Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   AMD10_RS16880 Genome accession   NZ_CP009007
Coordinates   3817240..3818976 (-) Length   578 a.a.
NCBI ID   WP_011052125.1    Uniprot ID   A0AAI7ZH88
Organism   Xanthomonas citri pv. citri strain MF20     
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 3795899..3821657 3817240..3818976 within 0


Gene organization within MGE regions


Location: 3795899..3821657
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AMD10_RS23980 (J172_03398) - 3795899..3797066 (+) 1168 Protein_3219 IS3 family transposase -
  AMD10_RS16795 (J172_03400) avrXacE2 3797826..3798896 (-) 1071 WP_011052114.1 type III secretion system effector avirulence protein AvrXacE2 -
  AMD10_RS16800 (J172_03401) - 3798981..3800258 (-) 1278 WP_011052115.1 lytic murein transglycosylase -
  AMD10_RS16805 (J172_03402) - 3800391..3803381 (-) 2991 WP_040107658.1 Tn3-like element TnXax1 family transposase -
  AMD10_RS16810 (J172_03403) - 3803390..3804664 (-) 1275 Protein_3223 site-specific integrase -
  AMD10_RS16820 (J172_03405) - 3804857..3805933 (+) 1077 WP_011052118.1 DNA-binding protein -
  AMD10_RS16825 (J172_03406) xopAI 3806067..3806957 (+) 891 WP_011052119.1 type III secretion system effector XopAI -
  AMD10_RS16830 (J172_03407) - 3807377..3808183 (-) 807 WP_015463520.1 hypothetical protein -
  AMD10_RS16835 (J172_03408) - 3808288..3808572 (+) 285 WP_016849322.1 hypothetical protein -
  AMD10_RS16840 (J172_03409) - 3808800..3809915 (+) 1116 WP_011052122.1 IS1595 family transposase -
  AMD10_RS16845 (J172_03410) - 3809870..3810385 (-) 516 WP_011052123.1 hypothetical protein -
  AMD10_RS16850 (J172_03411) sucD 3810472..3811347 (-) 876 WP_005921370.1 succinate--CoA ligase subunit alpha -
  AMD10_RS16855 (J172_03412) sucC 3811372..3812541 (-) 1170 WP_005915812.1 ADP-forming succinate--CoA ligase subunit beta -
  AMD10_RS16860 (J172_03413) - 3812773..3814386 (+) 1614 WP_003488599.1 HAMP domain-containing sensor histidine kinase -
  AMD10_RS16865 (J172_03414) pilR 3814711..3816105 (+) 1395 WP_015463522.1 sigma-54 dependent transcriptional regulator Regulator
  AMD10_RS16870 (J172_03416) - 3816328..3816495 (-) 168 WP_015463523.1 hypothetical protein -
  AMD10_RS16875 (J172_03417) pilB 3816627..3816746 (-) 120 WP_005915819.1 hypothetical protein Machinery gene
  AMD10_RS16880 (J172_03418) pilB 3817240..3818976 (-) 1737 WP_011052125.1 type IV-A pilus assembly ATPase PilB Machinery gene
  AMD10_RS16885 (J172_03419) - 3819040..3819495 (-) 456 WP_015463526.1 pilin -
  AMD10_RS16890 (J172_03420) - 3819605..3820045 (-) 441 WP_011052127.1 pilin -
  AMD10_RS16895 (J172_03421) pilC 3820401..3821657 (+) 1257 WP_040107659.1 type II secretion system F family protein Machinery gene

Sequence

Protein


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

>NTDB_id=126060 AMD10_RS16880 WP_011052125.1 3817240..3818976(-) (pilB) [Xanthomonas citri pv. citri strain MF20]
MNSVVTANLVGITGIARRLVQDGAVEEAVARSAMDQASAAKVPLPQWFAEKKLVTASQLAAANAVEFGMPLLDVSAFDAS
QNAVKLVSEELLQKHQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSALG
DDEEGMGDLDVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLNQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDGSAAKLGIDKLGYEPDQQK
LFLEAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
DNALLAEGFTPAQLAAGIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQAIGIRDLRQSALM
KAANGVTSLAEINRVTKD

Nucleotide


Download         Length: 1737 bp        

>NTDB_id=126060 AMD10_RS16880 WP_011052125.1 3817240..3818976(-) (pilB) [Xanthomonas citri pv. citri strain MF20]
ATGAATAGCGTCGTGACCGCAAATTTGGTTGGAATAACGGGCATCGCGCGTCGTCTGGTGCAAGATGGTGCGGTCGAAGA
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

Multiple sequence alignment