Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   K6979_RS04700 Genome accession   NZ_CP082218
Coordinates   1147261..1148994 (+) Length   577 a.a.
NCBI ID   WP_104604283.1    Uniprot ID   A0A2S7DNL6
Organism   Xanthomonas cucurbitae strain IL_234     
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 1134245..1156066 1147261..1148994 within 0


Gene organization within MGE regions


Location: 1134245..1156066
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  K6979_RS04640 (K6979_04630) - 1134245..1135345 (-) 1101 WP_159406553.1 IS5 family transposase -
  K6979_RS04645 (K6979_04635) - 1135719..1136111 (+) 393 WP_104604311.1 hypothetical protein -
  K6979_RS04650 (K6979_04640) - 1136199..1136588 (+) 390 WP_104604301.1 H-NS family nucleoid-associated regulatory protein -
  K6979_RS04655 (K6979_04645) glgX 1136716..1138848 (-) 2133 WP_104604299.1 glycogen debranching protein GlgX -
  K6979_RS04660 (K6979_04650) rimK 1139320..1140225 (+) 906 WP_104604297.1 30S ribosomal protein S6--L-glutamate ligase -
  K6979_RS04665 (K6979_04655) - 1140497..1140853 (+) 357 WP_146090337.1 hypothetical protein -
  K6979_RS04670 (K6979_04660) - 1140916..1141593 (+) 678 WP_003490678.1 response regulator transcription factor -
  K6979_RS04675 (K6979_04665) - 1142049..1143383 (+) 1335 WP_104604293.1 HAMP domain-containing sensor histidine kinase -
  K6979_RS04680 (K6979_04670) coaE 1143598..1144203 (-) 606 WP_104604291.1 dephospho-CoA kinase -
  K6979_RS04685 (K6979_04675) - 1144217..1145080 (-) 864 WP_104604289.1 A24 family peptidase -
  K6979_RS04690 (K6979_04680) pilC 1145087..1146349 (-) 1263 WP_104604287.1 type II secretion system F family protein Machinery gene
  K6979_RS04695 (K6979_04685) pilA 1146695..1147123 (+) 429 WP_104604285.1 pilin Machinery gene
  K6979_RS04700 (K6979_04690) pilB 1147261..1148994 (+) 1734 WP_104604283.1 type IV-A pilus assembly ATPase PilB Machinery gene
  K6979_RS04705 (K6979_04695) pilR 1149631..1151022 (-) 1392 WP_170066996.1 sigma-54 dependent transcriptional regulator Regulator
  K6979_RS04710 (K6979_04700) - 1151182..1152795 (-) 1614 WP_104604280.1 HAMP domain-containing sensor histidine kinase -
  K6979_RS04715 (K6979_04705) sucC 1153030..1154199 (+) 1170 WP_104604278.1 ADP-forming succinate--CoA ligase subunit beta -
  K6979_RS04720 (K6979_04710) sucD 1154224..1155099 (+) 876 WP_104604276.1 succinate--CoA ligase subunit alpha -
  K6979_RS04725 (K6979_04715) - 1155217..1155453 (-) 237 WP_158251453.1 hypothetical protein -
  K6979_RS04730 (K6979_04720) - 1155674..1156066 (+) 393 WP_167526931.1 endonuclease domain-containing protein -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62692.80 Da        Isoelectric Point: 5.9517

