Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   ABFU56_RS05670 Genome accession   NZ_CP155998
Coordinates   1322823..1324085 (-) Length   420 a.a.
NCBI ID   WP_057671824.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. campestris strain LMG 00574     
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 1275162..1333476 1322823..1324085 within 0


Gene organization within MGE regions


Location: 1275162..1333476
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFU56_RS05450 (ABFU56_05445) - 1275162..1277042 (+) 1881 WP_019237331.1 integrase arm-type DNA-binding domain-containing protein -
  ABFU56_RS05455 (ABFU56_05450) - 1277227..1277646 (+) 420 WP_019237332.1 hypothetical protein -
  ABFU56_RS05460 (ABFU56_05455) - 1277679..1278680 (+) 1002 WP_011038253.1 XVIPCD domain-containing protein -
  ABFU56_RS05465 (ABFU56_05460) - 1278751..1279401 (-) 651 WP_011038252.1 LysR substrate-binding domain-containing protein -
  ABFU56_RS05470 (ABFU56_05465) - 1279504..1279797 (+) 294 WP_011038251.1 helix-turn-helix domain-containing protein -
  ABFU56_RS05475 (ABFU56_05470) - 1279825..1280709 (-) 885 WP_057671621.1 LysR family transcriptional regulator -
  ABFU56_RS05480 (ABFU56_05475) - 1281462..1285487 (-) 4026 WP_075287146.1 helix-turn-helix domain-containing protein -
  ABFU56_RS05485 (ABFU56_05480) - 1286042..1289305 (-) 3264 WP_057671623.1 ATP-binding protein -
  ABFU56_RS05490 (ABFU56_05485) - 1289396..1289527 (+) 132 Protein_1062 IS5/IS1182 family transposase -
  ABFU56_RS05495 (ABFU56_05490) - 1290496..1292034 (+) 1539 WP_011038243.1 MASE1 domain-containing protein -
  ABFU56_RS05500 (ABFU56_05495) - 1293056..1293703 (+) 648 WP_016848927.1 hypothetical protein -
  ABFU56_RS05505 (ABFU56_05500) - 1293735..1294874 (+) 1140 WP_017117946.1 type IV secretion system protein -
  ABFU56_RS05510 (ABFU56_05505) - 1294952..1295491 (+) 540 WP_225443876.1 DUF4189 domain-containing protein -
  ABFU56_RS05515 (ABFU56_05510) - 1295889..1296419 (+) 531 WP_011038239.1 hypothetical protein -
  ABFU56_RS05520 (ABFU56_05515) - 1296416..1297075 (+) 660 WP_057671625.1 hypothetical protein -
  ABFU56_RS05525 (ABFU56_05520) - 1297072..1298454 (+) 1383 WP_057671628.1 DUF6792 domain-containing protein -
  ABFU56_RS05530 (ABFU56_05525) - 1298558..1298985 (+) 428 Protein_1070 type IV secretion system protein -
  ABFU56_RS05535 (ABFU56_05530) - 1299494..1300638 (+) 1145 WP_274349786.1 IS3 family transposase -
  ABFU56_RS05540 (ABFU56_05535) - 1301187..1301666 (+) 480 WP_075286085.1 RadC family protein -
  ABFU56_RS05545 (ABFU56_05540) - 1301737..1301928 (+) 192 WP_221261829.1 hypothetical protein -
  ABFU56_RS05550 (ABFU56_05545) - 1302008..1303110 (+) 1103 Protein_1074 IS3-like element IS1404 family transposase -
  ABFU56_RS05555 (ABFU56_05550) - 1303769..1303924 (+) 156 WP_186009287.1 hypothetical protein -
  ABFU56_RS05560 (ABFU56_05555) - 1304913..1305338 (+) 426 Protein_1076 XVIPCD domain-containing protein -
  ABFU56_RS05565 (ABFU56_05560) - 1305366..1305620 (-) 255 WP_057671639.1 hypothetical protein -
  ABFU56_RS05570 (ABFU56_05565) - 1305887..1306897 (+) 1011 Protein_1078 MobA/MobL family protein -
