Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   XB05_RS10815 Genome accession   NZ_CP011256
Coordinates   2562322..2563578 (+) Length   418 a.a.
NCBI ID   WP_046346034.1    Uniprot ID   -
Organism   Xanthomonas arboricola strain 17     
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)
ICE 2564170..2610227 2562322..2563578 flank 592


Gene organization within MGE regions


Location: 2562322..2610227
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  XB05_RS10815 (XB05_10815) pilC 2562322..2563578 (+) 1257 WP_046346034.1 type II secretion system F family protein Machinery gene
  XB05_RS10820 (XB05_10820) - 2563585..2564448 (+) 864 WP_046343941.1 A24 family peptidase -
  XB05_RS10825 (XB05_10825) coaE 2564462..2565073 (+) 612 WP_046343943.1 dephospho-CoA kinase -
  XB05_RS25140 - 2565574..2569941 (+) 4368 WP_240475951.1 RHS repeat-associated core domain-containing protein -
  XB05_RS24080 - 2569944..2570402 (+) 459 WP_144410818.1 hypothetical protein -
  XB05_RS10835 (XB05_10835) - 2570802..2571197 (+) 396 WP_080931356.1 SymE family type I addiction module toxin -
  XB05_RS10840 (XB05_10840) - 2571302..2572636 (-) 1335 WP_016904089.1 HAMP domain-containing sensor histidine kinase -
  XB05_RS10845 (XB05_10845) - 2572629..2573306 (-) 678 WP_006448355.1 response regulator transcription factor -
  XB05_RS10850 (XB05_10850) - 2573338..2573808 (-) 471 WP_046343948.1 hypothetical protein -
  XB05_RS10855 (XB05_10855) rimK 2574034..2574939 (-) 906 WP_167337518.1 30S ribosomal protein S6--L-glutamate ligase -
  XB05_RS10860 (XB05_10860) glgX 2575424..2577556 (+) 2133 WP_046343951.1 glycogen debranching protein GlgX -
  XB05_RS10865 (XB05_10865) - 2578206..2578598 (-) 393 WP_023904915.1 H-NS family nucleoid-associated regulatory protein -
  XB05_RS10870 (XB05_10870) - 2578687..2579073 (-) 387 WP_046343953.1 hypothetical protein -
  XB05_RS10875 (XB05_10875) - 2579812..2580174 (+) 363 WP_046343955.1 hypothetical protein -
  XB05_RS10880 (XB05_10880) - 2580219..2581805 (-) 1587 WP_046343957.1 MobA/MobL family protein -
  XB05_RS10885 (XB05_10885) - 2582065..2582370 (+) 306 WP_046346036.1 hypothetical protein -
  XB05_RS10890 (XB05_10890) - 2582466..2583458 (-) 993 WP_046343958.1 beta-propeller fold lactonase family protein -
  XB05_RS10895 (XB05_10895) - 2583580..2584497 (-) 918 WP_046343960.1 LysR family transcriptional regulator -
  XB05_RS10900 (XB05_10900) - 2584605..2585768 (+) 1164 WP_075285892.1 TDT family transporter -
  XB05_RS10905 (XB05_10905) - 2585770..2586372 (-) 603 WP_046343962.1 uracil-DNA glycosylase -
  XB05_RS25350 - 2586468..2586893 (-) 426 Protein_2217 XVIPCD domain-containing protein -
  XB05_RS24735 - 2587882..2588037 (-) 156 WP_167337519.1 hypothetical protein -
  XB05_RS25145 - 2588671..2588862 (-) 192 Protein_2219 hypothetical protein -
  XB05_RS10920 (XB05_10920) radC 2588932..2589411 (-) 480 WP_046343964.1 DNA repair protein RadC -
  XB05_RS10925 (XB05_10925) - 2589792..2590184 (+) 393 WP_240475952.1 GNAT family N-acetyltransferase -
  XB05_RS10930 (XB05_10930) - 2590761..2592467 (+) 1707 WP_046343965.1 hypothetical protein -
  XB05_RS10935 (XB05_10935) - 2592521..2593189 (+) 669 WP_046343967.1 hypothetical protein -
  XB05_RS10940 (XB05_10940) - 2593490..2594236 (-) 747 WP_046343968.1 hypothetical protein -
  XB05_RS10945 (XB05_10945) - 2594296..2595153 (+) 858 WP_046343969.1 hypothetical protein -
  XB05_RS10950 (XB05_10950) - 2595234..2595701 (+) 468 WP_046343971.1 hypothetical protein -
  XB05_RS10955 (XB05_10955) - 2595791..2596015 (-) 225 WP_046343973.1 hypothetical protein -
  XB05_RS24085 - 2597067..2597348 (-) 282 WP_144410819.1 hypothetical protein -
  XB05_RS24090 - 2597554..2598708 (-) 1155 WP_144410820.1 hypothetical protein -
  XB05_RS24095 - 2598771..2600114 (-) 1344 WP_144410821.1 hypothetical protein -
  XB05_RS25150 (XB05_10965) - 2600412..2600746 (-) 335 Protein_2231 hypothetical protein -
  XB05_RS10970 (XB05_10970) - 2601172..2601813 (+) 642 WP_144410822.1 hypothetical protein -
  XB05_RS22270 - 2602151..2603077 (-) 927 WP_144410823.1 hypothetical protein -
  XB05_RS10980 (XB05_10980) - 2603387..2604262 (-) 876 WP_046343977.1 small ribosomal subunit Rsm22 family protein -
  XB05_RS10985 (XB05_10985) - 2604326..2604784 (-) 459 WP_046343979.1 hypothetical protein -
  XB05_RS10990 (XB05_10990) - 2605143..2606534 (+) 1392 WP_046343981.1 site-specific integrase -
  XB05_RS10995 (XB05_10995) - 2606721..2607560 (+) 840 WP_240475953.1 site-specific integrase -
  XB05_RS11000 (XB05_11000) - 2607876..2608547 (-) 672 WP_046343985.1 STN domain-containing protein -
  XB05_RS11005 (XB05_11005) - 2608937..2609746 (-) 810 WP_046343987.1 OBAP family protein -