>NTDB_id=600279 K6979_RS04700 WP_104604283.1 1147261..1148994(+) (pilB) [Xanthomonas cucurbitae strain IL_234]
MSAVAANLVGITGIARRLVQDGALDETSARTAMDQAAAAKIPLPQWFSERKLVSASQLAAANAVEFGMPLMDVSVFDASQ
NAIKLVSEELLQKHQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNASLGSSLGG
DDEEMGDLDVSAGDEDMGAGGDAGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAPV
KLSQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDGSAAKLGIEKLGYEADQQKL
FLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQDPD
IIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKTSLPE
HALLAEGFTQQQIDQGITLYEAVGCDDCTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMK
AAHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=600279 K6979_RS04700 WP_104604283.1 1147261..1148994(+) (pilB) [Xanthomonas cucurbitae strain IL_234]
ATGAGTGCAGTCGCGGCGAACTTAGTAGGGATTACAGGCATTGCACGCCGCTTGGTGCAAGACGGAGCATTGGATGAAAC
AAGTGCCCGTACCGCCATGGACCAAGCTGCGGCGGCGAAGATTCCGCTTCCACAATGGTTCTCCGAGAGAAAGCTGGTTT
CAGCGTCTCAACTAGCAGCGGCAAACGCAGTCGAGTTCGGCATGCCGCTAATGGACGTATCGGTGTTCGACGCCAGCCAG
AACGCGATCAAGCTGGTCAGCGAGGAGTTGCTCCAGAAGCACCAGGTGCTGCCGCTGTTCAAGCGCGGGAACCGGTTGTT
CGTGGGGGTGAGCAACCCGACCCAGACCAGGGCGCTTGATGACATCAAGTTTCATACGAACCTGGTGGTCGAGCCGATCC
TGGTGGACGAGGACCAGATCCGTCGCACCTTGGAGCAATGGCAAGCTAGCAACGCATCGCTTGGTTCATCGCTGGGGGGC
GATGACGAAGAGATGGGCGACCTGGACGTCTCGGCCGGCGACGAAGACATGGGCGCCGGCGGGGATGCCGGGGTCGATGC
CAAGGGTGATGACACGCCGGTGGTGAAATTCGTCAACAAGGTGTTGGTGGATGCGATCCGGCGGGGAGCCTCCGATATCC
ATTTCGAGCCTTATGAAGACGACTACCGTGTTCGCTTGCGCATCGATGGGCTGCTGAAGAACGTGGCCAAGGCGCCGGTG
AAGCTGAGCCAGCGGATTGCGGCGCGGTTGAAGGTGATGTCGCAGCTGGATATCGCCGAGAAGCGGGTGCCGCAGGATGG
GCGCATCAAGCTTAATCTGTCCAAGACCAAACAGATCGACTTCCGTGTGAGTACCTTGCCGACGCTGTTCGGCGAGAAGG
TGGTGCTACGTATCCTGGATGGCAGTGCGGCCAAGCTGGGGATCGAGAAGCTAGGTTACGAGGCGGACCAGCAGAAGCTG
TTCCTGGATGCGATCCACAAGCCCTACGGGATGGTGCTGGTGACCGGGCCGACCGGTTCGGGCAAGACGGTGTCCTTGTA
TACGGCGCTGGGTATCCTCAACGATGAGACGCGCAACATCTCTACTGCCGAGGATCCGGTTGAAATTCGCCTGCCTGGCG
TCAATCAGGTGCAGCAGAACAACAAGCGCGGCATGACCTTTGCGGCGGCCTTGCGCTCGTTCCTGCGCCAGGACCCTGAC
ATCATCATGGTCGGCGAAATTCGCGACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGCCATATGGTGCT
GTCCACGTTGCATACCAACGATGCGCCACAGACCATCGCGCGCTTGATGAACATGGGGATTGCGCCGTACAACATCACCT
CGTCGGTGACCTTGGTCATTGCGCAGCGCCTGGCGCGGCGGTTGTGCAACAACTGCAAGCGCAAGACCAGCTTGCCAGAG
CATGCGTTGCTGGCCGAAGGGTTTACGCAACAGCAGATCGACCAGGGCATTACGCTGTATGAGGCGGTCGGTTGCGATGA
CTGCACCGAGGGCTACAAGGGCCGTACGGGTATCTACCAGGTCATGCCGATGACCGACGAGATCGGTGCGATCGTGCTGG
AAGGCGGCAATGCGATGCAGATCGCCGAGGCGGCGCAGAAGATCGGTATCCGCGACTTGCGGCAGTCGGCCTTGATGAAG
GCCGCGCATGGGGTGACCAGCCTGGCGGAGATCAATCGGGTGACCAAGGACTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(200-467)

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 A0A2S7DNL6

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

56.514

98.44

0.556
  pilB Acinetobacter baylyi ADP1

55.282

98.44

0.544
  pilB Legionella pneumophila strain ERS1305867

52.34

100

0.523
  pilB Vibrio cholerae strain A1552

48.955

99.48

0.487
  pilF Neisseria gonorrhoeae MS11

48.768

98.44

0.48
  pilB Vibrio campbellii strain DS40M4

46.127

98.44

0.454
  pilB Vibrio parahaemolyticus RIMD 2210633

46.099

97.747

0.451
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

39.36

92.028

0.362