Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   IXO1088_RS17580 Genome accession   NZ_CP040687
Coordinates   3794000..3795733 (-) Length   577 a.a.
NCBI ID   WP_011408072.1    Uniprot ID   A0A0K0GIN1
Organism   Xanthomonas oryzae pv. oryzae strain IXO1088     
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 3786839..3811812 3794000..3795733 within 0


Gene organization within MGE regions


Location: 3786839..3811812
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  IXO1088_RS17545 (IXO1088_018440) - 3786839..3787330 (-) 492 WP_027703282.1 hypothetical protein -
  IXO1088_RS17550 (IXO1088_018445) sucD 3787503..3788378 (-) 876 WP_011258368.1 succinate--CoA ligase subunit alpha -
  IXO1088_RS17555 (IXO1088_018450) sucC 3788403..3789572 (-) 1170 WP_011258367.1 ADP-forming succinate--CoA ligase subunit beta -
  IXO1088_RS17560 (IXO1088_018455) - 3789806..3791419 (+) 1614 WP_011258366.1 HAMP domain-containing sensor histidine kinase -
  IXO1088_RS17565 (IXO1088_018460) pilR 3791690..3793141 (+) 1452 WP_171970756.1 sigma-54 dependent transcriptional regulator Regulator
  IXO1088_RS17570 (IXO1088_018465) - 3793214..3793420 (+) 207 WP_027703281.1 YhfG family protein -
  IXO1088_RS24585 - 3793482..3793643 (+) 162 WP_153296778.1 hypothetical protein -
  IXO1088_RS24590 - 3793731..3793991 (+) 261 WP_011408073.1 Fic family protein -
  IXO1088_RS17580 (IXO1088_018475) pilB 3794000..3795733 (-) 1734 WP_011408072.1 type IV-A pilus assembly ATPase PilB Machinery gene
  IXO1088_RS17585 (IXO1088_018480) - 3795768..3797294 (-) 1527 WP_041182621.1 membrane protein -
  IXO1088_RS17590 (IXO1088_018485) - 3797264..3797893 (-) 630 WP_011408070.1 hypothetical protein -
  IXO1088_RS17595 (IXO1088_018490) - 3797904..3799493 (-) 1590 WP_075240477.1 phosphoethanolamine transferase -
  IXO1088_RS17600 (IXO1088_018495) pilA2 3799628..3800053 (-) 426 WP_011408068.1 pilin Machinery gene
  IXO1088_RS17605 (IXO1088_018500) pilC 3800408..3801667 (+) 1260 WP_011408067.1 type II secretion system F family protein Machinery gene
  IXO1088_RS17610 (IXO1088_018505) - 3801674..3802537 (+) 864 WP_011258358.1 A24 family peptidase -
  IXO1088_RS17615 (IXO1088_018510) coaE 3802551..3803159 (+) 609 WP_011258357.1 dephospho-CoA kinase -
  IXO1088_RS17620 (IXO1088_018515) - 3803230..3804549 (+) 1320 WP_115862282.1 IS701-like element ISXo15 family transposase -
  IXO1088_RS17625 (IXO1088_018520) - 3804791..3805753 (+) 963 WP_041182297.1 IS1595-like element ISXo2 family transposase -
  IXO1088_RS17630 (IXO1088_018525) - 3806190..3806492 (-) 303 WP_158645227.1 hypothetical protein -
  IXO1088_RS17635 (IXO1088_018530) - 3806526..3807482 (-) 957 WP_041182719.1 IS30-like element IS1112b family transposase -
  IXO1088_RS17640 (IXO1088_018535) - 3807721..3809039 (-) 1319 Protein_3375 IS701 family transposase -
  IXO1088_RS17645 (IXO1088_018540) - 3809154..3809522 (-) 369 WP_011408064.1 DUF6869 domain-containing protein -
  IXO1088_RS17650 (IXO1088_018545) - 3809528..3811036 (-) 1509 WP_075240223.1 RHS repeat-associated core domain-containing protein -
  IXO1088_RS17655 (IXO1088_018550) - 3811038..3811367 (-) 330 WP_143685531.1 hypothetical protein -
  IXO1088_RS17660 (IXO1088_018555) - 3811364..3811663 (-) 300 WP_125168747.1 hypothetical protein -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62970.00 Da        Isoelectric Point: 5.4513

>NTDB_id=366526 IXO1088_RS17580 WP_011408072.1 3794000..3795733(-) (pilB) [Xanthomonas oryzae pv. oryzae strain IXO1088]
MNSVSTTNLVGITGIARRLVQDGALEETAARTAMEQAAAAKVPLPQWFAENRLVSASQLAAANAVEFGMPLMDVSVFDAN
QNAVKLVSEELLQKYHVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNASFGSSLG
NDDEEMGDLDVSTGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLSQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDGSAAKLGIDKLGYEPDQQK
LFLEAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
EHALLAEGFTPEQVANMELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMK
ASQGVTSLAEINRVTKD

