Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   JH283_RS05560 Genome accession   NZ_CP066921
Coordinates   1333209..1334471 (-) Length   420 a.a.
NCBI ID   WP_104570928.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. raphani strain 5055     
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 1322467..1346618 1333209..1334471 within 0


Gene organization within MGE regions


Location: 1322467..1346618
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JH283_RS05505 (JH283_05475) - 1322964..1323194 (-) 231 WP_181920809.1 hypothetical protein -
  JH283_RS05510 (JH283_05480) - 1323258..1323404 (+) 147 WP_076054137.1 hypothetical protein -
  JH283_RS05515 (JH283_05485) - 1323588..1323983 (+) 396 WP_042594933.1 hypothetical protein -
  JH283_RS05520 (JH283_05490) - 1324074..1324466 (+) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  JH283_RS05525 (JH283_05495) glgX 1325000..1327129 (-) 2130 WP_274299339.1 glycogen debranching protein GlgX -
  JH283_RS05530 (JH283_05500) rimK 1327625..1328500 (+) 876 WP_076054142.1 30S ribosomal protein S6--L-glutamate ligase -
  JH283_RS05535 (JH283_05505) - 1329150..1329827 (+) 678 WP_003490678.1 response regulator transcription factor -
  JH283_RS05540 (JH283_05510) - 1329820..1331154 (+) 1335 WP_019237347.1 HAMP domain-containing sensor histidine kinase -
  JH283_RS05545 (JH283_05515) - 1331253..1331523 (-) 271 Protein_1075 SymE family type I addiction module toxin -
  JH283_RS05550 (JH283_05520) coaE 1331702..1332325 (-) 624 WP_225042504.1 dephospho-CoA kinase -
  JH283_RS05555 (JH283_05525) - 1332339..1333202 (-) 864 WP_011038216.1 A24 family peptidase -
  JH283_RS05560 (JH283_05530) pilC 1333209..1334471 (-) 1263 WP_104570928.1 type II secretion system F family protein Machinery gene
  JH283_RS05565 (JH283_05535) pilA/pilAI 1334822..1335220 (+) 399 WP_104570927.1 pilin Machinery gene
  JH283_RS05570 (JH283_05540) - 1335321..1335743 (+) 423 WP_104570926.1 pilin -
  JH283_RS05575 (JH283_05545) - 1335802..1337622 (+) 1821 WP_147308815.1 hypothetical protein -
  JH283_RS05580 (JH283_05550) - 1337746..1338504 (+) 759 WP_274299340.1 class I SAM-dependent methyltransferase -
  JH283_RS05585 (JH283_05555) - 1339001..1339687 (+) 687 WP_258872788.1 glycosyltransferase family 9 protein -
  JH283_RS05590 (JH283_05560) - 1339690..1340532 (-) 843 WP_147308817.1 glycosyltransferase -
  JH283_RS05595 (JH283_05565) - 1340526..1341698 (-) 1173 WP_181920810.1 glycosyltransferase -
  JH283_RS05600 (JH283_05570) - 1341683..1342546 (-) 864 WP_116921534.1 glycosyltransferase -
  JH283_RS05605 (JH283_05575) - 1342596..1343447 (-) 852 WP_108133901.1 glycosyltransferase family 2 protein -
  JH283_RS05610 (JH283_05580) pilB 1343603..1345336 (+) 1734 WP_274299341.1 type IV-A pilus assembly ATPase PilB Machinery gene
  JH283_RS05615 (JH283_05585) - 1345519..1346256 (-) 738 WP_274299342.1 zeta toxin family protein -
  JH283_RS05620 (JH283_05590) - 1346256..1346612 (-) 357 WP_139328384.1 hypothetical protein -

Sequence

Protein


Download         Length: 420 a.a.        Molecular weight: 45799.15 Da        Isoelectric Point: 10.2311

