Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   NKJ47_RS06520 Genome accession   NZ_CP100647
Coordinates   1596488..1598227 (+) Length   579 a.a.
NCBI ID   WP_254460688.1    Uniprot ID   -
Organism   Xanthomonas sacchari strain DD13     
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 1590642..1610303 1596488..1598227 within 0


Gene organization within MGE regions


Location: 1590642..1610303
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  NKJ47_RS06495 - 1590642..1592474 (+) 1833 WP_254460683.1 hypothetical protein -
  NKJ47_RS06500 - 1592534..1593742 (-) 1209 WP_254460684.1 glycosyltransferase -
  NKJ47_RS06505 - 1593739..1594689 (-) 951 WP_254460685.1 YbhN family protein -
  NKJ47_RS06510 - 1594686..1595474 (-) 789 WP_254460686.1 class I SAM-dependent methyltransferase -
  NKJ47_RS06515 - 1595497..1596354 (-) 858 WP_254460687.1 glycosyltransferase family 2 protein -
  NKJ47_RS06520 pilB 1596488..1598227 (+) 1740 WP_254460688.1 type IV-A pilus assembly ATPase PilB Machinery gene
  NKJ47_RS06525 pilR 1598474..1599862 (-) 1389 WP_254460689.1 sigma-54 dependent transcriptional regulator Regulator
  NKJ47_RS06530 - 1599945..1601558 (-) 1614 WP_254460690.1 ATP-binding protein -
  NKJ47_RS06535 sucC 1601940..1603109 (+) 1170 WP_010342227.1 ADP-forming succinate--CoA ligase subunit beta -
  NKJ47_RS06540 sucD 1603132..1604007 (+) 876 WP_010342226.1 succinate--CoA ligase subunit alpha -
  NKJ47_RS06545 - 1604208..1605485 (-) 1278 WP_254460691.1 DUF2254 domain-containing protein -
  NKJ47_RS06550 - 1605737..1607833 (+) 2097 WP_254460692.1 pyrroloquinoline quinone-dependent dehydrogenase -
  NKJ47_RS06555 - 1608526..1610163 (+) 1638 WP_254460693.1 NAD+ synthase -

Sequence

Protein


Download         Length: 579 a.a.        Molecular weight: 62846.10 Da        Isoelectric Point: 5.6445

>NTDB_id=705947 NKJ47_RS06520 WP_254460688.1 1596488..1598227(+) (pilB) [Xanthomonas sacchari strain DD13]
MNAAVSANLVGITGIARRLVQDGVLEEAAARTAMAQAAEAKVPLPQWFSEKKLVTAAQLAAANAVEFGMPLMDVSVFDAS
QNAMKLVSEELLQKYQVLPLFKRGTRLFVGISNPTQTRALDDIKFHTNLTVEAILVDEDQIRRTLEQWQASNDSLGSALG
DDEGMDNLDVGGGDEDMGGGSSGDTGIDAKGEDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKSVAKA
PVKLNQRIAARLKVMAQLDIAEKRVPQDGRIKLNLSKNKQIDFRVSTLPTLFGEKIVLRILDGSAAKLGIDKLGYEPEQQ
KLFLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDDTRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQD
PDIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRPVQL
PEKALLAEGFTEAEIAAGIQLYEAVGCDECTEGYKGRTGIYQVMPMNDEIAAIVLQGGNAMDIASAAQKIGVRDLRQSAL
LKARNGITSLAEINRVTKD

