Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   ABFU79_RS05145 Genome accession   NZ_CP155970
Coordinates   1225450..1227186 (+) Length   578 a.a.
NCBI ID   WP_040940802.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. raphani strain bglFP 6792     
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 1204151..1234907 1225450..1227186 within 0


Gene organization within MGE regions


Location: 1204151..1234907
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFU79_RS05035 (ABFU79_05025) - 1204151..1204522 (+) 372 WP_323540342.1 hypothetical protein -
  ABFU79_RS05040 (ABFU79_05030) - 1204822..1205052 (-) 231 WP_407470239.1 hypothetical protein -
  ABFU79_RS05045 (ABFU79_05035) - 1205116..1205262 (+) 147 WP_076054137.1 hypothetical protein -
  ABFU79_RS05050 (ABFU79_05040) - 1205446..1205841 (+) 396 WP_042594933.1 hypothetical protein -
  ABFU79_RS05055 (ABFU79_05045) - 1205932..1206324 (+) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  ABFU79_RS05060 (ABFU79_05050) glgX 1206850..1208979 (-) 2130 WP_228431836.1 glycogen debranching protein GlgX -
  ABFU79_RS05065 (ABFU79_05055) rimK 1209472..1210347 (+) 876 WP_116921527.1 30S ribosomal protein S6--L-glutamate ligase -
  ABFU79_RS05070 (ABFU79_05060) - 1210997..1211674 (+) 678 WP_003490678.1 response regulator transcription factor -
  ABFU79_RS05075 (ABFU79_05065) - 1211667..1213001 (+) 1335 WP_019237347.1 HAMP domain-containing sensor histidine kinase -
  ABFU79_RS05080 (ABFU79_05070) - 1213100..1213355 (-) 256 Protein_986 SymE family type I addiction module toxin -
  ABFU79_RS05085 (ABFU79_05075) coaE 1213549..1214172 (-) 624 WP_225042504.1 dephospho-CoA kinase -
  ABFU79_RS05090 (ABFU79_05080) - 1214186..1215049 (-) 864 WP_040940797.1 A24 family peptidase -
  ABFU79_RS05095 (ABFU79_05085) pilC 1215056..1216318 (-) 1263 WP_104570928.1 type II secretion system F family protein Machinery gene
  ABFU79_RS05100 (ABFU79_05090) pilA/pilAI 1216669..1217067 (+) 399 WP_104570927.1 pilin Machinery gene
  ABFU79_RS05105 (ABFU79_05095) - 1217168..1217590 (+) 423 WP_104570926.1 pilin -
  ABFU79_RS05110 (ABFU79_05100) - 1217649..1219469 (+) 1821 WP_323540341.1 hypothetical protein -
  ABFU79_RS05115 (ABFU79_05105) - 1219593..1220351 (+) 759 WP_323534158.1 class I SAM-dependent methyltransferase -
  ABFU79_RS05120 (ABFU79_05110) - 1220848..1221534 (+) 687 WP_258872788.1 glycosyltransferase family 9 protein -
  ABFU79_RS05125 (ABFU79_05115) - 1221537..1222379 (-) 843 WP_147308817.1 glycosyltransferase -
  ABFU79_RS05130 (ABFU79_05120) - 1222373..1223545 (-) 1173 WP_181920810.1 glycosyltransferase -
  ABFU79_RS05135 (ABFU79_05125) - 1223530..1224393 (-) 864 WP_323540340.1 glycosyltransferase -
  ABFU79_RS05140 (ABFU79_05130) - 1224443..1225294 (-) 852 WP_108133901.1 glycosyltransferase family 2 protein -
  ABFU79_RS05145 (ABFU79_05135) pilB 1225450..1227186 (+) 1737 WP_040940802.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFU79_RS05150 (ABFU79_05140) pilR 1228571..1229965 (-) 1395 WP_012437607.1 sigma-54 dependent transcriptional regulator Regulator
  ABFU79_RS05155 (ABFU79_05145) - 1230174..1231784 (-) 1611 WP_323540339.1 ATP-binding protein -
  ABFU79_RS05160 (ABFU79_05150) sucC 1232018..1233187 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ABFU79_RS05165 (ABFU79_05155) sucD 1233212..1234087 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  ABFU79_RS05170 (ABFU79_05160) - 1234191..1234601 (+) 411 WP_029628876.1 CopG family ribbon-helix-helix protein -
  ABFU79_RS05175 (ABFU79_05165) - 1234605..1234907 (+) 303 WP_323540338.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 578 a.a.        Molecular weight: 62780.99 Da        Isoelectric Point: 5.6058