  ABFU56_RS05575 (ABFU56_05570) - 1306972..1308080 (+) 1109 WP_192012246.1 IS3 family transposase -
  ABFU56_RS05580 (ABFU56_05575) - 1308099..1308686 (+) 588 Protein_1080 hypothetical protein -
  ABFU56_RS05585 (ABFU56_05580) - 1308759..1309127 (-) 369 WP_225443877.1 transcriptional regulator -
  ABFU56_RS05590 (ABFU56_05585) - 1309135..1309416 (-) 282 WP_011348355.1 DUF6516 family protein -
  ABFU56_RS05595 (ABFU56_05590) - 1309482..1309823 (-) 342 WP_081020748.1 hypothetical protein -
  ABFU56_RS05600 (ABFU56_05595) - 1310549..1310899 (+) 351 WP_225443878.1 hypothetical protein -
  ABFU56_RS05605 (ABFU56_05600) - 1311198..1311428 (-) 231 WP_157382680.1 hypothetical protein -
  ABFU56_RS05610 (ABFU56_05605) - 1311492..1311638 (+) 147 WP_040940792.1 hypothetical protein -
  ABFU56_RS05615 (ABFU56_05610) - 1311823..1312218 (+) 396 WP_042594933.1 hypothetical protein -
  ABFU56_RS05620 (ABFU56_05615) - 1312309..1312701 (+) 393 WP_012437593.1 H-NS family nucleoid-associated regulatory protein -
  ABFU56_RS05625 (ABFU56_05620) glgX 1313236..1315365 (-) 2130 WP_057671651.1 glycogen debranching protein GlgX -
  ABFU56_RS05630 (ABFU56_05625) rimK 1315858..1316733 (+) 876 WP_016945000.1 30S ribosomal protein S6--L-glutamate ligase -
  ABFU56_RS05635 (ABFU56_05630) - 1317383..1318060 (+) 678 WP_003490678.1 response regulator transcription factor -
  ABFU56_RS05640 (ABFU56_05635) - 1318053..1319387 (+) 1335 WP_057671653.1 HAMP domain-containing sensor histidine kinase -
  ABFU56_RS05645 (ABFU56_05640) - 1319530..1320021 (-) 492 WP_057671655.1 GNAT family N-acetyltransferase -
  ABFU56_RS05650 (ABFU56_05645) - 1320018..1320308 (-) 291 WP_011038219.1 DUF1778 domain-containing protein -
  ABFU56_RS05655 (ABFU56_05650) - 1320383..1320784 (-) 402 WP_040940795.1 SymE family type I addiction module toxin -
  ABFU56_RS05660 (ABFU56_05655) coaE 1321316..1321939 (-) 624 WP_011038217.1 dephospho-CoA kinase -
  ABFU56_RS05665 (ABFU56_05660) - 1321953..1322816 (-) 864 WP_057671659.1 A24 family peptidase -
  ABFU56_RS05670 (ABFU56_05665) pilC 1322823..1324085 (-) 1263 WP_057671824.1 type II secretion system F family protein Machinery gene
  ABFU56_RS05675 (ABFU56_05670) pilA 1324427..1324855 (+) 429 WP_407470115.1 pilin Machinery gene
  ABFU56_RS05680 (ABFU56_05675) pilB 1324991..1326721 (+) 1731 WP_057671826.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFU56_RS05690 (ABFU56_05685) pilR 1327140..1328534 (-) 1395 WP_057671663.1 sigma-54 dependent transcriptional regulator Regulator
  ABFU56_RS05695 (ABFU56_05690) - 1328743..1330353 (-) 1611 WP_057671664.1 PAS domain-containing sensor histidine kinase -
  ABFU56_RS05700 (ABFU56_05695) sucC 1330587..1331756 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ABFU56_RS05705 (ABFU56_05700) sucD 1331781..1332656 (+) 876 WP_057671668.1 succinate--CoA ligase subunit alpha -
  ABFU56_RS05710 (ABFU56_05705) - 1332760..1333170 (+) 411 WP_029217117.1 CopG family ribbon-helix-helix protein -
  ABFU56_RS05715 (ABFU56_05710) - 1333174..1333476 (+) 303 WP_011038207.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 420 a.a.        Molecular weight: 46232.76 Da        Isoelectric Point: 10.2689