Nucleotide


Download         Length: 1740 bp        

>NTDB_id=705947 NKJ47_RS06520 WP_254460688.1 1596488..1598227(+) (pilB) [Xanthomonas sacchari strain DD13]
ATGAACGCAGCTGTATCGGCCAACCTTGTCGGCATCACCGGTATCGCCCGTCGCCTCGTCCAAGACGGGGTGTTGGAGGA
GGCCGCAGCGCGGACCGCGATGGCCCAGGCGGCCGAGGCCAAGGTGCCGCTGCCGCAGTGGTTCTCCGAGAAGAAGCTGG
TCACCGCCGCGCAGCTGGCCGCCGCCAATGCGGTCGAGTTCGGCATGCCGTTGATGGATGTCTCGGTTTTCGACGCCAGC
CAGAATGCGATGAAGCTGGTCAGCGAGGAGTTGCTGCAGAAGTACCAGGTGCTGCCGCTGTTCAAGCGCGGCACGCGCCT
GTTCGTCGGCATCAGCAACCCGACCCAGACGCGGGCGCTGGACGACATCAAGTTCCACACCAACCTGACGGTCGAGGCCA
TCCTGGTCGATGAGGACCAGATCCGCCGCACCTTGGAACAGTGGCAGGCCAGCAACGATTCGCTCGGCAGTGCCTTGGGC
GACGACGAGGGCATGGACAACCTCGATGTCGGCGGCGGCGACGAGGACATGGGTGGGGGGAGCAGCGGCGACACCGGCAT
CGATGCCAAGGGCGAAGACACCCCGGTCGTCAAGTTCGTGAACAAGGTGCTGGTCGATGCGATCCGCCGTGGCGCCTCCG
ACATCCATTTCGAGCCCTACGAAGACGACTACCGGGTGCGCCTGCGTATCGACGGCCTGCTCAAGAGCGTGGCCAAGGCG
CCGGTCAAGCTCAACCAGCGCATCGCCGCGCGCCTCAAGGTGATGGCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCA
GGACGGCCGCATCAAGCTCAACCTGTCCAAGAACAAGCAGATCGATTTCCGCGTCAGCACGCTGCCGACGCTGTTCGGCG
AGAAGATCGTGCTGCGTATCCTCGACGGCAGCGCAGCCAAGCTGGGCATCGACAAGCTCGGCTACGAGCCCGAGCAGCAG
AAACTGTTCCTGGATGCGATCCACAAGCCGTACGGCATGGTCCTGGTCACCGGCCCCACCGGCTCGGGCAAGACGGTGTC
GCTGTACACCGCGCTGGGCATCCTCAACGACGACACCCGCAACATCTCCACCGCCGAGGATCCGGTCGAAATCCGCCTGC
CCGGGGTCAACCAGGTCCAGCAGAACAACAAGCGCGGCATGACCTTCGCCGCGGCGCTGCGCTCATTCCTGCGCCAGGAT
CCGGACATCATCATGGTCGGCGAAATTCGCGACCTGGAGACCGCCGAGATCGCGATCAAGGCGGCGCAGACCGGCCACAT
GGTGCTGTCCACCCTGCACACCAACGACGCGCCGCAGACCATCGCGCGCCTGATGAACATGGGCATCGCGCCCTACAACA
TCACCAGTTCGGTGACCCTGGTCATCGCCCAGCGCCTGGCGCGACGCCTATGCAACAACTGCAAGCGCCCGGTCCAGTTG
CCGGAGAAGGCCTTGCTGGCCGAGGGCTTCACCGAGGCGGAGATCGCCGCCGGCATCCAGCTGTACGAGGCGGTCGGCTG
CGACGAGTGCACCGAGGGCTACAAGGGCCGGACCGGCATCTACCAGGTCATGCCGATGAACGACGAGATCGCGGCGATCG
TGCTGCAGGGCGGCAACGCGATGGACATCGCCAGCGCCGCGCAGAAGATCGGCGTCCGCGACCTGCGCCAGTCGGCCCTG
CTCAAGGCCCGCAACGGCATCACCAGTTTGGCCGAGATCAATCGGGTGACGAAGGATTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(202-469)

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 baylyi ADP1

55.009

98.273

0.541
  pilB Acinetobacter baumannii D1279779

54.72

98.791

0.541
  pilB Legionella pneumophila strain ERS1305867

51.489

98.618

0.508
  pilB Vibrio cholerae strain A1552

49.306

99.482

0.491
  pilF Neisseria gonorrhoeae MS11

49.123

98.446

0.484
  pilB Vibrio parahaemolyticus RIMD 2210633

46.06

98.618

0.454
  pilB Vibrio campbellii strain DS40M4

45.28

98.791

0.447
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.186

100

0.383
  pilB/pilB1 Synechocystis sp. PCC 6803

36.23

100

0.382