Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   XCCCN08v2_RS05230 Genome accession   NZ_CP101176
Coordinates   1240161..1241867 (+) Length   568 a.a.
NCBI ID   WP_187305920.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. campestris strain CN08     
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 1224045..1248622 1240161..1241867 within 0


Gene organization within MGE regions


Location: 1224045..1248622
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  XCCCN08v2_RS05140 - 1224045..1224461 (+) 417 WP_227971334.1 hypothetical protein -
  XCCCN08v2_RS05145 - 1224751..1224981 (-) 231 WP_157769280.1 hypothetical protein -
  XCCCN08v2_RS05150 - 1225045..1225200 (+) 156 WP_075285405.1 hypothetical protein -
  XCCCN08v2_RS05155 - 1225377..1225772 (+) 396 WP_016945003.1 hypothetical protein -
  XCCCN08v2_RS05160 - 1225863..1226255 (+) 393 WP_012437593.1 H-NS family nucleoid-associated regulatory protein -
  XCCCN08v2_RS05165 glgX 1226780..1228909 (-) 2130 WP_016945001.1 glycogen debranching protein GlgX -
  XCCCN08v2_RS05170 rimK 1229402..1230277 (+) 876 WP_016945000.1 30S ribosomal protein S6--L-glutamate ligase -
  XCCCN08v2_RS05175 - 1230927..1231604 (+) 678 WP_003490678.1 response regulator transcription factor -
  XCCCN08v2_RS05180 - 1231597..1232931 (+) 1335 WP_162808569.1 HAMP domain-containing sensor histidine kinase -
  XCCCN08v2_RS05185 - 1233074..1233565 (-) 492 WP_011038220.1 GNAT family N-acetyltransferase -
  XCCCN08v2_RS05190 - 1233562..1233852 (-) 291 WP_011038219.1 DUF1778 domain-containing protein -
  XCCCN08v2_RS05195 - 1233927..1234328 (-) 402 WP_040940795.1 SymE family type I addiction module toxin -
  XCCCN08v2_RS05200 - 1234471..1235579 (+) 1109 WP_087942068.1 IS3 family transposase -
  XCCCN08v2_RS05205 coaE 1236064..1236687 (-) 624 WP_075285407.1 dephospho-CoA kinase -
  XCCCN08v2_RS05210 - 1236701..1237564 (-) 864 WP_075285408.1 A24 family peptidase -
  XCCCN08v2_RS05215 pilC 1237570..1238826 (-) 1257 WP_075285409.1 type II secretion system F family protein Machinery gene
  XCCCN08v2_RS05220 - 1239163..1239612 (+) 450 WP_075285410.1 pilin -
  XCCCN08v2_RS05225 - 1239728..1240102 (+) 375 WP_269467167.1 pilin -
  XCCCN08v2_RS05230 pilB 1240161..1241867 (+) 1707 WP_187305920.1 type IV-A pilus assembly ATPase PilB Machinery gene
  XCCCN08v2_RS05235 pilR 1242285..1243679 (-) 1395 WP_162808570.1 sigma-54 dependent transcriptional regulator Regulator
  XCCCN08v2_RS05240 - 1243889..1245499 (-) 1611 WP_040940804.1 HAMP domain-containing sensor histidine kinase -
  XCCCN08v2_RS05245 sucC 1245733..1246902 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  XCCCN08v2_RS05250 sucD 1246927..1247802 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  XCCCN08v2_RS05255 - 1247906..1248316 (+) 411 WP_029628876.1 DNA-binding protein -
  XCCCN08v2_RS05260 - 1248320..1248622 (+) 303 WP_011038207.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 568 a.a.        Molecular weight: 61805.86 Da        Isoelectric Point: 5.7640