Sequence

Protein


Download         Length: 418 a.a.        Molecular weight: 46013.40 Da        Isoelectric Point: 10.2301

>NTDB_id=143985 XB05_RS10815 WP_046346034.1 2562322..2563578(+) (pilC) [Xanthomonas arboricola strain 17]
MSAVRNDLKKQPTDRSISQLQVFVWEGTDKRGVKMKGEQNAKSINMLRAELRRQGITPNIVKLKPKPLFGAAGKKITAKE
IAFFSRQMATMMKSGVPIVGSLEIIGEGHKNPRMRKMVGQVRTDIEGGSSLYEAISKHPVQFDELYRNLVRAGEGAGVLE
TVLDTIASYKENIEALKGKIKKALFYPAMVIAVAILVSAILLIFVVPQFEEVFKGFGADLPAFTQLLVNASRFMVSYWWL
MLLGTLGAIFGFTFAYKRSPAMQHRMDRLILKVPVVGQIMHNSSIARFARTTAVTFKAGVPLVEALSIVAGATGNKVYEE
AVLRMRDDVSVGYPVNVSMKQVNLFPHMVIQMTAIGEEAGALDAMLFKVAEYFEQEVNNAVDALSSLLEPLIMVFIGTIV
GGMVIGMYLPIFKLASVV

Nucleotide


Download         Length: 1257 bp        

>NTDB_id=143985 XB05_RS10815 WP_046346034.1 2562322..2563578(+) (pilC) [Xanthomonas arboricola strain 17]
ATGTCGGCAGTCCGCAATGATCTAAAAAAGCAGCCCACAGATCGCAGCATCAGTCAGTTGCAAGTCTTCGTGTGGGAGGG
CACTGACAAGCGTGGCGTCAAGATGAAAGGCGAGCAGAACGCTAAAAGTATCAACATGTTACGAGCAGAGCTTAGGCGTC
AGGGCATTACGCCTAACATTGTAAAGCTCAAGCCGAAGCCACTTTTTGGCGCCGCTGGCAAAAAAATTACTGCTAAAGAA
ATTGCATTCTTTAGCCGGCAGATGGCGACTATGATGAAATCTGGGGTACCTATTGTGGGTTCGCTAGAAATCATTGGCGA
GGGCCATAAAAATCCCCGCATGAGAAAGATGGTCGGCCAGGTTCGGACTGATATTGAGGGCGGCTCGTCCCTGTATGAGG
CCATAAGTAAGCACCCCGTGCAGTTTGACGAACTCTATAGAAACCTCGTTCGTGCTGGCGAGGGTGCTGGTGTTCTTGAA
ACCGTTCTCGATACCATCGCTAGCTACAAAGAAAATATTGAAGCACTCAAAGGGAAAATAAAAAAAGCGCTTTTCTATCC
AGCAATGGTAATTGCGGTAGCAATACTTGTAAGCGCGATACTTCTAATTTTTGTTGTGCCGCAATTTGAAGAAGTATTCA
AAGGTTTTGGCGCCGACTTACCCGCTTTTACCCAGCTACTTGTAAACGCTTCGAGATTCATGGTTTCTTACTGGTGGCTC
ATGCTGCTCGGGACGCTTGGGGCGATTTTTGGCTTTACTTTTGCTTACAAGCGCTCACCTGCAATGCAGCACCGCATGGA
CCGGTTGATTCTCAAGGTTCCAGTTGTCGGCCAAATCATGCACAACAGCTCGATTGCACGGTTCGCTCGTACAACTGCAG
TAACCTTCAAAGCAGGTGTTCCTCTCGTAGAAGCACTTAGCATTGTGGCAGGCGCAACTGGCAATAAAGTGTATGAAGAG
GCGGTGCTTCGGATGCGCGATGACGTGTCAGTTGGCTACCCTGTCAACGTATCAATGAAACAGGTAAATTTGTTTCCACA
CATGGTTATTCAAATGACCGCCATTGGGGAAGAAGCAGGCGCACTTGATGCAATGCTTTTTAAGGTGGCCGAATATTTCG
AACAGGAAGTCAATAATGCTGTTGACGCTCTTAGCAGTTTGCTTGAGCCACTTATCATGGTGTTCATAGGCACGATTGTT
GGCGGAATGGTCATCGGCATGTATCTCCCAATCTTCAAACTCGCTTCTGTGGTGTAA

Domains

Predicted by InterproScan.

Type II secretion system (T2SS), protein F (T2SSF)

(288-410)

Type II secretion system (T2SS), protein F (T2SSF)

(84-207)


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
  pilC Pseudomonas stutzeri DSM 10701

53.652

94.976

0.51
  pilC Legionella pneumophila strain ERS1305867

51.358

96.89

0.498
  pilC Acinetobacter baylyi ADP1

52.01

95.215

0.495
  pilC Acinetobacter baumannii D1279779

50.882

94.976

0.483
  pilG Neisseria gonorrhoeae MS11

44.724

95.215

0.426
  pilG Neisseria meningitidis 44/76-A

44.221

95.215

0.421
  pilC Vibrio cholerae strain A1552

40.351

95.455

0.385
  pilC Vibrio campbellii strain DS40M4

38.75

95.694

0.371
  pilC Thermus thermophilus HB27

38.653

95.933

0.371

Multiple sequence alignment