Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   ABFU65_RS05065 Genome accession   NZ_CP155964
Coordinates   1202199..1203905 (+) Length   568 a.a.
NCBI ID   WP_323550509.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. raphani strain BR25     
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 1193455..1212566 1202199..1203905 within 0
IScluster/Tn 1204816..1205614 1202199..1203905 flank 911


Gene organization within MGE regions


Location: 1193455..1212566
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFU65_RS05025 (ABFU65_05025) coaE 1193455..1194078 (-) 624 WP_323549481.1 dephospho-CoA kinase -
  ABFU65_RS05030 (ABFU65_05030) - 1194092..1194955 (-) 864 WP_011038216.1 A24 family peptidase -
  ABFU65_RS05035 (ABFU65_05035) pilC 1194962..1196221 (-) 1260 WP_323549480.1 type II secretion system F family protein Machinery gene
  ABFU65_RS05040 (ABFU65_05040) pilA2 1196576..1196995 (+) 420 WP_323549479.1 pilin Machinery gene
  ABFU65_RS05045 (ABFU65_05045) - 1197077..1198978 (+) 1902 WP_323549478.1 hypothetical protein -
  ABFU65_RS05050 (ABFU65_05050) - 1198975..1199433 (+) 459 WP_323549477.1 GtrA family protein -
  ABFU65_RS05055 (ABFU65_05055) - 1199439..1200983 (+) 1545 WP_323552249.1 NAD(P)/FAD-dependent oxidoreductase -
  ABFU65_RS05060 (ABFU65_05060) galE 1201079..1202056 (+) 978 WP_323550507.1 UDP-glucose 4-epimerase GalE -
  ABFU65_RS05065 (ABFU65_05065) pilB 1202199..1203905 (+) 1707 WP_323550509.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFU65_RS05070 (ABFU65_05070) - 1204088..1204717 (-) 630 WP_407472217.1 toxin -
  ABFU65_RS05075 (ABFU65_05075) - 1204816..1205614 (+) 799 WP_087941972.1 IS5 family transposase -
  ABFU65_RS05080 (ABFU65_05080) - 1205676..1206038 (-) 363 WP_148263072.1 hypothetical protein -
  ABFU65_RS05085 (ABFU65_05085) pilR 1206230..1207624 (-) 1395 WP_043921909.1 sigma-54 dependent transcriptional regulator Regulator
  ABFU65_RS05090 (ABFU65_05090) - 1207833..1209443 (-) 1611 WP_014508702.1 PAS domain-containing sensor histidine kinase -
  ABFU65_RS05095 (ABFU65_05095) sucC 1209677..1210846 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ABFU65_RS05100 (ABFU65_05100) sucD 1210871..1211746 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  ABFU65_RS05105 (ABFU65_05105) - 1211850..1212260 (+) 411 WP_029628876.1 CopG family ribbon-helix-helix protein -
  ABFU65_RS05110 (ABFU65_05110) - 1212264..1212566 (+) 303 WP_323475834.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 568 a.a.        Molecular weight: 61545.54 Da        Isoelectric Point: 5.9537

>NTDB_id=1000371 ABFU65_RS05065 WP_323550509.1 1202199..1203905(+) (pilB) [Xanthomonas campestris pv. raphani strain BR25]
MGITGLARRLVQDGALDEGAARDAMAKAAAAKQPLPSWLAQNKVVGASQLAAANAVEFGMPLMDVSAFDASQNAVKLVSE
ELLQKHQVLPLFKRGNRLFVGVSNPTQTKALDDIKFHTNLVVEPILVDEDQIRRTLEQWQAGNASFGSALGGDDEEMGDL
DVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAPVKLSQRIAA
RLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQKLFLDAIHKP
YGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDPDIIMVGEIR
DLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLPEHALLAEGF
TPEQVANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMKASHGVTSLA
EINRVTKD

