Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   JH280_RS16315 Genome accession   NZ_CP066922
Coordinates   3750208..3751941 (-) Length   577 a.a.
NCBI ID   WP_228431843.1    Uniprot ID   -
Organism   Xanthomonas campestris strain 5053     
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 3752045..3770021 3750208..3751941 flank 104


Gene organization within MGE regions


Location: 3750208..3770021
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JH280_RS16315 (JH280_16255) pilB 3750208..3751941 (-) 1734 WP_228431843.1 type IV-A pilus assembly ATPase PilB Machinery gene
  JH280_RS16320 (JH280_16260) - 3752045..3752683 (-) 639 WP_076054160.1 methionine biosynthesis protein MetW -
  JH280_RS16325 (JH280_16265) - 3752676..3753722 (-) 1047 WP_081390738.1 glycosyltransferase family 2 protein -
  JH280_RS16330 (JH280_16270) - 3753719..3754513 (-) 795 WP_076057322.1 glycosyltransferase family A protein -
  JH280_RS16335 (JH280_16275) - 3754518..3754898 (-) 381 WP_228431841.1 SMR family transporter -
  JH280_RS16340 (JH280_16280) comP 3755239..3755655 (+) 417 WP_274347446.1 pilin Machinery gene
  JH280_RS16345 (JH280_16285) - 3755740..3757722 (+) 1983 WP_274347447.1 hypothetical protein -
  JH280_RS16350 (JH280_16290) pilC 3757911..3759113 (+) 1203 WP_274349048.1 type II secretion system F family protein Machinery gene
  JH280_RS16355 (JH280_16295) - 3759120..3759983 (+) 864 WP_012437600.1 A24 family peptidase -
  JH280_RS16360 (JH280_16300) coaE 3759997..3760620 (+) 624 WP_274347448.1 dephospho-CoA kinase -
  JH280_RS21805 - 3760852..3761069 (+) 218 Protein_3144 SymE family type I addiction module toxin -
  JH280_RS16365 (JH280_16305) - 3761169..3762503 (-) 1335 WP_227971331.1 HAMP domain-containing sensor histidine kinase -
  JH280_RS16370 (JH280_16310) - 3762496..3763173 (-) 678 WP_003490678.1 response regulator transcription factor -
  JH280_RS16375 (JH280_16315) rimK 3763823..3764698 (-) 876 WP_076054142.1 30S ribosomal protein S6--L-glutamate ligase -
  JH280_RS16380 (JH280_16320) glgX 3765192..3767321 (+) 2130 WP_274347449.1 glycogen debranching protein GlgX -
  JH280_RS16385 (JH280_16325) - 3767851..3768243 (-) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  JH280_RS16390 (JH280_16330) - 3768334..3768729 (-) 396 WP_011038225.1 hypothetical protein -
  JH280_RS16395 (JH280_16335) - 3768913..3769059 (-) 147 WP_076054137.1 hypothetical protein -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62857.00 Da        Isoelectric Point: 5.4508

>NTDB_id=523207 JH280_RS16315 WP_228431843.1 3750208..3751941(-) (pilB) [Xanthomonas campestris strain 5053]
MNSVVTANLVGITGIARRLVQDGALDEGAARAAMDQAATAKVPLPQWFSEKKLVTASQLAAANSVEFGMPLLDVSSFDPN
QNAIKLVSEELLQKFQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSSMG
DDDDEMGDLDVSTGDEEMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLNQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQK
LFLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
EHALLAEGFTPEQVANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMK
ASHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=523207 JH280_RS16315 WP_228431843.1 3750208..3751941(-) (pilB) [Xanthomonas campestris strain 5053]
ATGAATAGCGTCGTCACCGCCAACTTGGTTGGCATCACGGGCATTGCCCGGCGGCTTGTGCAGGACGGTGCTCTGGATGA
AGGCGCGGCGCGTGCTGCGATGGATCAGGCCGCTACTGCCAAGGTCCCGTTGCCGCAATGGTTCTCAGAGAAGAAGCTGG
TGACCGCTTCGCAATTAGCAGCTGCCAACTCAGTGGAGTTCGGGATGCCGCTACTTGATGTGTCATCGTTCGACCCTAAT
CAGAATGCAATCAAGTTGGTTAGCGAAGAACTGCTGCAAAAGTTTCAAGTGCTGCCCCTGTTCAAGCGCGGTAATCGGTT
GTTTGTGGGGGTGAGCAACCCGACCCAGACCCGGGCGCTGGACGACATCAAGTTTCACACCAATTTGGTGGTCGAGCCGA
TCCTGGTCGACGAGGACCAGATCCGTCGCACATTGGAGCAGTGGCAGGCCAGCAATGCGGCGCTCGGCTCTTCGATGGGC
GACGACGATGATGAAATGGGGGATCTGGACGTCTCCACCGGGGACGAGGAGATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGCGATGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCGGACA
TCCATTTCGAGCCCTATGAAGATGACTACCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCG
GTGAAGCTCAACCAGCGCATCGCGGCGCGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGA
CGGACGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGTGTGAGCACCTTGCCAACCCTGTTCGGCGAGA
AGGTGGTACTGCGTATCCTGGACGCCAGTGCGGCCAAGCTTGGTATCGAGAAGCTGGGCTATGAGGCGGACCAACAGAAG
CTGTTCCTGGATGCGATACACAAGCCCTACGGCATGGTGCTGGTGACTGGGCCGACCGGTTCGGGCAAGACGGTGTCGCT
GTATACCGCACTCGGGATTCTCAACGACGAGACCCGCAATATTTCCACGGCCGAGGATCCGGTTGAAATCCGCCTGCCCG
GCGTCAACCAGGTGCAGCAGAACGTCAAGCGGGGCATGACGTTTGCCGCTGCGCTGCGGTCGTTCCTGCGTCAGGACCCG
GACATCATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAAATTGCGATCAAGGCGGCGCAGACCGGCCACATGGT
GCTGTCGACACTGCACACCAACGATGCGCCGCAGACCATCGCGCGTCTAATGAACATGGGCATCGCGCCGTACAACATCA
CCTCGTCGGTGACCCTGGTCATCGCGCAGCGCCTGGCGCGGCGGCTGTGCAACAACTGTAAGCGCAAGTCGACGCTGCCG
GAACATGCGCTGCTGGCGGAAGGCTTTACGCCGGAGCAGGTTGCGAACATCGAGCTCTATGAAGCGGTCGGTTGCGATGA
GTGCACCGAAGGCTACAAGGGCCGTACCGGCATCTATCAAGTGATGCCGATGACCGACGAAATCGGCGCGATCGTGCTGG
AAGGCGGCAATGCGATGCAGATCGCCGAGGCTGCGCAGAAGATCGGTATCCGCGACTTGCGCCAGTCAGCGTTGATGAAG
GCTTCGCACGGGGTGACCAGCCTGGCCGAGATCAATCGTGTGACCAAGGACTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(201-468)

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

(50-153)


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 baumannii D1279779

55.634

98.44

0.548
  pilB Acinetobacter baylyi ADP1

55.634

98.44

0.548
  pilB Legionella pneumophila strain ERS1305867

51.408

98.44

0.506
  pilF Neisseria gonorrhoeae MS11

48.944

98.44

0.482
  pilB Vibrio cholerae strain A1552

49.546

95.494

0.473
  pilB Vibrio campbellii strain DS40M4

45.47

99.48

0.452
  pilB Vibrio parahaemolyticus RIMD 2210633

45.826

97.574

0.447
  pilB/pilB1 Synechocystis sp. PCC 6803

35.738

100

0.378