Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   NYR95_RS17055 Genome accession   NZ_CP103837
Coordinates   3913454..3915187 (-) Length   577 a.a.
NCBI ID   WP_316687911.1    Uniprot ID   -
Organism   Xanthomonas dyei strain 22-321     
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 3915342..3952203 3913454..3915187 flank 155


Gene organization within MGE regions


Location: 3913454..3952203
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  NYR95_RS17055 (NYR95_17040) pilB 3913454..3915187 (-) 1734 WP_316687911.1 type IV-A pilus assembly ATPase PilB Machinery gene
  NYR95_RS17060 (NYR95_17045) - 3915342..3916193 (+) 852 WP_316687912.1 glycosyltransferase family 2 protein -
  NYR95_RS17065 (NYR95_17050) - 3916245..3917105 (+) 861 WP_316687913.1 glycosyltransferase family 2 protein -
  NYR95_RS17070 (NYR95_17055) - 3917090..3918265 (+) 1176 WP_316687914.1 glycosyltransferase -
  NYR95_RS17075 (NYR95_17060) - 3918259..3919101 (+) 843 WP_316687915.1 glycosyltransferase -
  NYR95_RS17080 (NYR95_17065) - 3919104..3920030 (-) 927 WP_316687916.1 glycosyltransferase family 9 protein -
  NYR95_RS17085 (NYR95_17070) - 3920287..3921045 (-) 759 WP_316687917.1 class I SAM-dependent methyltransferase -
  NYR95_RS17090 (NYR95_17075) - 3921169..3922989 (-) 1821 WP_316687918.1 hypothetical protein -
  NYR95_RS17095 (NYR95_17080) - 3923048..3923470 (-) 423 WP_316687919.1 pilin -
  NYR95_RS17100 (NYR95_17090) pilA/pilAI 3923571..3923969 (-) 399 WP_316687920.1 pilin Machinery gene
  NYR95_RS17105 (NYR95_17095) pilC 3924320..3925582 (+) 1263 WP_316687921.1 type II secretion system F family protein Machinery gene
  NYR95_RS17110 (NYR95_17100) - 3925589..3926452 (+) 864 WP_115513691.1 A24 family peptidase -
  NYR95_RS17115 (NYR95_17105) coaE 3926466..3927086 (+) 621 WP_316687922.1 dephospho-CoA kinase -
  NYR95_RS17120 (NYR95_17110) - 3927240..3932021 (+) 4782 WP_316687923.1 RHS repeat-associated core domain-containing protein -
  NYR95_RS17125 (NYR95_17115) - 3932658..3933061 (+) 404 Protein_3272 SymE family type I addiction module toxin -
  NYR95_RS17130 (NYR95_17120) - 3933137..3933427 (+) 291 WP_228325572.1 DUF1778 domain-containing protein -
  NYR95_RS17135 (NYR95_17125) - 3933424..3933915 (+) 492 WP_316687924.1 GNAT family N-acetyltransferase -
  NYR95_RS17140 (NYR95_17130) - 3934060..3935394 (-) 1335 WP_316687925.1 HAMP domain-containing sensor histidine kinase -
  NYR95_RS17145 (NYR95_17135) - 3935387..3936064 (-) 678 WP_003490678.1 response regulator transcription factor -
  NYR95_RS17150 (NYR95_17140) - 3936083..3936667 (-) 585 WP_316688070.1 hypothetical protein -
  NYR95_RS17155 (NYR95_17145) rimK 3936771..3937676 (-) 906 WP_167455844.1 30S ribosomal protein S6--L-glutamate ligase -
  NYR95_RS17160 (NYR95_17150) glgX 3938144..3940276 (+) 2133 WP_316688074.1 glycogen debranching protein GlgX -
  NYR95_RS17165 (NYR95_17155) - 3940831..3941223 (-) 393 WP_104617555.1 H-NS family nucleoid-associated regulatory protein -
  NYR95_RS17170 (NYR95_17160) - 3941312..3941704 (-) 393 WP_316688076.1 hypothetical protein -
  NYR95_RS17175 (NYR95_17165) - 3942247..3942792 (-) 546 WP_104617557.1 hypothetical protein -
  NYR95_RS17180 (NYR95_17170) - 3942962..3943246 (+) 285 WP_316688080.1 hypothetical protein -
  NYR95_RS17185 (NYR95_17175) - 3943855..3944196 (+) 342 WP_316688082.1 hypothetical protein -
  NYR95_RS17190 (NYR95_17180) - 3944261..3944542 (+) 282 WP_228325566.1 DUF6516 family protein -
  NYR95_RS17195 (NYR95_17185) - 3944550..3944918 (+) 369 WP_316688084.1 transcriptional regulator -
  NYR95_RS17200 (NYR95_17190) - 3944992..3945627 (-) 636 Protein_3287 hypothetical protein -
  NYR95_RS17205 (NYR95_17195) - 3945697..3946799 (+) 1103 WP_316688085.1 IS3 family transposase -
  NYR95_RS17210 (NYR95_17200) - 3947000..3947677 (+) 678 WP_316688086.1 hypothetical protein -
  NYR95_RS17215 (NYR95_17205) - 3947899..3949389 (+) 1491 WP_316688088.1 hypothetical protein -
  NYR95_RS17220 (NYR95_17210) - 3949708..3950517 (-) 810 WP_316688091.1 hypothetical protein -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62769.92 Da        Isoelectric Point: 5.6058

