Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   JH263_RS16260 Genome accession   NZ_CP067002
Coordinates   3662143..3663849 (-) Length   568 a.a.
NCBI ID   WP_228943908.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. campestris strain 39-3     
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 3655694..3720056 3662143..3663849 within 0


Gene organization within MGE regions


Location: 3655694..3720056
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JH263_RS16235 (JH263_16170) - 3655694..3656104 (-) 411 WP_029628876.1 DNA-binding protein -
  JH263_RS16240 (JH263_16175) sucD 3656208..3657083 (-) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  JH263_RS16245 (JH263_16180) sucC 3657108..3658277 (-) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  JH263_RS16250 (JH263_16185) - 3658511..3660121 (+) 1611 WP_040940804.1 HAMP domain-containing sensor histidine kinase -
  JH263_RS16255 (JH263_16190) pilR 3660331..3661725 (+) 1395 WP_274497633.1 sigma-54 dependent transcriptional regulator Regulator
  JH263_RS16260 (JH263_16195) pilB 3662143..3663849 (-) 1707 WP_228943908.1 type IV-A pilus assembly ATPase PilB Machinery gene
  JH263_RS16265 (JH263_16200) - 3663908..3664318 (-) 411 WP_075285411.1 pilin -
  JH263_RS16270 (JH263_16205) - 3664398..3664847 (-) 450 WP_274514260.1 pilin -
  JH263_RS16275 (JH263_16210) pilC 3665184..3666440 (+) 1257 WP_075285409.1 type II secretion system F family protein Machinery gene
  JH263_RS16280 (JH263_16215) - 3666447..3667310 (+) 864 WP_274514261.1 A24 family peptidase -
  JH263_RS16285 (JH263_16220) coaE 3667324..3667947 (+) 624 WP_274514262.1 dephospho-CoA kinase -
  JH263_RS16290 (JH263_16225) - 3668479..3668880 (+) 402 WP_274514263.1 SymE family type I addiction module toxin -
  JH263_RS16295 (JH263_16230) - 3668955..3669245 (+) 291 WP_011038219.1 DUF1778 domain-containing protein -
  JH263_RS16300 (JH263_16235) - 3669242..3669733 (+) 492 WP_227971330.1 GNAT family N-acetyltransferase -
  JH263_RS16305 (JH263_16240) - 3669876..3671210 (-) 1335 WP_012437598.1 HAMP domain-containing sensor histidine kinase -
  JH263_RS16310 (JH263_16245) - 3671203..3671880 (-) 678 WP_003490678.1 response regulator transcription factor -
  JH263_RS16315 (JH263_16250) - 3671911..3672384 (-) 474 WP_012437597.1 hypothetical protein -
  JH263_RS16320 (JH263_16255) rimK 3672607..3673482 (-) 876 WP_016945000.1 30S ribosomal protein S6--L-glutamate ligase -
  JH263_RS16325 (JH263_16260) glgX 3673978..3676107 (+) 2130 WP_016945001.1 glycogen debranching protein GlgX -
  JH263_RS16330 (JH263_16265) - 3676632..3677024 (-) 393 WP_012437593.1 H-NS family nucleoid-associated regulatory protein -
  JH263_RS16335 (JH263_16270) - 3677115..3677510 (-) 396 WP_016945003.1 hypothetical protein -
  JH263_RS16340 (JH263_16275) - 3677687..3677842 (-) 156 WP_075285405.1 hypothetical protein -
  JH263_RS16345 (JH263_16280) - 3677906..3678136 (+) 231 WP_157769280.1 hypothetical protein -
  JH263_RS16350 (JH263_16285) - 3678426..3678842 (-) 417 WP_227971334.1 hypothetical protein -
  JH263_RS16355 (JH263_16290) - 3679091..3679330 (+) 240 WP_274514264.1 hypothetical protein -
  JH263_RS16360 (JH263_16295) - 3679407..3679772 (+) 366 WP_116670930.1 hypothetical protein -
  JH263_RS16365 (JH263_16300) - 3679816..3681408 (-) 1593 WP_274514265.1 MobA/MobL family protein -
  JH263_RS16370 (JH263_16305) - 3681667..3681993 (+) 327 WP_274514266.1 hypothetical protein -
  JH263_RS16375 (JH263_16310) - 3682260..3682529 (+) 270 WP_258873713.1 HNH endonuclease -
  JH263_RS16380 (JH263_16315) - 3682649..3683083 (+) 435 WP_258873711.1 hypothetical protein -