>NTDB_id=709145 XCCCN08v2_RS05230 WP_187305920.1 1240161..1241867(+) (pilB) [Xanthomonas campestris pv. campestris strain CN08]
MGITGIARRLVQDGSLEEGAARSAMDQAAAAKIPLPQWFAERKLVSAAQLAAANAVEFGMPLMDVSVFDASQNAVKLVSE
ELLQKHQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSSMGDDDEGMGDL
DVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAPVKLNQRIAA
RLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQKLFLDAIHKP
YGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDPDIIMVGEIR
DLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLPEHALLAEGF
TPEQVANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMKASHGVTSLA
EINRVTKD

Nucleotide


Download         Length: 1707 bp        

>NTDB_id=709145 XCCCN08v2_RS05230 WP_187305920.1 1240161..1241867(+) (pilB) [Xanthomonas campestris pv. campestris strain CN08]
ATCGGAATAACTGGAATAGCCCGTCGTTTGGTACAGGACGGCTCATTGGAAGAAGGCGCTGCGCGTTCAGCAATGGACCA
GGCTGCTGCCGCAAAAATTCCACTGCCTCAGTGGTTTGCTGAAAGAAAATTAGTATCTGCAGCTCAGCTCGCCGCAGCTA
ATGCCGTAGAGTTCGGCATGCCGCTGATGGATGTGTCGGTGTTTGACGCCAGCCAGAACGCGGTCAAGTTGGTCAGTGAG
GAGTTGCTTCAGAAGCATCAGGTGCTGCCGCTGTTCAAGCGCGGCAACCGGTTGTTTGTGGGGGTGAGCAACCCAACCCA
GACCCGTGCGCTGGACGACATCAAGTTCCATACTAATCTTGTGGTCGAGCCGATCCTCGTCGACGAGGATCAGATCCGGC
GCACCTTGGAGCAGTGGCAGGCCAGCAATGCGGCGCTCGGTTCGTCGATGGGGGACGACGACGAGGGGATGGGAGACCTA
GACGTGTCCGCCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGATGCCAAGGGCGATGACACGCCGGTGGT
GAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCGGACATCCATTTCGAGCCGTATGAAGACGACT
ACCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCGGTGAAGCTCAACCAGCGCATCGCGGCG
CGCTTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAAGACGGGCGCATCAAGCTCAACCTGTCCAA
GACCAAGCAGATCGACTTCCGTGTGAGTACCTTGCCGACCCTGTTCGGCGAGAAGGTGGTGCTGCGTATCCTGGACGCCA
GTGCGGCCAAGCTCGGTATCGAGAAGCTGGGCTATGAGGCGGACCAGCAGAAGCTGTTCCTGGATGCGATCCACAAGCCC
TACGGCATGGTGCTGGTGACCGGGCCGACTGGTTCGGGCAAGACGGTGTCGCTGTATACCGCGCTCGGGATTCTCAACGA
CGAGACGCGCAATATTTCCACTGCTGAGGATCCGGTCGAAATCCGCTTGCCCGGCGTCAATCAGGTGCAGCAGAACGTCA
AGCGGGGCATGACGTTTGCGGCGGCGCTGCGCTCGTTCCTGCGTCAGGACCCGGACATCATCATGGTCGGCGAAATCCGC
GACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGCCACATGGTGCTGTCGACGTTGCACACCAACGATGC
GCCGCAGACCATTGCGCGTCTGATGAACATGGGCATCGCGCCGTACAACATCACCTCGTCGGTGACCCTGGTCATCGCGC
AGCGCTTGGCACGGCGGCTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCGGAACATGCGCTGCTGGCGGAAGGCTTT
ACGCCGGAGCAGGTTGCGAACATCGAGCTCTATGAGGCGGTCGGTTGCGATGAATGCACGGAAGGCTACAAGGGCCGCAC
CGGTATCTATCAGGTGATGCCGATGACGGACGAAATCGGCGCGATCGTGCTGGAAGGCGGCAATGCGATGCAGATCGCCG
AGGCCGCGCAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCGTTGATGAAGGCTTCGCACGGCGTGACCAGCCTGGCC
GAGATCAATCGTGTGACCAAGGACTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(192-459)

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

(40-144)


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

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