>NTDB_id=1000952 ABFU56_RS05670 WP_057671824.1 1322823..1324085(-) (pilC) [Xanthomonas campestris pv. campestris strain LMG 00574]
MSVVRNAIKKQVVDRSTGQQLQLFLWEGTDKRGIKMKGEQTARNMNMLRAELRRQGINPSVVKPKPKPLFGAAGKKITPK
DIAFFSRQMATMMKSGVPIVSSLEIIGEGHKNPRMKKMVGQVRTDIEGGSSLYESISRHPVQFDELYRNLVRAGEGAGVL
ETVLDTVATYKENIEALKGKIKKALFYPAMVIAVALIVSAILLIFVVPQFEEVFKGFGAELPAFTQMIVGASRFMVSYWW
IMLFVVAGSIIGFIFAYKRSPSMQHAMDRLILRVPVIGQIMHNSSIARFARTTAVTFKAGVPLVEALGIVAGATGNRVYE
DAVLRMRDDVSVGYPVNMAMKQVNLFPHMVIQMTAIGEEAGALDTMLFKVAEYFEQEVNNAVDALSSLLEPMIMVFIGVV
VGGMVIGMYLPIFKLGAVVG

Nucleotide


Download         Length: 1263 bp        

>NTDB_id=1000952 ABFU56_RS05670 WP_057671824.1 1322823..1324085(-) (pilC) [Xanthomonas campestris pv. campestris strain LMG 00574]
ATGTCTGTCGTACGCAATGCTATTAAGAAGCAAGTAGTCGACCGCAGTACTGGTCAACAGCTACAGCTGTTTCTTTGGGA
AGGAACCGATAAGCGCGGAATCAAGATGAAAGGCGAGCAGACTGCGCGCAACATGAATATGTTGCGCGCGGAACTTCGTC
GTCAAGGTATCAATCCGTCGGTAGTCAAACCCAAACCCAAGCCGCTGTTCGGTGCTGCAGGCAAGAAAATTACGCCAAAA
GACATTGCATTTTTCAGTCGCCAGATGGCGACTATGATGAAATCAGGGGTGCCGATTGTAAGCTCGCTTGAGATCATCGG
TGAGGGCCACAAAAATCCACGCATGAAAAAGATGGTGGGCCAAGTGAGAACGGATATCGAGGGCGGCTCATCTCTTTATG
AATCAATCAGCAGACATCCCGTGCAGTTTGATGAGCTCTACCGAAACCTCGTCCGAGCAGGTGAAGGTGCAGGCGTTCTA
GAGACAGTGCTAGATACAGTTGCCACTTACAAAGAAAACATAGAGGCCCTTAAGGGAAAGATTAAGAAGGCCCTGTTTTA
TCCAGCCATGGTGATTGCAGTCGCCCTTATTGTCAGCGCCATCCTGCTCATTTTTGTGGTCCCTCAATTCGAAGAGGTTT
TTAAGGGTTTCGGCGCCGAGTTACCCGCCTTCACCCAAATGATTGTAGGAGCATCACGCTTCATGGTGAGCTACTGGTGG
ATCATGCTGTTCGTTGTAGCAGGCTCCATCATTGGCTTCATCTTTGCTTATAAACGCTCACCAAGCATGCAGCATGCCAT
GGATAGGCTGATATTGAGAGTGCCTGTTATCGGGCAAATCATGCATAACAGCTCGATTGCGCGCTTCGCACGCACGACTG
CGGTTACCTTTAAAGCCGGAGTCCCATTAGTGGAAGCATTAGGCATTGTTGCTGGCGCCACCGGCAACCGCGTCTACGAA
GATGCGGTACTCCGTATGCGCGACGATGTATCTGTTGGCTACCCGGTCAACATGGCGATGAAACAGGTAAACCTGTTCCC
ACACATGGTTATTCAAATGACTGCGATTGGCGAAGAAGCGGGCGCTCTTGATACCATGCTCTTCAAGGTGGCGGAATACT
TCGAGCAAGAGGTAAACAATGCAGTAGATGCACTTAGCAGCCTGCTCGAACCGATGATTATGGTCTTTATTGGCGTCGTC
GTAGGCGGTATGGTCATCGGCATGTATCTTCCGATCTTCAAACTCGGCGCAGTGGTTGGATAA

Domains

Predicted by InterproScan.

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

(85-208)

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

(289-411)


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

54.408

94.524

0.514
  pilC Legionella pneumophila strain ERS1305867

52.882

95

0.502
  pilC Acinetobacter baylyi ADP1

51.244

95.714

0.49
  pilC Acinetobacter baumannii D1279779

49.628

95.952

0.476
  pilG Neisseria gonorrhoeae MS11

44.638

95.476

0.426
  pilG Neisseria meningitidis 44/76-A

44.14

95.476

0.421
  pilC Vibrio campbellii strain DS40M4

40.786

96.905

0.395
  pilC Vibrio cholerae strain A1552

40.75

95.238

0.388

Multiple sequence alignment