Nucleotide


Download         Length: 1707 bp        

>NTDB_id=1000371 ABFU65_RS05065 WP_323550509.1 1202199..1203905(+) (pilB) [Xanthomonas campestris pv. raphani strain BR25]
ATCGGCATCACCGGCTTGGCTCGTCGCCTGGTTCAGGATGGTGCGCTGGACGAAGGCGCTGCTCGCGATGCCATGGCTAA
GGCTGCAGCAGCCAAGCAGCCTTTACCAAGCTGGCTTGCGCAGAACAAAGTCGTAGGGGCCTCCCAATTAGCGGCCGCCA
ACGCAGTCGAATTCGGTATGCCATTGATGGATGTCTCGGCATTTGATGCTAGCCAGAATGCGGTGAAGCTGGTCAGTGAG
GAACTGCTCCAGAAGCATCAGGTGTTGCCGCTGTTCAAGCGCGGCAACCGATTGTTTGTGGGAGTGAGCAATCCAACCCA
GACTAAGGCGTTGGACGACATCAAGTTCCATACCAACTTGGTGGTGGAGCCCATCCTGGTCGATGAGGACCAGATCCGTA
GGACGTTGGAGCAATGGCAGGCAGGAAACGCGTCCTTTGGCTCGGCGCTTGGTGGCGACGACGAGGAGATGGGGGACCTA
GACGTGTCCGCCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGAGTCGATGCCAAGGGCGATGACACGCCGGTGGT
GAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCGGACATCCATTTCGAGCCTTATGAAGACGACT
ACCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCGGTGAAGCTCAGCCAGCGCATTGCGGCG
CGTTTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGACGGGCGCATCAAGCTCAACCTGTCCAA
GACCAAGCAGATCGACTTCCGCGTGAGCACCTTGCCGACCTTGTTCGGCGAGAAGGTGGTGTTGCGTATCCTGGACGCCA
GTGCGGCCAAGCTCGGTATCGAGAAGCTGGGTTACGAGGCGGATCAGCAGAAGCTGTTCCTGGATGCGATCCACAAGCCC
TACGGCATGGTGCTGGTGACCGGGCCGACTGGTTCGGGCAAGACGGTGTCGCTGTATACCGCGCTCGGGATTCTCAACGA
CGAGACCCGCAATATTTCCACGGCCGAGGATCCGGTCGAAATCCGCCTGCCCGGCGTCAATCAGGTGCAGCAGAACGTCA
AGCGGGGCATGACGTTTGCGGCGGCGTTGCGCTCGTTCCTGCGTCAGGACCCGGACATCATCATGGTCGGCGAAATCCGC
GACCTTGAGACGGCCGAGATTGCGATCAAGGCAGCGCAGACGGGCCACATGGTGCTGTCGACACTGCACACCAACGATGC
GCCGCAAACCATTGCGCGTCTGATGAACATGGGTATCGCGCCGTACAACATCACCTCGTCGGTGACCCTGGTCATCGCGC
AGCGCCTGGCGCGGCGGCTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCGGAACATGCGCTGCTGGCGGAAGGCTTT
ACGCCGGAGCAGGTTGCGAACATCGAGCTCTATGAGGCGGTCGGTTGCGATGAATGCACGGAAGGCTACAAGGGCCGCAC
CGGTATCTATCAGGTGATGCCGATGACGGACGAAATCGGTGCGATCGTGCTGGAAGGCGGCAATGCGATGCAGATCGCCG
AGGCTGCGCAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCGTTGATGAAGGCTTCGCACGGCGTGACCAGCCTGGCC
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)

(39-141)


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

56.162

100

0.562
  pilB Legionella pneumophila strain ERS1305867

52.465

100

0.525
  pilF Neisseria gonorrhoeae MS11

49.296

100

0.493
  pilB Vibrio cholerae strain A1552

50.182

96.831

0.486
  pilB Vibrio campbellii strain DS40M4

46.221

100

0.463
  pilB Vibrio parahaemolyticus RIMD 2210633

46.195

99.472

0.46
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.764

94.014

0.364
  pilF Thermus thermophilus HB27

38.868

93.31

0.363

Multiple sequence alignment