  JH263_RS16385 (JH263_16320) - 3683131..3683583 (+) 453 WP_274514267.1 hypothetical protein -
  JH263_RS16390 - 3683595..3684398 (+) 804 WP_274514268.1 HNH endonuclease -
  JH263_RS16395 (JH263_16330) - 3684410..3685060 (-) 651 WP_116670935.1 hypothetical protein -
  JH263_RS16400 (JH263_16335) - 3685100..3689122 (-) 4023 WP_274514269.1 hypothetical protein -
  JH263_RS16405 (JH263_16340) - 3689160..3689798 (-) 639 WP_116670799.1 DUF1629 domain-containing protein -
  JH263_RS16410 (JH263_16345) - 3689932..3691296 (-) 1365 WP_116670798.1 hypothetical protein -
  JH263_RS16415 (JH263_16350) - 3691299..3693389 (-) 2091 WP_274514270.1 DUF87 domain-containing protein -
  JH263_RS16420 (JH263_16355) - 3693403..3694293 (-) 891 WP_116670796.1 DNA adenine methylase -
  JH263_RS16425 (JH263_16360) - 3694511..3694702 (-) 192 WP_116670795.1 hypothetical protein -
  JH263_RS16430 (JH263_16365) - 3694772..3694927 (-) 156 Protein_3170 JAB domain-containing protein -
  JH263_RS16435 (JH263_16370) - 3694992..3696124 (+) 1133 WP_087942069.1 IS3-like element IS476 family transposase -
  JH263_RS16440 (JH263_16375) - 3696350..3696997 (+) 648 WP_033836538.1 hypothetical protein -
  JH263_RS16445 (JH263_16380) - 3697029..3698165 (+) 1137 WP_274514271.1 type IV secretion system protein -
  JH263_RS16450 (JH263_16385) - 3698209..3698739 (+) 531 WP_237352374.1 DUF4189 domain-containing protein -
  JH263_RS16455 (JH263_16390) - 3699117..3699647 (+) 531 WP_237352373.1 hypothetical protein -
  JH263_RS16460 (JH263_16395) - 3699713..3700303 (+) 591 WP_104599556.1 hypothetical protein -
  JH263_RS16465 (JH263_16400) - 3700300..3701670 (+) 1371 WP_274514272.1 DUF6792 domain-containing protein -
  JH263_RS16470 - 3702125..3702400 (+) 276 WP_274514788.1 DUF4189 domain-containing protein -
  JH263_RS16475 (JH263_16410) - 3702479..3703018 (+) 540 WP_274514273.1 DUF4189 domain-containing protein -
  JH263_RS16480 (JH263_16415) mobH 3703145..3705067 (-) 1923 WP_274514274.1 MobH family relaxase -
  JH263_RS16485 (JH263_16420) - 3705518..3706474 (+) 957 WP_274514275.1 GGDEF domain-containing protein -
  JH263_RS16490 (JH263_16425) - 3706578..3706868 (+) 291 WP_274514276.1 hypothetical protein -
  JH263_RS16495 (JH263_16430) - 3707024..3707950 (-) 927 WP_274514277.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  JH263_RS16500 (JH263_16435) - 3707943..3708701 (-) 759 WP_237352372.1 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
  JH263_RS16510 (JH263_16445) - 3710156..3710650 (+) 495 WP_274514278.1 hypothetical protein -
  JH263_RS16515 (JH263_16450) - 3710647..3712359 (+) 1713 WP_274514279.1 ATP-dependent helicase -
  JH263_RS16520 (JH263_16455) - 3712645..3713442 (+) 798 WP_274514280.1 hypothetical protein -
  JH263_RS16525 (JH263_16460) - 3713872..3714756 (+) 885 WP_029996258.1 LysR family transcriptional regulator -
  JH263_RS16530 (JH263_16465) - 3714784..3715077 (-) 294 WP_274514281.1 helix-turn-helix transcriptional regulator -
  JH263_RS16535 (JH263_16470) - 3715180..3715830 (+) 651 WP_274514282.1 LysR substrate-binding domain-containing protein -
  JH263_RS16540 (JH263_16475) - 3715901..3716899 (-) 999 WP_274514283.1 XVIPCD domain-containing protein -
  JH263_RS16545 (JH263_16480) - 3716927..3717349 (-) 423 WP_274514284.1 hypothetical protein -
  JH263_RS16550 (JH263_16485) - 3717554..3717991 (-) 438 WP_274514285.1 hypothetical protein -
  JH263_RS16555 (JH263_16490) - 3718176..3720056 (-) 1881 WP_274514286.1 integrase arm-type DNA-binding domain-containing protein -

Sequence

Protein


Download         Length: 568 a.a.        Molecular weight: 61777.84 Da        Isoelectric Point: 5.7640

