Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   JH299_RS16205 Genome accession   NZ_CP066928
Coordinates   3655139..3656845 (-) Length   568 a.a.
NCBI ID   WP_175611860.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. incanae strain CFBP1371     
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 3647635..3690119 3655139..3656845 within 0


Gene organization within MGE regions


Location: 3647635..3690119
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JH299_RS16170 (JH299_16130) - 3647635..3648045 (-) 411 WP_029628876.1 DNA-binding protein -
  JH299_RS16175 (JH299_16135) sucD 3648149..3649024 (-) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  JH299_RS16180 (JH299_16140) sucC 3649049..3650218 (-) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  JH299_RS16185 (JH299_16145) - 3650452..3652062 (+) 1611 WP_076037049.1 HAMP domain-containing sensor histidine kinase -
  JH299_RS16190 (JH299_16150) pilR 3652271..3653665 (+) 1395 WP_043921909.1 sigma-54 dependent transcriptional regulator Regulator
  JH299_RS16195 (JH299_16155) - 3653863..3654219 (+) 357 WP_139328384.1 hypothetical protein -
  JH299_RS16200 (JH299_16160) - 3654219..3654956 (+) 738 WP_070690009.1 zeta toxin family protein -
  JH299_RS16205 (JH299_16165) pilB 3655139..3656845 (-) 1707 WP_175611860.1 type IV-A pilus assembly ATPase PilB Machinery gene
  JH299_RS16210 (JH299_16170) pilA/pilAI 3657028..3657435 (-) 408 WP_076037052.1 pilin Machinery gene
  JH299_RS16215 (JH299_16175) pilC 3657780..3659036 (+) 1257 WP_076037882.1 type II secretion system F family protein Machinery gene
  JH299_RS16220 (JH299_16180) - 3659043..3659906 (+) 864 WP_040940797.1 A24 family peptidase -
  JH299_RS16225 (JH299_16185) coaE 3659920..3660543 (+) 624 WP_076037053.1 dephospho-CoA kinase -
  JH299_RS16230 (JH299_16190) - 3661072..3661473 (+) 402 WP_076037054.1 SymE family type I addiction module toxin -
  JH299_RS16235 (JH299_16195) - 3661549..3661839 (+) 291 WP_014508712.1 DUF1778 domain-containing protein -
  JH299_RS16240 (JH299_16200) - 3661836..3662327 (+) 492 WP_011038220.1 GNAT family N-acetyltransferase -
  JH299_RS16245 (JH299_16205) - 3662470..3663804 (-) 1335 WP_019237347.1 HAMP domain-containing sensor histidine kinase -
  JH299_RS16250 (JH299_16210) - 3663797..3664474 (-) 678 WP_003490678.1 response regulator transcription factor -
  JH299_RS16255 (JH299_16215) rimK 3665124..3665999 (-) 876 WP_076037055.1 30S ribosomal protein S6--L-glutamate ligase -
  JH299_RS16260 (JH299_16220) glgX 3666492..3668621 (+) 2130 WP_016945001.1 glycogen debranching protein GlgX -
  JH299_RS16265 (JH299_16225) - 3669152..3669544 (-) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  JH299_RS16270 (JH299_16230) - 3669635..3670030 (-) 396 WP_011038225.1 hypothetical protein -
  JH299_RS16275 (JH299_16235) - 3670215..3670361 (-) 147 WP_076037056.1 hypothetical protein -
  JH299_RS16280 - 3670479..3670820 (-) 342 WP_228438057.1 hypothetical protein -
  JH299_RS16285 (JH299_16245) - 3670953..3671324 (-) 372 WP_076037057.1 hypothetical protein -
  JH299_RS16290 (JH299_16250) - 3672027..3672368 (+) 342 WP_070689991.1 hypothetical protein -
  JH299_RS16295 (JH299_16255) - 3672433..3672714 (+) 282 WP_076037058.1 DUF6516 family protein -
  JH299_RS16300 (JH299_16260) - 3672722..3673090 (+) 369 WP_065628137.1 transcriptional regulator -
  JH299_RS16305 (JH299_16265) - 3673162..3673953 (-) 792 WP_076037059.1 hypothetical protein -
  JH299_RS16310 (JH299_16270) - 3674069..3675171 (+) 1103 WP_100101058.1 IS3-like element IS1404 family transposase -
  JH299_RS16315 (JH299_16275) - 3675330..3675983 (-) 654 WP_147309026.1 hypothetical protein -
  JH299_RS16320 (JH299_16280) - 3676601..3676945 (+) 345 WP_228438129.1 hypothetical protein -
  JH299_RS16325 (JH299_16285) - 3676942..3677358 (+) 417 WP_076037060.1 hypothetical protein -
  JH299_RS16330 (JH299_16290) xopAE 3677568..3679199 (-) 1632 WP_076037061.1 type III secretion system effector XopAE -
  JH299_RS16335 (JH299_16295) - 3679782..3680060 (+) 279 WP_139328385.1 hypothetical protein -
  JH299_RS16340 (JH299_16300) - 3680494..3680718 (-) 225 WP_175611669.1 hypothetical protein -
  JH299_RS16345 (JH299_16305) - 3681263..3682663 (+) 1401 WP_076037063.1 site-specific integrase -
  JH299_RS16350 (JH299_16310) - 3682865..3683338 (+) 474 WP_139328386.1 hypothetical protein -
  JH299_RS16355 (JH299_16315) - 3683465..3684337 (+) 873 WP_139328387.1 hypothetical protein -
  JH299_RS16360 (JH299_16320) - 3684573..3684896 (-) 324 WP_175611861.1 helix-turn-helix transcriptional regulator -
  JH299_RS16370 (JH299_16330) - 3686939..3687737 (+) 799 WP_100097398.1 IS5 family transposase -
  JH299_RS16375 (JH299_16335) - 3688257..3688481 (+) 225 WP_139328388.1 hypothetical protein -