>NTDB_id=1000477 ABFU79_RS05145 WP_040940802.1 1225450..1227186(+) (pilB) [Xanthomonas campestris pv. raphani strain bglFP 6792]
MNAVISANLVGITGIARRLVQDGALDETAARTAMEQAASARVPLPQWFAERKLVTASQLAAANAVEFGMPLMDVSVFDAS
QNAVKLVSEELLQKYQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSSMG
DDDEGMGDLDVSTGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLSQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQK
LFLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKAPLP
EHALLAEGFTAEQIAAGIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQRIGIRDLRQSALV
KAAHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1737 bp        

>NTDB_id=1000477 ABFU79_RS05145 WP_040940802.1 1225450..1227186(+) (pilB) [Xanthomonas campestris pv. raphani strain bglFP 6792]
ATGAACGCAGTGATCTCAGCCAATCTCGTTGGCATAACCGGCATAGCTCGTCGGCTGGTTCAAGACGGCGCACTTGATGA
AACGGCGGCCCGTACCGCCATGGAGCAAGCTGCTTCAGCCAGGGTTCCTCTGCCCCAGTGGTTTGCGGAGAGAAAGTTAG
TGACTGCATCCCAGCTTGCCGCCGCAAACGCGGTTGAGTTTGGCATGCCTCTGATGGACGTTTCCGTGTTCGATGCCAGC
CAGAACGCGGTCAAGCTGGTCAGCGAGGAGTTGCTCCAGAAGTACCAGGTGCTACCGCTGTTCAAGCGCGGCAACCGGTT
GTTCGTGGGGGTGAGCAATCCGACCCAGACCAGGGCGCTGGACGACATCAAGTTCCATACCAATCTGGTGGTCGAGCCGA
TCCTGGTCGACGAGGATCAGATCCGTCGCACCTTGGAGCAGTGGCAGGCCAGCAATGCGGCGCTTGGCTCGTCGATGGGT
GACGACGACGAGGGGATGGGGGATCTGGACGTCTCCACCGGCGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGCGACGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCGTCCGACA
TCCATTTCGAGCCGTACGAAGACGACTACCGGGTGCGCTTGCGGATCGATGGCCTCCTGAAGAATGTGGCCAAGGCGCCG
GTGAAGTTGAGCCAGCGCATTGCGGCGCGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGA
TGGGCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGTGTGAGCACCTTGCCGACCCTGTTCGGCGAGA
AGGTGGTGCTGCGTATCCTGGACGCGAGTGCGGCCAAGCTGGGCATTGAGAAGCTGGGCTATGAGGCGGATCAGCAAAAG
CTGTTCCTGGATGCGATCCACAAGCCTTACGGCATGGTGCTGGTGACCGGGCCAACCGGTTCGGGCAAGACGGTGTCGTT
GTATACGGCGCTGGGCATCCTCAACGATGAGACGCGCAACATCTCCACGGCCGAGGATCCGGTCGAAATCCGCTTGCCTG
GTGTCAATCAGGTGCAGCAAAACGTCAAGCGCGGCATGACGTTTGCTGCGGCGTTGCGCTCGTTCCTGCGCCAGGATCCG
GACATCATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGTCACATGGT
GTTGTCGACGCTGCATACCAACGATGCGCCACAGACCATCGCGCGTCTGATGAACATGGGCATTGCGCCGTACAACATCA
CTTCGTCGGTGACCTTGGTCATTGCGCAGCGTCTGGCGCGGCGTTTGTGCAACAACTGCAAGCGCAAGGCGCCGCTGCCG
GAGCATGCGTTGCTGGCCGAAGGGTTTACCGCAGAGCAGATCGCTGCCGGAATCGAACTGTACGAGGCGGTCGGCTGCGA
TGAGTGCACCGAAGGCTACAAGGGGCGTACCGGTATCTACCAGGTGATGCCGATGACCGACGAGATCGGCGCGATCGTAC
TGGAAGGCGGCAACGCGATGCAGATCGCCGAGGCGGCGCAGAGGATCGGCATCCGCGATTTGCGGCAGTCGGCGCTGGTG
AAGGCGGCGCATGGGGTGACGAGCCTGGCGGAGATCAATCGGGTGACGAAGGACTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(201-468)

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

(50-153)


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

98.27

0.548
  pilB Acinetobacter baylyi ADP1

55.106

98.27

0.542
  pilB Legionella pneumophila strain ERS1305867

52.021

98.443

0.512
  pilB Vibrio cholerae strain A1552

49.043

99.481

0.488
  pilF Neisseria gonorrhoeae MS11

47.887

98.27

0.471
  pilB Vibrio campbellii strain DS40M4

45.694

98.443

0.45
  pilB Vibrio parahaemolyticus RIMD 2210633

45.745

97.578

0.446
  pilB/pilB1 Synechocystis sp. PCC 6803

35.61

100

0.379
  pilF Thermus thermophilus HB27

40.499

90.138

0.365

Multiple sequence alignment