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=366526 IXO1088_RS17580 WP_011408072.1 3794000..3795733(-) (pilB) [Xanthomonas oryzae pv. oryzae strain IXO1088]
ATGAATTCAGTATCTACAACCAACCTCGTTGGCATCACCGGCATCGCTCGTCGCCTTGTGCAGGATGGCGCCCTGGAGGA
AACCGCTGCGCGGACAGCGATGGAACAGGCGGCCGCTGCCAAGGTGCCGCTGCCGCAGTGGTTTGCCGAGAACAGGCTGG
TGTCGGCGTCGCAGCTTGCGGCGGCCAATGCAGTGGAATTTGGCATGCCACTGATGGATGTGTCTGTGTTCGACGCTAAC
CAGAACGCAGTCAAGCTAGTCAGCGAGGAGTTGCTCCAGAAGTACCATGTGCTGCCGCTGTTCAAGCGCGGCAATCGGTT
GTTTGTGGGAGTGAGCAACCCGACTCAGACCCGTGCACTTGATGACATCAAGTTTCATACGAATCTGGTCGTCGAGCCGA
TTCTTGTCGATGAGGACCAAATCCGTCGCACATTGGAGCAGTGGCAGGCAAGCAATGCCTCATTTGGATCATCGCTTGGC
AACGACGACGAGGAAATGGGGGATCTGGACGTCTCCACCGGCGACGAAGACATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGCGACGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGGGCCTCGGACA
TCCATTTCGAGCCGTACGAAGACGACTACCGGGTGCGGTTGCGGATCGACGGGTTGCTGAAGAACGTGGCCAAGGCGCCG
GTGAAGCTGAGCCAGCGCATCGCGGCGCGTTTGAAGGTGATGTCGCAGCTGGATATCGCCGAGAAGCGGGTGCCGCAGGA
CGGGCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGTGTCAGCACCTTGCCGACCCTGTTCGGTGAGA
AGGTGGTGCTGCGTATCCTGGACGGCAGCGCGGCCAAGCTGGGCATCGACAAGCTGGGCTACGAGCCGGACCAACAGAAG
CTGTTCCTGGAAGCGATCCACAAGCCGTACGGCATGGTGCTGGTGACCGGGCCGACCGGCTCGGGCAAGACGGTGTCGCT
GTACACGGCGCTGGGCATCCTCAACGATGAGACGCGCAACATCTCCACCGCCGAGGATCCGGTCGAAATTCGCCTGCCTG
GCGTCAACCAGGTGCAGCAGAACAACAAGCGCGGCATGACCTTCGCCGCGGCGCTGCGTTCGTTCCTGCGACAGGATCCG
GACATCATCATGGTTGGCGAAATCCGCGACCTGGAAACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGTCACATGGT
GCTGTCCACGCTGCATACCAACGATGCGCCGCAGACCATCGCGCGTCTGATGAACATGGGGATCGCGCCGTACAACATCA
CCTCGTCGGTGACCTTGGTGATCGCGCAGCGTCTGGCGCGGCGGTTGTGCAATAACTGCAAGCGCAAGTCGACGTTGCCG
GAGCATGCACTGCTGGCGGAAGGCTTTACGCCGGAGCAGGTCGCGAATATGGAGCTTTATGAAGCCGTGGGTTGCGACGA
GTGCACCGAGGGCTACAAGGGCCGTACCGGTATCTATCAGGTGATGCCGATGACCGACGAAATCGGCGCGATCGTGCTGG
AAGGCGGCAATGCGATGCAGATTGCCGAGGCCGCTCAGAAGATCGGCATCCGGGACTTGCGGCAGTCGGCGTTGATGAAG
GCCTCGCAAGGCGTGACCAGCCTGGCCGAGATCAATCGGGTGACCAAGGACTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(201-468)

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

(49-152)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A0K0GIN1

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

57.042

98.44

0.562
  pilB Acinetobacter baumannii D1279779

56.69

98.44

0.558
  pilB Legionella pneumophila strain ERS1305867

52.465

98.44

0.516
  pilB Vibrio cholerae strain A1552

49.74

100

0.497
  pilF Neisseria gonorrhoeae MS11

49.648

98.44

0.489
  pilB Vibrio campbellii strain DS40M4

46.046

98.614

0.454
  pilB Vibrio parahaemolyticus RIMD 2210633

46.359

97.574

0.452
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

39.394

91.508

0.36

Multiple sequence alignment