Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   KDR_RS09890 Genome accession   NZ_CP150840
Coordinates   1986901..1989564 (-) Length   887 a.a.
NCBI ID   WP_027479822.1    Uniprot ID   -
Organism   Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 strain ATCC 13939     
Function   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 1973553..1986838 1986901..1989564 flank 63
IScluster/Tn 1984767..1986375 1986901..1989564 flank 526


Gene organization within MGE regions


Location: 1973553..1989564
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  KDR_RS09810 - 1973553..1974293 (-) 741 WP_162177654.1 hypothetical protein -
  KDR_RS09815 - 1974355..1974909 (-) 555 WP_010888585.1 hypothetical protein -
  KDR_RS09820 - 1974928..1976061 (-) 1134 WP_010888586.1 permease prefix domain 1-containing protein -
  KDR_RS09825 - 1976067..1976390 (-) 324 WP_010888587.1 PadR family transcriptional regulator -
  KDR_RS09830 - 1976564..1978126 (-) 1563 WP_010888588.1 ABC transporter substrate-binding protein -
  KDR_RS09835 - 1978273..1978935 (+) 663 WP_010888589.1 hypothetical protein -
  KDR_RS09840 - 1979043..1979489 (+) 447 WP_051618937.1 hypothetical protein -
  KDR_RS09845 - 1979486..1980487 (+) 1002 WP_010888591.1 ADP-ribosylglycohydrolase family protein -
  KDR_RS09850 - 1980484..1981041 (+) 558 WP_010888592.1 nucleotidyltransferase family protein -
  KDR_RS09855 - 1981116..1982315 (+) 1200 WP_010888593.1 acetyl-CoA C-acetyltransferase -
  KDR_RS09860 - 1982504..1983187 (+) 684 WP_028328057.1 ankyrin repeat domain-containing protein -
  KDR_RS09865 - 1983265..1983777 (+) 513 WP_010888595.1 hypothetical protein -
  KDR_RS09870 - 1983840..1984646 (-) 807 Protein_1936 type IV pilus twitching motility protein PilT -
  KDR_RS09875 tnpA 1984740..1985162 (+) 423 WP_010887312.1 IS200/IS605-like element ISDra2 family transposase -
  KDR_RS09880 tnpB 1985170..1986375 (+) 1206 WP_231885333.1 IS200/IS605 family element RNA-guided endonuclease TnpB -
  KDR_RS09885 - 1986368..1986838 (-) 471 Protein_1939 ATPase, T2SS/T4P/T4SS family -
  KDR_RS09890 pilB 1986901..1989564 (-) 2664 WP_027479822.1 ATPase, T2SS/T4P/T4SS family Machinery gene

Sequence

Protein


Download         Length: 887 a.a.        Molecular weight: 97248.06 Da        Isoelectric Point: 4.8389

