Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   JH275_RS05520 Genome accession   NZ_CP066966
Coordinates   1301209..1302465 (-) Length   418 a.a.
NCBI ID   WP_011038215.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. campestris strain 08305     
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 1247619..1301502 1301209..1302465 flank -293


Gene organization within MGE regions


Location: 1247619..1302465
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JH275_RS05270 (JH275_05250) - 1247619..1249499 (+) 1881 WP_019237331.1 integrase arm-type DNA-binding domain-containing protein -
  JH275_RS05275 (JH275_05255) - 1249684..1250103 (+) 420 WP_019237332.1 hypothetical protein -
  JH275_RS05280 (JH275_05260) - 1250136..1251137 (+) 1002 WP_011038253.1 XVIPCD domain-containing protein -
  JH275_RS05285 (JH275_05265) - 1251208..1251858 (-) 651 WP_011038252.1 LysR substrate-binding domain-containing protein -
  JH275_RS05290 (JH275_05270) - 1251961..1252254 (+) 294 WP_011038251.1 helix-turn-helix transcriptional regulator -
  JH275_RS05295 (JH275_05275) - 1252282..1253166 (-) 885 WP_011038250.1 LysR family transcriptional regulator -
  JH275_RS05300 (JH275_05280) - 1253956..1255323 (+) 1368 WP_011035783.1 IS5-like element IS1478 family transposase -
  JH275_RS05305 (JH275_05285) - 1255640..1256620 (+) 981 WP_011036443.1 IS5-like element IS1646 family transposase -
  JH275_RS05310 (JH275_05290) - 1256711..1260619 (-) 3909 WP_274495701.1 helix-turn-helix domain-containing protein -
  JH275_RS05315 (JH275_05295) - 1260939..1261271 (-) 333 Protein_1025 integrase core domain-containing protein -
  JH275_RS05320 (JH275_05300) - 1261302..1262404 (-) 1103 Protein_1026 IS3-like element IS1404 family transposase -
  JH275_RS05325 (JH275_05305) - 1262473..1262808 (-) 336 Protein_1027 DDE-type integrase/transposase/recombinase -
  JH275_RS05330 (JH275_05310) - 1262881..1263989 (+) 1109 WP_087942070.1 IS3 family transposase -
  JH275_RS05335 (JH275_05315) - 1264006..1264841 (-) 836 Protein_1029 IS3-like element ISXca1 family transposase -
  JH275_RS05340 (JH275_05320) - 1264905..1265162 (-) 258 Protein_1030 hypothetical protein -
  JH275_RS05345 (JH275_05325) - 1265159..1265818 (-) 660 WP_011038238.1 hypothetical protein -
  JH275_RS05350 (JH275_05330) - 1265815..1266345 (-) 531 WP_011038239.1 hypothetical protein -
  JH275_RS05355 (JH275_05335) - 1266743..1267282 (-) 540 WP_225443876.1 DUF4189 domain-containing protein -
  JH275_RS05360 (JH275_05340) - 1267360..1268499 (-) 1140 WP_011038241.1 type IV secretion system protein -
  JH275_RS05365 (JH275_05345) - 1268531..1269178 (-) 648 WP_016848927.1 hypothetical protein -
  JH275_RS05370 (JH275_05350) - 1270200..1271738 (-) 1539 WP_011038243.1 MASE1 domain-containing protein -
  JH275_RS05375 (JH275_05355) - 1272706..1272867 (-) 162 Protein_1037 IS5/IS1182 family transposase -
  JH275_RS05380 (JH275_05360) - 1272928..1276191 (+) 3264 WP_011038245.1 ATP-binding protein -
  JH275_RS05385 (JH275_05365) - 1276516..1276991 (+) 476 Protein_1039 IS3-like element ISXca1 family transposase -
  JH275_RS05395 (JH275_05375) - 1278202..1278489 (+) 288 Protein_1041 transposase -
  JH275_RS05400 (JH275_05380) mobH 1278520..1279512 (-) 993 Protein_1042 MobH family relaxase -
  JH275_RS05405 (JH275_05385) - 1279963..1280919 (+) 957 WP_228442279.1 GGDEF domain-containing protein -
  JH275_RS05410 (JH275_05390) - 1281023..1281313 (+) 291 WP_019237341.1 hypothetical protein -
  JH275_RS05415 (JH275_05395) - 1281469..1282395 (-) 927 WP_011038232.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  JH275_RS05420 (JH275_05400) - 1282388..1283146 (-) 759 WP_011038231.1 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
  JH275_RS05425 (JH275_05405) - 1283371..1283730 (+) 360 WP_029628872.1 DUF3742 family protein -
  JH275_RS05430 (JH275_05410) - 1283742..1285265 (-) 1524 WP_029628873.1 conjugal transfer protein TraG N-terminal domain-containing protein -
  JH275_RS05435 (JH275_05415) - 1285281..1285628 (-) 348 WP_011269554.1 hypothetical protein -
  JH275_RS05440 (JH275_05420) - 1285625..1286962 (-) 1338 WP_309545238.1 integrating conjugative element protein -
  JH275_RS05445 (JH275_05425) - 1287036..1287974 (-) 939 WP_011038228.1 TIGR03756 family integrating conjugative element protein -
  JH275_RS05455 - 1289444..1289755 (+) 312 WP_228428745.1 hypothetical protein -
  JH275_RS05460 (JH275_05440) - 1289873..1290028 (+) 156 WP_011038226.1 hypothetical protein -
  JH275_RS05465 (JH275_05445) - 1290205..1290600 (+) 396 WP_011038225.1 hypothetical protein -
  JH275_RS05470 (JH275_05450) - 1290691..1291083 (+) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  JH275_RS05475 (JH275_05455) glgX 1291622..1293751 (-) 2130 WP_011038223.1 glycogen debranching protein GlgX -
  JH275_RS05480 (JH275_05460) rimK 1294244..1295119 (+) 876 WP_011038222.1 30S ribosomal protein S6--L-glutamate ligase -
  JH275_RS05485 (JH275_05465) - 1295769..1296446 (+) 678 WP_003490678.1 response regulator transcription factor -
  JH275_RS05490 (JH275_05470) - 1296439..1297773 (+) 1335 WP_019237347.1 HAMP domain-containing sensor histidine kinase -
  JH275_RS05495 (JH275_05475) - 1297916..1298407 (-) 492 WP_011038220.1 GNAT family N-acetyltransferase -
  JH275_RS05500 (JH275_05480) - 1298404..1298694 (-) 291 WP_011038219.1 DUF1778 domain-containing protein -
  JH275_RS05505 (JH275_05485) - 1298769..1299170 (-) 402 WP_019237348.1 SymE family type I addiction module toxin -
  JH275_RS05510 (JH275_05490) coaE 1299702..1300325 (-) 624 WP_011038217.1 dephospho-CoA kinase -
  JH275_RS05515 (JH275_05495) - 1300339..1301202 (-) 864 WP_011038216.1 A24 family peptidase -
  JH275_RS05520 (JH275_05500) pilC 1301209..1302465 (-) 1257 WP_011038215.1 type II secretion system F family protein Machinery gene

