Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   I6N98_RS04310 Genome accession   NZ_CP066167
Coordinates   942056..943771 (-) Length   571 a.a.
NCBI ID   WP_198570570.1    Uniprot ID   -
Organism   Spongiibacter nanhainus strain csc3.9     
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 944651..954540 942056..943771 flank 880


Gene organization within MGE regions


Location: 942056..954540
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  I6N98_RS04310 (I6N98_04310) pilB 942056..943771 (-) 1716 WP_198570570.1 type IV-A pilus assembly ATPase PilB Machinery gene
  I6N98_RS04315 (I6N98_04315) pilA2 944169..944600 (+) 432 WP_198570571.1 pilin Machinery gene
  I6N98_RS04320 (I6N98_04320) - 944651..946606 (+) 1956 WP_198570572.1 hypothetical protein -
  I6N98_RS04325 (I6N98_04325) - 946603..947457 (+) 855 WP_198570573.1 glycosyltransferase family 2 protein -
  I6N98_RS04330 (I6N98_04330) - 947528..949216 (+) 1689 WP_198570574.1 ATP-binding cassette domain-containing protein -
  I6N98_RS04335 (I6N98_04335) - 949431..950465 (+) 1035 WP_198570575.1 glycosyltransferase -
  I6N98_RS04340 (I6N98_04340) - 950636..952162 (+) 1527 WP_198570576.1 stealth conserved region 3 domain-containing protein -
  I6N98_RS04345 (I6N98_04345) - 952180..953205 (-) 1026 WP_198571544.1 stealth family protein -
  I6N98_RS04350 (I6N98_04350) - 953329..954540 (-) 1212 WP_198570577.1 glycosyltransferase -

Sequence

Protein


Download         Length: 571 a.a.        Molecular weight: 62622.69 Da        Isoelectric Point: 5.0356

>NTDB_id=517930 I6N98_RS04310 WP_198570570.1 942056..943771(-) (pilB) [Spongiibacter nanhainus strain csc3.9]
MNSSQVPLTGLARRLVYDGILEEDAVRKAQEAANKDKKSLVSHLVEKKLADGLNLAEAAADEFGIPFLDLRVFTLDLAPH
KLVDNKLVKTHRALPLWKRGKRLFVGMSDPTNLHALDQIKFNTGLNTEPIVVEESALAVAIDKYLSAQEESLTDSLGGMD
DVDLESLDVEAVDEDGGEVDLSGADEAPVVKFVNKVLVDAIRGGASDIHFEPYERVYRVRFRTDGILHEVARPPVSLGFR
LAARLKVMSQMDISERRIPQDGRIKMKLSKTRAIDFRVNTLPTLWGEKVVLRILDPSSAQMGIDALGYEPDQKQLYMEAL
DEPQGMILVTGPTGSGKTVSLYTGLNILNTPERNISTAEDPVEINLEGINQVHVNNKVGLGFAEALRSFLRQDPDIIMVG
EIRDLETAEIAIKAAQTGHLVLSTLHTNSAPETLTRLLNMGVPAFNVATSVSLIIAQRLARRLCKECSVPADIPHETLLE
EGFSEEMLDGASILKPVGCDHCNGGYKGRVGIYEVVRITPDISRIIMENGNSLVIAEQARKEGFANLRTSALRKCAQGVT
SLEEVNRVTKD

