Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   H8Z72_RS16795 Genome accession   NZ_CP060470
Coordinates   3875964..3877700 (-) Length   578 a.a.
NCBI ID   WP_011052125.1    Uniprot ID   A0AAI7ZH88
Organism   Xanthomonas citri pv. citri strain DAR73889     
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 3853939..3888047 3875964..3877700 within 0


Gene organization within MGE regions


Location: 3853939..3888047
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  H8Z72_RS16705 (H8Z72_16690) avrXacE2 3853939..3855009 (-) 1071 WP_011052114.1 type III secretion system effector avirulence protein AvrXacE2 -
  H8Z72_RS16710 (H8Z72_16695) - 3855094..3856371 (-) 1278 WP_052462048.1 lytic murein transglycosylase -
  H8Z72_RS16715 (H8Z72_16700) - 3856505..3859495 (-) 2991 WP_015472512.1 Tn3 family transposase -
  H8Z72_RS16720 (H8Z72_16705) - 3859504..3860777 (-) 1274 Protein_3276 site-specific integrase -
  H8Z72_RS16725 (H8Z72_16710) - 3860970..3862053 (+) 1084 Protein_3277 DNA-binding protein -
  H8Z72_RS16730 (H8Z72_16715) xopE 3862187..3863263 (+) 1077 WP_041471283.1 XopE/AvrPphe family type III secretion system effector -
  H8Z72_RS16735 (H8Z72_16720) - 3863594..3864675 (+) 1082 Protein_3279 DNA-binding protein -
  H8Z72_RS16740 (H8Z72_16725) xopAI 3864809..3865699 (+) 891 WP_011052119.1 type III secretion system effector XopAI -
  H8Z72_RS16745 (H8Z72_16730) - 3866119..3866925 (-) 807 WP_015463520.1 hypothetical protein -
  H8Z72_RS16750 (H8Z72_16735) - 3867030..3867314 (+) 285 WP_016849322.1 hypothetical protein -
  H8Z72_RS16755 (H8Z72_16740) - 3867542..3868657 (+) 1116 WP_011052122.1 IS1595 family transposase -
  H8Z72_RS24655 (H8Z72_16745) - 3868612..3869127 (-) 516 WP_011052123.1 hypothetical protein -
  H8Z72_RS16765 (H8Z72_16750) sucD 3869214..3870089 (-) 876 WP_005921370.1 succinate--CoA ligase subunit alpha -
  H8Z72_RS16770 (H8Z72_16755) sucC 3870114..3871283 (-) 1170 WP_005915812.1 ADP-forming succinate--CoA ligase subunit beta -
  H8Z72_RS16775 (H8Z72_16760) - 3871515..3873128 (+) 1614 WP_003488599.1 HAMP domain-containing sensor histidine kinase -
  H8Z72_RS16780 (H8Z72_16765) pilR 3873453..3874847 (+) 1395 WP_005930970.1 sigma-54 dependent transcriptional regulator Regulator
  H8Z72_RS16785 (H8Z72_16770) - 3875052..3875219 (-) 168 WP_015463523.1 hypothetical protein -
  H8Z72_RS16790 (H8Z72_16775) pilB 3875351..3875470 (-) 120 WP_005915819.1 hypothetical protein Machinery gene
  H8Z72_RS16795 (H8Z72_16780) pilB 3875964..3877700 (-) 1737 WP_011052125.1 type IV-A pilus assembly ATPase PilB Machinery gene
  H8Z72_RS16800 (H8Z72_16785) - 3877764..3878219 (-) 456 WP_015463526.1 pilin -
  H8Z72_RS16805 (H8Z72_16790) - 3878329..3878769 (-) 441 WP_015471735.1 pilin -
  H8Z72_RS16810 (H8Z72_16795) pilC 3879128..3880384 (+) 1257 WP_040107659.1 type II secretion system F family protein Machinery gene
  H8Z72_RS16815 (H8Z72_16800) - 3880391..3881254 (+) 864 WP_003491180.1 A24 family peptidase -
  H8Z72_RS16820 (H8Z72_16805) coaE 3881268..3881876 (+) 609 WP_011052129.1 dephospho-CoA kinase -
  H8Z72_RS16825 (H8Z72_16810) - 3882100..3886623 (+) 4524 WP_040153736.1 RHS repeat domain-containing protein -
  H8Z72_RS16830 (H8Z72_16815) - 3887258..3887623 (+) 366 WP_076605127.1 SymE family type I addiction module toxin -
  H8Z72_RS16835 (H8Z72_16820) - 3887637..3887882 (+) 246 Protein_3299 transposase -

Sequence

Protein


Download         Length: 578 a.a.        Molecular weight: 62517.63 Da        Isoelectric Point: 5.4526