>NTDB_id=725867 NYR95_RS17055 WP_316687911.1 3913454..3915187(-) (pilB) [Xanthomonas dyei strain 22-321]
MNAVVSANLVGITGIARRLVQDGALDEAAARTAMEQAASARVPLPQWFAEKKLVTAAQLAAANAVEFGMPLMDVSVFDAS
QNAVKLVSEELLQKYQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRALEQWQASNASLGSSLG
NDDDEMGDLDVSSGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLSQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQK
LFLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
EHALLAEGFTPEQIANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQRVGIRDLRQSALMK
ASHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=725867 NYR95_RS17055 WP_316687911.1 3913454..3915187(-) (pilB) [Xanthomonas dyei strain 22-321]
ATGAACGCAGTGGTCTCAGCCAATCTCGTTGGCATAACCGGCATAGCTCGTCGGCTCGTGCAGGATGGCGCACTTGATGA
AGCGGCGGCCCGCACCGCCATGGAGCAAGCTGCTTCAGCAAGAGTCCCACTGCCACAATGGTTTGCAGAGAAGAAGCTGG
TCACTGCAGCCCAGCTTGCCGCTGCAAATGCGGTCGAGTTCGGCATGCCCCTGATGGACGTTTCCGTGTTCGATGCTAGC
CAGAACGCGGTTAAGCTGGTCAGTGAGGAGTTGCTCCAGAAGTACCAAGTGCTGCCGCTGTTCAAGCGCGGCAACCGGTT
GTTCGTGGGGGTGAGCAACCCGACCCAGACCCGGGCGCTGGACGATATCAAGTTCCATACCAATCTGGTGGTCGAGCCTA
TCCTGGTCGACGAGGACCAGATCCGGCGCGCTCTGGAACAATGGCAGGCGAGCAATGCGTCGCTTGGCTCGTCGTTGGGG
AACGACGATGACGAGATGGGGGATCTGGACGTCTCGTCCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGGGACGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGCGCCTCCGACA
TCCATTTCGAGCCGTATGAAGACGACTATCGGGTGCGCTTGCGCATCGATGGGTTGCTGAAGAACGTGGCCAAGGCGCCG
GTGAAGTTGAGTCAGCGCATTGCGGCGCGCCTGAAGGTGATGTCGCAGCTGGATATCGCGGAAAAGCGGGTGCCGCAGGA
CGGGCGAATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGTGTGAGCACGTTGCCGACGCTGTTCGGCGAGA
AGGTGGTGTTGCGTATCCTGGACGCCAGCGCAGCCAAGCTGGGGATCGAGAAGCTGGGCTACGAGGCGGACCAGCAGAAG
CTGTTCCTGGATGCGATCCACAAGCCCTATGGCATGGTGCTGGTGACCGGGCCGACCGGTTCGGGCAAGACGGTGTCGTT
GTATACGGCGCTAGGCATCCTCAACGACGAGACGCGCAATATTTCCACGGCCGAGGATCCGGTCGAAATCCGCTTGCCCG
GCGTGAATCAGGTGCAGCAGAACGTCAAGCGCGGCATGACGTTTGCGGCGGCGCTGCGCTCGTTCCTGCGCCAGGATCCG
GACATCATCATGGTCGGCGAAATCCGCGACCTTGAGACAGCCGAGATCGCGATCAAGGCGGCGCAGACCGGCCATATGGT
GCTGTCGACGCTGCATACCAACGATGCGCCGCAGACCATCGCGCGTCTGATGAATATGGGCATTGCGCCTTACAACATCA
CCTCGTCGGTCACGCTGGTGATCGCGCAGCGTCTGGCGCGGCGGCTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCG
GAGCATGCGCTGCTGGCGGAAGGCTTCACGCCCGAGCAGATCGCGAACATCGAGCTGTATGAGGCGGTGGGCTGCGATGA
GTGTACCGAGGGGTACAAGGGTCGTACAGGTATCTATCAGGTCATGCCGATGACCGACGAGATCGGCGCGATCGTGCTGG
AAGGCGGCAATGCGATGCAGATTGCCGAGGCCGCACAGAGGGTAGGTATCCGCGATCTGCGCCAGTCGGCGTTGATGAAG
GCTTCGCATGGGGTAACCAGCCTGGCGGAGATCAATCGGGTGACCAAGGACTGA

Domains

Predicted by InterproScan.

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

(49-153)

Type II/IV secretion system protein (T2SSE)

(201-468)


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

55.634

98.44

0.548
  pilB Acinetobacter baumannii D1279779

55.458

98.44

0.546
  pilB Legionella pneumophila strain ERS1305867

51.937

98.44

0.511
  pilB Vibrio cholerae strain A1552

49.215

99.307

0.489
  pilF Neisseria gonorrhoeae MS11

48.063

98.44

0.473
  pilB Vibrio campbellii strain DS40M4

46.221

98.614

0.456
  pilB Vibrio parahaemolyticus RIMD 2210633

46.004

97.574

0.449
  pilB/pilB1 Synechocystis sp. PCC 6803

35.738

100

0.378
  pilF Thermus thermophilus HB27

40.077

89.948

0.36