Sequence

Protein


Download         Length: 418 a.a.        Molecular weight: 45907.37 Da        Isoelectric Point: 10.3359

>NTDB_id=523657 JH275_RS05520 WP_011038215.1 1301209..1302465(-) (pilC) [Xanthomonas campestris pv. campestris strain 08305]
MSIARSSMKKQPIDRNVNEMVPFVWEGTDKRGIKMKGEQPARNANMLRAELRRQGITPLVVKTKPKPLFGAAGKKISSKD
IAFFSRQMATMMKSGVPIVGSLEIIGEGHKNPRMKKMVGQIRTDIEGGSSLHEAISRHPVQFDDLYRNLVRAGEGAGVLE
TVLDTVANYKENIEALKGKIKKALFYPAMVMAVAIIVSGILLVFVVPQFEDVFKGFGAELPAFTQMIVAASRFMVSYWWL
MLLGSIAAIAGFIFAYKRSPRMRHGMDRLVLKVPVIGQIMHNSSIARFARTTAVTFKAGVPLVEALSIVAGATGNKVYEE
AVLRMRDDVSVGYPVNMAMKQVNLFPHMVVQMTSIGEEAGALDAMLFKVAEYFEQEVNNAVDALSSLLEPLIMVFIGTIV
GGMVIGMYLPIFKLGSVV