>NTDB_id=476288 H8Z72_RS16795 WP_011052125.1 3875964..3877700(-) (pilB) [Xanthomonas citri pv. citri strain DAR73889]
MNSVVTANLVGITGIARRLVQDGAVEEAVARSAMDQASAAKVPLPQWFAEKKLVTASQLAAANAVEFGMPLLDVSAFDAS
QNAVKLVSEELLQKHQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSALG
DDEEGMGDLDVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLNQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDGSAAKLGIDKLGYEPDQQK
LFLEAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
DNALLAEGFTPAQLAAGIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQAIGIRDLRQSALM
KAANGVTSLAEINRVTKD

Nucleotide


Download         Length: 1737 bp        

>NTDB_id=476288 H8Z72_RS16795 WP_011052125.1 3875964..3877700(-) (pilB) [Xanthomonas citri pv. citri strain DAR73889]
ATGAATAGCGTCGTGACCGCAAATTTGGTTGGAATAACGGGCATCGCGCGTCGTCTGGTGCAAGACGGTGCGGTCGAAGA
AGCAGTTGCGCGATCTGCGATGGATCAGGCATCTGCGGCAAAGGTTCCTCTGCCGCAATGGTTTGCTGAGAAGAAGTTGG
TCACTGCTTCCCAGCTCGCCGCTGCGAATGCGGTCGAGTTCGGCATGCCACTGTTGGACGTGTCGGCGTTCGACGCCAGC
CAAAACGCGGTCAAGCTGGTAAGTGAGGAGCTACTTCAGAAGCACCAAGTGCTACCGCTGTTCAAGCGCGGCAACCGGCT
GTTCGTAGGGGTGAGCAATCCGACCCAGACCCGGGCGCTGGATGACATCAAGTTTCATACGAACTTGGTAGTCGAGCCCA
TCCTTGTGGATGAAGATCAGATCCGTCGCACCCTGGAGCAATGGCAGGCCAGCAATGCTGCGCTGGGCTCCGCGCTCGGT
GACGACGAGGAGGGCATGGGGGATCTGGACGTCTCGGCCGGCGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTTGA
TGCCAAGGGCGACGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCAGGCGGGGAGCCTCGGACA
TCCATTTCGAGCCGTATGAAGACGACTACCGGGTGCGCTTGCGCATCGATGGCTTGTTGAAGAACGTGGCCAAGGCGCCG
GTGAAGCTGAACCAGCGCATCGCAGCGCGGTTGAAGGTGATGTCGCAGCTGGATATCGCCGAGAAGCGGGTGCCGCAGGA
CGGGCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGTGTCAGCACCTTGCCGACCCTGTTCGGCGAGA
AGGTGGTGCTGCGTATCCTGGACGGCAGCGCGGCCAAGCTGGGCATCGACAAGCTGGGCTACGAGCCGGACCAACAGAAG
CTGTTCCTGGAAGCGATCCACAAGCCCTATGGCATGGTGCTGGTGACCGGGCCGACCGGCTCGGGCAAGACGGTGTCGTT
GTACACCGCGCTGGGAATTCTCAACGACGAGACGCGCAATATCTCCACCGCGGAGGATCCGGTCGAAATCCGCTTGCCTG
GCGTCAATCAGGTGCAGCAGAACAACAAGCGTGGCATGACCTTCGCCGCGGCTTTGCGCTCGTTCCTGCGCCAGGATCCG
GACATCATCATGGTCGGCGAAATCCGTGACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACGGGTCACATGGT
GCTGTCGACGTTGCACACCAACGATGCGCCGCAGACCATCGCACGTCTGATGAACATGGGCATCGCGCCCTACAACATCA
CCTCGTCGGTGACGCTGGTGATCGCGCAGCGGCTGGCGCGGCGCTTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCT
GACAACGCATTGCTGGCCGAAGGATTCACGCCTGCCCAGCTTGCCGCCGGGATCGAGCTGTATGAGGCGGTCGGTTGCGA
TGAGTGCACCGAAGGCTACAAGGGGCGTACCGGTATCTACCAGGTAATGCCGATGACCGACGAGATCGGCGCGATCGTGC
TGGAAGGCGGCAATGCGATGCAGATCGCCGAGGCCGCGCAGGCGATCGGTATCCGCGATTTGCGGCAGTCGGCGCTGATG
AAGGCTGCGAATGGGGTGACCAGCCTGGCCGAGATCAATCGTGTGACGAAGGACTAA

Domains

Predicted by InterproScan.

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

(49-153)

Type II/IV secretion system protein (T2SSE)

(201-468)


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

56.514

98.27

0.555
  pilB Acinetobacter baylyi ADP1

55.81

98.27

0.548
  pilB Legionella pneumophila strain ERS1305867

52.021

98.443

0.512
  pilB Vibrio cholerae strain A1552

49.306

99.654

0.491
  pilF Neisseria gonorrhoeae MS11

49.12

98.27

0.483
  pilB Vibrio parahaemolyticus RIMD 2210633

46.964

96.886

0.455
  pilB Vibrio campbellii strain DS40M4

45.518

98.443

0.448