Nucleotide


Download         Length: 1716 bp        

>NTDB_id=517930 I6N98_RS04310 WP_198570570.1 942056..943771(-) (pilB) [Spongiibacter nanhainus strain csc3.9]
ATGAATAGTTCACAGGTCCCGCTAACCGGCTTGGCGCGCAGGTTAGTCTATGATGGCATACTGGAAGAAGATGCCGTCCG
AAAGGCGCAAGAAGCGGCCAACAAAGATAAGAAAAGCTTGGTTTCTCACTTGGTTGAGAAAAAGCTCGCTGATGGTCTGA
ATTTGGCCGAGGCCGCAGCTGATGAGTTTGGCATACCTTTCTTAGACCTCCGCGTCTTTACCCTGGACCTTGCGCCCCAC
AAGCTTGTGGACAATAAACTGGTCAAGACCCACCGAGCTCTGCCCTTGTGGAAACGGGGCAAGCGTCTGTTTGTGGGCAT
GTCTGATCCCACCAACCTCCACGCCCTTGATCAGATTAAGTTCAACACTGGCCTCAATACCGAACCGATAGTCGTGGAGG
AAAGTGCTCTCGCCGTCGCTATAGACAAATACCTTAGTGCCCAGGAAGAGTCTTTGACAGATAGCCTGGGCGGCATGGAT
GACGTAGACCTAGAAAGCCTTGATGTAGAAGCCGTTGATGAAGACGGCGGCGAAGTTGACCTATCGGGCGCTGATGAGGC
CCCGGTGGTCAAATTCGTTAATAAAGTGCTGGTTGACGCCATTCGAGGCGGCGCTTCAGATATTCACTTTGAGCCCTATG
AGCGAGTCTACCGGGTTCGCTTCCGTACCGACGGTATTTTGCACGAAGTAGCCCGTCCGCCAGTGTCTTTGGGATTTCGG
CTAGCAGCACGCCTCAAGGTCATGTCGCAAATGGACATTTCAGAACGGCGCATCCCACAGGATGGCCGCATTAAGATGAA
GCTGTCCAAGACTCGCGCCATCGACTTCCGGGTGAATACGCTGCCTACCCTATGGGGTGAGAAGGTAGTACTACGGATTT
TGGACCCCAGTTCGGCTCAGATGGGCATCGACGCCCTTGGCTACGAGCCAGATCAGAAACAGTTGTACATGGAGGCTCTG
GACGAGCCCCAGGGCATGATACTGGTCACCGGACCTACCGGCTCGGGTAAGACTGTGTCGTTGTATACCGGTCTCAACAT
TCTGAACACCCCCGAGCGTAATATCTCCACCGCAGAGGACCCCGTTGAGATCAACCTGGAGGGGATCAACCAGGTCCACG
TAAACAATAAGGTAGGGTTGGGCTTTGCTGAAGCGCTGCGCTCCTTCCTCCGTCAGGATCCGGATATCATTATGGTGGGG
GAGATACGGGACCTGGAAACGGCGGAAATCGCTATCAAAGCCGCGCAAACCGGGCACCTGGTGCTCTCTACCCTCCACAC
CAATAGTGCCCCAGAAACACTGACACGCCTACTCAACATGGGCGTACCAGCTTTTAACGTCGCGACCTCGGTCAGCCTGA
TTATTGCCCAGCGTTTGGCCCGCCGGCTATGTAAAGAGTGTTCTGTGCCAGCCGATATCCCGCATGAGACCCTTCTTGAG
GAAGGCTTTAGCGAGGAAATGCTCGATGGGGCGTCTATTCTTAAGCCGGTGGGCTGCGACCACTGTAACGGCGGATACAA
GGGCCGGGTGGGCATTTACGAGGTTGTGCGTATTACACCAGACATTTCTCGTATTATTATGGAGAATGGTAATTCGCTGG
TAATTGCCGAGCAGGCCCGCAAAGAAGGGTTCGCCAACTTGCGCACCTCGGCGCTTAGAAAGTGTGCTCAGGGCGTCACC
AGCCTAGAAGAAGTCAACCGTGTGACCAAGGATTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(195-462)

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

(44-150)


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

62.367

99.124

0.618
  pilB Acinetobacter baylyi ADP1

60.071

99.124

0.595
  pilB Legionella pneumophila strain ERS1305867

56.085

99.299

0.557
  pilB Vibrio campbellii strain DS40M4

49.562

100

0.496
  pilF Neisseria gonorrhoeae MS11

48.866

100

0.49
  pilB Vibrio cholerae strain A1552

52.841

92.469

0.489
  pilB Vibrio parahaemolyticus RIMD 2210633

53.668

90.718

0.487
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

39.421

96.848

0.382
  pilF Thermus thermophilus HB27

38.42

97.548

0.375
  pilB/pilB1 Synechocystis sp. PCC 6803

42.376

88.441

0.375