Nucleotide


Download         Length: 1257 bp        

>NTDB_id=523657 JH275_RS05520 WP_011038215.1 1301209..1302465(-) (pilC) [Xanthomonas campestris pv. campestris strain 08305]
ATGTCAATCGCTCGTAGCAGCATGAAGAAGCAGCCGATAGACCGGAACGTAAACGAGATGGTCCCATTTGTCTGGGAGGG
TACGGACAAGCGCGGCATCAAGATGAAGGGGGAACAACCTGCTCGCAACGCGAACATGCTCCGCGCTGAGCTTCGGCGGC
AGGGCATCACACCTTTAGTTGTAAAGACGAAGCCTAAGCCGCTTTTCGGCGCCGCTGGCAAGAAAATTTCTTCAAAAGAT
ATCGCATTTTTCAGTCGCCAGATGGCAACAATGATGAAGTCGGGCGTACCTATTGTTGGATCGCTTGAAATCATCGGAGA
GGGGCACAAAAATCCCCGCATGAAAAAAATGGTTGGTCAAATTAGGACCGACATTGAAGGAGGGTCTTCACTCCATGAAG
CAATTTCTAGGCATCCAGTCCAATTCGACGACCTCTATCGAAATTTGGTACGAGCAGGCGAAGGTGCCGGCGTTCTAGAA
ACCGTTTTAGACACAGTTGCAAATTACAAAGAAAACATTGAAGCACTGAAGGGAAAAATAAAGAAAGCTTTATTTTATCC
TGCAATGGTAATGGCCGTTGCAATTATTGTGAGCGGAATATTACTTGTATTTGTTGTCCCGCAATTTGAAGACGTATTCA
AAGGATTCGGAGCAGAACTACCAGCTTTCACTCAGATGATCGTCGCGGCGTCGCGTTTCATGGTGTCTTATTGGTGGCTT
ATGCTACTTGGTAGCATCGCAGCAATTGCAGGATTCATTTTTGCTTACAAGCGCTCGCCTCGCATGCGACATGGAATGGA
TAGATTGGTCTTGAAGGTCCCAGTCATTGGCCAGATCATGCATAATAGCTCTATCGCCCGATTTGCGCGAACCACTGCCG
TTACGTTCAAAGCTGGCGTTCCTTTAGTTGAAGCCTTGAGCATTGTGGCTGGCGCCACCGGTAATAAAGTTTATGAGGAA
GCTGTGCTTCGTATGCGCGATGATGTCTCGGTAGGCTACCCTGTCAACATGGCGATGAAGCAGGTCAATCTTTTCCCACA
CATGGTGGTTCAGATGACCTCGATCGGCGAAGAAGCTGGCGCCCTGGATGCCATGTTGTTCAAAGTGGCTGAATATTTCG
AGCAAGAAGTTAATAACGCCGTGGATGCATTGAGCAGCTTACTGGAACCATTGATCATGGTTTTTATTGGCACAATTGTG
GGCGGCATGGTCATTGGCATGTATCTTCCCATCTTCAAACTTGGCTCAGTGGTCTAA

Domains

Predicted by InterproScan.

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

(84-207)

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

(288-410)


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

53.788

94.737

0.51
  pilC Acinetobacter baylyi ADP1

53.401

94.976

0.507
  pilC Acinetobacter baumannii D1279779

51.741

96.172

0.498
  pilC Legionella pneumophila strain ERS1305867

50.493

97.129

0.49
  pilG Neisseria gonorrhoeae MS11

44.836

94.976

0.426
  pilG Neisseria meningitidis 44/76-A

44.332

94.976

0.421
  pilC Vibrio cholerae strain A1552

42.172

94.737

0.4
  pilC Vibrio campbellii strain DS40M4

39.141

94.737

0.371