>NTDB_id=524141 JH263_RS16260 WP_228943908.1 3662143..3663849(-) (pilB) [Xanthomonas campestris pv. campestris strain 39-3]
MGITGIARRLVQDGSLEEGAARSAMDQAAAAKIPLPQWFAEKKLVSAAQLAAANAVEFGMPLMDVSVFDASQNAVKLVSE
ELLQKHQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSSMGDDDEGMGDL
DVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAPVKLNQRIAA
RLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQKLFLDAIHKP
YGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDPDIIMVGEIR
DLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLPEHALLAEGF
TPEQVANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMKASHGVTSLA
EINRVTKD

Nucleotide


Download         Length: 1707 bp        

>NTDB_id=524141 JH263_RS16260 WP_228943908.1 3662143..3663849(-) (pilB) [Xanthomonas campestris pv. campestris strain 39-3]
ATCGGAATAACTGGAATAGCCCGTCGTTTGGTACAGGACGGCTCATTGGAAGAAGGCGCTGCGCGTTCAGCAATGGACCA
GGCTGCTGCCGCAAAAATTCCACTGCCTCAGTGGTTTGCTGAAAAAAAATTAGTATCTGCAGCTCAGCTCGCCGCAGCTA
ATGCCGTAGAGTTCGGCATGCCGCTGATGGATGTGTCGGTGTTCGATGCCAGTCAGAATGCAGTCAAGCTGGTGAGTGAG
GAGTTGCTCCAGAAGCATCAGGTGCTGCCGCTGTTCAAGCGCGGCAACCGGTTGTTTGTGGGGGTAAGCAACCCGACCCA
GACCCGTGCGCTTGACGACATCAAGTTCCATACTAATCTTGTGGTCGAGCCGATCCTCGTCGACGAGGACCAGATCCGGC
GCACCTTGGAGCAGTGGCAGGCCAGCAATGCGGCGCTCGGTTCGTCGATGGGTGACGACGACGAGGGGATGGGAGACCTA
GACGTGTCCGCCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGATGCCAAGGGCGATGACACGCCGGTGGT
GAAATTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCGGACATCCATTTCGAGCCGTATGAAGACGACT
ACCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCGGTGAAGCTCAACCAGCGCATCGCGGCG
CGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGACGGGCGCATCAAGCTCAACCTGTCCAA
GACCAAGCAGATCGACTTCCGTGTGAGCACCTTGCCGACCTTGTTCGGCGAGAAGGTGGTGTTGCGTATCCTGGACGCCA
GTGCGGCCAAGCTCGGTATCGAGAAGCTGGGTTACGAGGCGGATCAGCAGAAGCTGTTCCTGGATGCGATCCACAAGCCC
TACGGCATGGTGCTGGTGACCGGGCCGACTGGTTCGGGCAAGACGGTGTCGCTGTATACCGCGCTCGGGATTCTCAACGA
CGAGACGCGCAATATTTCCACGGCTGAGGATCCGGTCGAAATCCGCTTGCCCGGCGTCAATCAGGTGCAGCAGAACGTCA
AGCGGGGCATGACGTTTGCGGCGGCGCTGCGCTCGTTCCTGCGTCAGGACCCGGACATCATCATGGTCGGCGAAATCCGC
GACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACGGGCCATATGGTGCTGTCGACACTGCACACCAACGATGC
GCCGCAGACCATTGCGCGTCTGATGAACATGGGTATCGCGCCGTACAACATCACCTCGTCGGTGACGCTGGTCATCGCGC
AGCGCCTGGCGCGGCGGCTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCGGAACATGCGCTGCTGGCGGAAGGCTTT
ACGCCGGAGCAGGTTGCGAACATCGAGCTCTATGAGGCGGTCGGTTGCGATGAATGCACGGAAGGCTACAAGGGCCGCAC
CGGTATCTATCAGGTGATGCCGATGACGGACGAAATCGGCGCGATCGTGCTGGAAGGCGGCAATGCGATGCAGATCGCCG
AGGCCGCGCAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCGTTGATGAAGGCTTCGCACGGGGTGACCAGCCTGGCT
GAGATCAATCGGGTGACCAAGGACTGA

Domains

Predicted by InterproScan.

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

(40-144)

Type II/IV secretion system protein (T2SSE)

(192-459)


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

56.162

100

0.562
  pilB Acinetobacter baylyi ADP1

55.458

100

0.555
  pilB Legionella pneumophila strain ERS1305867

52.641

100

0.526
  pilF Neisseria gonorrhoeae MS11

48.592

100

0.486
  pilB Vibrio cholerae strain A1552

49.548

97.359

0.482
  pilB Vibrio campbellii strain DS40M4

46.397

100

0.465
  pilB Vibrio parahaemolyticus RIMD 2210633

46.691

98.415

0.46