Sequence

Protein


Download         Length: 568 a.a.        Molecular weight: 61935.98 Da        Isoelectric Point: 5.5885

>NTDB_id=523277 JH299_RS16205 WP_175611860.1 3655139..3656845(-) (pilB) [Xanthomonas campestris pv. incanae strain CFBP1371]
MGITGIARRLVQDGALEESIARTAMDQASASKIPLPQWFADKKLVSAAQLAAANAVEFGMPLMDVSVFDASQNAVKLVSE
ELLQKHQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSSLGDDDDEMGDL
DVSTGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAPVKLNQRIAA
RLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQKLFLDAIHKP
YGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDPDIIMVGEIR
DLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLPEHALLAEGF
TPEQVANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMKASHGVTSLA
EINRVTKD

Nucleotide


Download         Length: 1707 bp        

>NTDB_id=523277 JH299_RS16205 WP_175611860.1 3655139..3656845(-) (pilB) [Xanthomonas campestris pv. incanae strain CFBP1371]
GTGGGAATCACTGGCATCGCGAGACGTCTAGTTCAAGACGGCGCTCTTGAAGAATCGATTGCTCGAACTGCGATGGATCA
AGCCTCAGCGTCTAAAATTCCACTGCCTCAATGGTTCGCCGATAAGAAGCTGGTGTCAGCGGCGCAACTCGCGGCAGCTA
ATGCAGTTGAGTTCGGTATGCCGCTGATGGATGTGTCGGTGTTCGACGCCAGCCAGAACGCGGTCAAGCTGGTCAGTGAG
GAGTTGCTTCAGAAGCATCAGGTGCTGCCGCTGTTCAAGCGCGGCAATCGCTTGTTCGTGGGGGTAAGCAACCCGACCCA
GACCAGGGCGCTGGACGACATCAAGTTTCACACCAATTTGGTGGTCGAGCCGATTTTGGTCGACGAGGACCAGATCCGTC
GCACCTTGGAGCAGTGGCAGGCCAGCAATGCGGCGCTCGGCTCCTCGCTCGGCGACGACGATGATGAAATGGGGGATCTG
GACGTCTCCACCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGATGCCAAGGGCGATGACACGCCGGTGGT
GAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCCGACATCCATTTCGAGCCGTATGAAGACGACT
ACCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCGGTGAAGCTCAATCAGCGCATCGCGGCG
CGCCTGAAGGTGATGTCGCAGCTGGATATCGCCGAGAAGCGGGTGCCGCAGGACGGACGCATCAAGCTCAACCTGTCCAA
GACCAAGCAGATCGACTTTCGCGTGAGCACCTTGCCAACCCTGTTCGGCGAGAAGGTGGTGTTGCGTATCCTGGACGCCA
GTGCGGCCAAGCTCGGTATCGAGAAGCTGGGTTACGAGGCGGATCAGCAGAAGCTGTTCCTGGATGCGATCCACAAGCCC
TACGGCATGGTGCTGGTGACCGGGCCGACTGGTTCGGGCAAGACGGTGTCGCTGTATACCGCGCTCGGGATTCTCAACGA
CGAGACGCGCAATATTTCCACGGCTGAGGATCCGGTCGAAATCCGCCTGCCCGGCGTCAATCAGGTGCAGCAGAACGTCA
AGCGGGGCATGACGTTTGCGGCGGCGCTGCGCTCGTTCCTGCGTCAGGACCCGGACATCATCATGGTCGGCGAAATCCGC
GACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGCCACATGGTGCTGTCGACACTGCACACCAACGATGC
GCCGCAGACCATTGCGCGTCTGATGAACATGGGCATCGCGCCGTACAACATCACCTCGTCGGTGACGCTGGTCATCGCGC
AGCGCTTGGCGCGGCGCTTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCGGAACATGCGCTGCTGGCGGAAGGCTTT
ACGCCGGAGCAGGTTGCGAACATCGAGCTCTATGAAGCGGTCGGTTGCGATGAATGCACGGAAGGCTACAAAGGCCGTAC
CGGCATCTATCAGGTGATGCCGATGACGGACGAAATCGGCGCGATCGTGCTGGAAGGCGGCAATGCGATGCAGATCGCCG
AGGCTGCGCAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCGTTAATGAAGGCTTCGCACGGCGTGACCAGCCTGGCC
GAAATCAATCGGGTGACGAAGGATTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(192-459)

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

(41-144)


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

55.81

100

0.558
  pilB Acinetobacter baylyi ADP1

55.634

100

0.556
  pilB Legionella pneumophila strain ERS1305867

52.113

100

0.521
  pilF Neisseria gonorrhoeae MS11

48.944

100

0.489
  pilB Vibrio cholerae strain A1552

49.817

96.127

0.479
  pilB Vibrio campbellii strain DS40M4

46.397

100

0.465
  pilB Vibrio parahaemolyticus RIMD 2210633

46.181

99.12

0.458
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.679

93.31

0.361