>NTDB_id=972874 KDR_RS09890 WP_027479822.1 1986901..1989564(-) (pilB) [Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 strain ATCC 13939]
MALSIGDRRLGAILLDQGYLGDNDLQRALERHSEVGGRLADVLIDSGMVGEKRIARAIEEALGIPLVNLLAVQPDPAALR
SIRPQTALNLQAFPFALEGDRLRVALVDPLSSFSIETLEDDSGFDIEPYQALREEVMWAIATHYPELGLEIVVPSGASDA
GRTGGKLGERLITHGYITDAQLQVALDAQQQTGEALGATLISQRAITEDQLYEVLAEQEGTTFLPNPSGFHPGEEVLGSM
LRADALRLLAVPVDETEQGVTVLTSDPRKRPDIDALIGRPVQLMLTRPRDIERLIEQFYPQRGRLGEQLVQEGTLSRDQL
REALQVQAREGKVKPLGEVITELGFASPDEVDSALQKQNVGGGRLEDTLVQSGKLSPEMLARSLAAQLGYEFLDPIQNPP
DPKVALMIPEATARRYVVVPVRLQGNSLVVAMKDPRNVFALDDLKLITGKEILPAVMAEKDIIRLIERYFGEKGFEKLNK
ELAERNKTQQSQEADLSVADESAIVQVVDSIIREAALQDASDIHIETTEDAVKVRYRIDGALREQNSFPKGAAQQIMARL
KIMGHLDIAERRVPQDGRVRFKKGSIDLDLRLSTLPTVYGEKAVMRLLQKASNIPELEQLGFSEYNYARYTEIIERPNGI
FLVTGPTGSGKSFTCFSTLKRIAKPEKNTTTIEDPIEYEVPGIVQSQVNNSTGMTFARALRAFLRQDPDIIFVGEIRDQE
TAKIAVEAALTGHMVLATLHTNDAPGAVTRLEEMGIENFNISAAVMGVLAQRLVRRVCSECKQPTNADPEVLRRLGISER
DIRGANLMRGTGCPRCGGTGYKGRMGIHELMVMDDSLRRTIGAGRPAAEIRDVALGESGLRSLRQDGIEKALQGLTTLEE
VLAVTAS

