGTTCAAGTTGTACGAGCCGGCGGGATGCCCGGACTGCAC
CGAAGGCTACAAGGGACGTACCGGCATCTACCAGGTCATGCCCATGACCGACGAAATCCAGGCCATCGTGCTGGAGGGCG
GCAACGCGATGCAGATCGCGGCCGCCGCCATCAAGTCCGGCGTCAACGACTTGCGCCGCTCCGCACTGATCAAGGTGATG
AACGGCGTCACCGGCCTGGCCGAAATCAACCGCGTAACCAAGGACTAA

Domains

Predicted by InterproScan.

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

(48-152)

Type II/IV secretion system protein (T2SSE)

(199-466)


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

55.088

99.13

0.546
  pilB Acinetobacter baumannii D1279779

54.246

100

0.544
  pilB Legionella pneumophila strain ERS1305867

50.963

99.304

0.506
  pilB Vibrio cholerae strain A1552

52.335

89.391

0.468
  pilF Neisseria gonorrhoeae MS11

52.227

85.913

0.449
  pilB Vibrio parahaemolyticus RIMD 2210633

49.425

90.783

0.449
  pilB Vibrio campbellii strain DS40M4

51.125

85.043

0.435

Multiple sequence alignment