Nucleotide


Download         Length: 2664 bp        

>NTDB_id=972874 KDR_RS09890 WP_027479822.1 1986901..1989564(-) (pilB) [Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 strain ATCC 13939]
TTGGCTCTTTCGATTGGTGACCGCCGCCTGGGCGCGATTTTGCTGGACCAGGGGTATCTGGGCGACAACGACTTGCAGCG
GGCGCTGGAGCGGCACTCCGAGGTGGGGGGCCGCCTCGCTGACGTGCTGATCGACTCCGGCATGGTGGGCGAAAAACGCA
TCGCCCGCGCCATCGAGGAAGCGCTCGGCATTCCGCTGGTCAACCTGCTGGCGGTGCAGCCCGACCCGGCGGCGCTGCGC
TCGATTCGGCCCCAGACGGCCCTCAACTTGCAGGCGTTTCCCTTCGCGCTCGAAGGTGACCGGCTGCGGGTGGCGCTGGT
GGACCCGCTGTCGAGCTTTTCGATCGAGACGCTTGAAGACGACAGCGGCTTCGACATCGAACCGTATCAGGCGCTGCGCG
AGGAAGTGATGTGGGCCATCGCCACGCACTACCCCGAGCTTGGCCTGGAGATCGTGGTGCCCAGCGGGGCCAGCGACGCC
GGGCGCACCGGAGGCAAGCTCGGTGAGCGGCTGATCACGCACGGCTACATCACCGACGCACAGCTTCAGGTGGCGCTCGA
CGCGCAGCAGCAGACCGGCGAGGCGCTCGGGGCGACCCTGATCTCGCAGCGGGCCATCACCGAAGACCAGCTCTACGAGG
TGCTCGCCGAACAGGAAGGCACCACCTTCCTTCCCAACCCCAGCGGTTTTCACCCCGGCGAGGAAGTCCTCGGCAGCATG
CTGCGCGCCGACGCCCTGCGCCTGCTCGCGGTGCCGGTGGACGAAACCGAGCAGGGCGTGACGGTCCTGACGAGCGACCC
GCGCAAGCGCCCCGACATCGACGCGCTCATCGGGCGCCCAGTGCAGTTGATGCTCACGCGCCCGCGCGACATCGAGCGCC
TGATTGAGCAGTTCTACCCGCAACGGGGCCGCCTCGGCGAGCAACTCGTGCAGGAAGGCACGCTGTCGCGCGACCAGTTG
CGCGAGGCGCTTCAGGTGCAGGCCCGTGAGGGCAAGGTCAAGCCGCTCGGCGAGGTCATCACCGAACTCGGATTCGCCAG
CCCCGACGAGGTGGATTCGGCGCTGCAAAAGCAGAACGTCGGCGGAGGCCGCCTGGAAGACACCCTGGTGCAGTCAGGCA
AGCTCAGCCCCGAGATGCTCGCCCGCTCGCTCGCCGCGCAGCTCGGCTACGAGTTCCTCGACCCCATCCAGAACCCGCCG
GACCCCAAGGTCGCGCTGATGATTCCCGAGGCCACCGCCCGCCGCTACGTAGTGGTGCCGGTCAGGCTCCAGGGCAACTC
GCTCGTCGTCGCCATGAAAGACCCGCGCAACGTGTTTGCGCTCGACGACCTCAAGCTGATTACCGGCAAAGAAATCCTGC
CCGCCGTGATGGCGGAAAAAGACATCATCCGCCTGATCGAGCGCTACTTCGGGGAAAAGGGCTTCGAGAAGCTCAACAAG
GAACTCGCCGAGCGCAACAAGACCCAGCAGTCGCAGGAAGCCGACCTCTCGGTGGCCGACGAGAGCGCCATCGTGCAGGT
GGTGGACTCGATTATCCGCGAGGCCGCGCTGCAAGACGCCTCGGACATTCACATCGAAACCACCGAGGACGCCGTCAAGG
TGCGCTACCGCATCGACGGTGCGCTGCGCGAGCAGAACTCCTTTCCCAAGGGCGCGGCGCAGCAGATCATGGCCCGCCTC
AAGATCATGGGCCACCTCGACATCGCCGAGCGCCGCGTGCCGCAAGACGGGCGCGTGCGCTTCAAGAAGGGCAGCATCGA
CCTCGACCTGCGTCTCTCGACCCTGCCCACCGTGTACGGCGAGAAAGCCGTCATGCGTCTGCTGCAAAAGGCGAGCAACA
TCCCCGAACTCGAGCAGCTCGGCTTTTCCGAGTACAACTACGCCCGCTACACCGAGATTATCGAGCGGCCCAACGGCATT
TTTCTGGTCACCGGGCCGACGGGGTCGGGCAAGTCGTTCACCTGTTTTTCGACCCTCAAGCGCATCGCCAAGCCCGAGAA
AAACACCACGACCATCGAAGACCCCATCGAGTACGAGGTGCCGGGCATCGTGCAGTCGCAGGTGAACAACTCGACCGGGA
TGACCTTTGCCCGCGCCCTGCGCGCCTTCCTGCGTCAGGACCCCGACATCATCTTCGTGGGCGAAATCCGTGACCAGGAA
ACCGCCAAGATTGCGGTGGAAGCGGCGCTCACCGGCCACATGGTGCTCGCCACTCTGCACACCAACGACGCGCCAGGCGC
CGTGACCCGCCTTGAGGAAATGGGCATCGAGAACTTCAACATCTCGGCGGCCGTGATGGGCGTGCTCGCGCAGCGGCTGG
TGCGCCGGGTGTGCAGCGAGTGCAAGCAGCCCACCAACGCCGACCCCGAGGTGCTCCGGCGGCTCGGCATCAGCGAGCGC
GATATTCGCGGCGCGAATCTGATGCGCGGGACCGGCTGTCCCCGCTGCGGCGGCACCGGCTACAAGGGCCGCATGGGGAT
CCACGAGCTGATGGTGATGGACGACTCGCTGCGCCGCACCATCGGGGCCGGGCGGCCCGCCGCCGAAATCCGCGACGTGG
CGCTGGGCGAAAGCGGCCTGCGGAGCCTGCGCCAGGACGGCATCGAAAAGGCCCTGCAAGGCCTGACCACCCTTGAAGAA
GTGCTGGCCGTCACCGCGAGCTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(511-776)

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

(369-472)

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

(200-303)

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

(43-146)


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 Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

100

100

1
  pilF Thermus thermophilus HB27

56.229

100

0.565

Multiple sequence alignment