>NTDB_id=523176 JH283_RS05560 WP_104570928.1 1333209..1334471(-) (pilC) [Xanthomonas campestris pv. raphani strain 5055]
MSAVRSTTKNKPASISAEQQMSPFVWEGTDKRGVKMKGEQVARNANMLRAELRRQGITPSVVKAKPKPLFGAAGKKITPK
EIAFFSRQMATMMKSGVPIVGSLEIIGNGHKNPRMKQMVGQIRTDIEGGSSLHEAVSKHPVQFDELYRNLIKAGEGAGVL
ETVLDTIASYKENLEALKGKIKKALFYPAMVVAVALLVSSILLIWVVPQFEDVFKGFGAELPAFTQLIVNASRFMVSYWW
LMLLVIVGSLVGFIFAYKRSLAMQHGMDRLVLKVPIIGQIMHNSSIARFARTTAVTFKAGVPLVEALGIVAGATGNSVYE
KAVLRMREDVSVGYPVNVSMKQVNLFPHMVIQMTAIGEEAGALDAMLFKVAEYYEQEVNNAVDALSSLIEPLIMVFIGTV
VGGMVIGMYLPIFKLASVVG

Nucleotide


Download         Length: 1263 bp        

>NTDB_id=523176 JH283_RS05560 WP_104570928.1 1333209..1334471(-) (pilC) [Xanthomonas campestris pv. raphani strain 5055]
ATGTCGGCAGTCCGCAGCACCACCAAAAACAAACCGGCGAGCATCAGCGCCGAACAGCAGATGAGTCCGTTCGTCTGGGA
GGGAACAGACAAGCGCGGTGTGAAGATGAAAGGTGAACAGGTCGCCCGCAACGCCAATATGTTGCGTGCGGAACTCCGCC
GGCAGGGCATTACGCCCAGCGTTGTTAAGGCAAAGCCTAAGCCACTGTTCGGGGCGGCAGGCAAGAAGATCACGCCGAAG
GAAATTGCGTTCTTCAGCCGTCAGATGGCCACTATGATGAAGTCGGGCGTCCCGATTGTCGGGTCGCTGGAGATCATCGG
CAATGGTCACAAAAACCCGCGCATGAAGCAGATGGTCGGGCAGATCCGTACCGACATCGAGGGCGGCTCTTCGCTGCACG
AAGCGGTAAGCAAGCATCCGGTGCAGTTCGACGAGCTGTACCGCAACCTGATCAAGGCGGGCGAAGGCGCTGGTGTGCTG
GAAACCGTCCTGGATACTATCGCCTCATACAAAGAGAACCTGGAAGCCCTTAAGGGCAAAATCAAGAAGGCCCTGTTCTA
CCCTGCCATGGTCGTGGCAGTTGCCCTGCTGGTCAGCTCGATCCTGTTGATCTGGGTTGTTCCGCAGTTCGAGGATGTGT
TCAAGGGATTTGGCGCGGAACTGCCGGCATTCACCCAACTGATCGTCAATGCGTCCAGATTCATGGTCTCGTATTGGTGG
CTGATGCTGCTTGTGATCGTCGGCTCGCTTGTGGGCTTCATCTTTGCCTACAAGCGATCACTTGCAATGCAGCATGGCAT
GGATCGGTTGGTACTCAAGGTACCCATCATCGGCCAGATCATGCACAACAGCTCGATTGCGCGTTTTGCGCGCACTACCG
CGGTGACCTTCAAGGCAGGCGTGCCGCTGGTCGAAGCACTGGGCATCGTCGCTGGCGCCACCGGCAACTCGGTGTACGAG
AAAGCAGTATTGCGCATGCGCGAGGATGTGTCGGTGGGCTATCCGGTCAACGTGTCGATGAAACAGGTCAACCTGTTTCC
GCATATGGTGATCCAGATGACGGCGATCGGCGAGGAGGCGGGCGCATTGGACGCCATGCTGTTCAAAGTTGCCGAATACT
ACGAGCAGGAAGTGAACAATGCGGTGGACGCACTGAGCAGCCTCATCGAACCCCTGATCATGGTGTTCATTGGTACAGTA
GTCGGCGGCATGGTCATCGGCATGTACCTGCCCATCTTCAAGCTCGCTTCGGTAGTTGGATAA

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 Acinetobacter baylyi ADP1

52.488

95.714

0.502
  pilC Legionella pneumophila strain ERS1305867

51.095

97.857

0.5
  pilC Pseudomonas stutzeri DSM 10701

52.513

94.762

0.498
  pilC Acinetobacter baumannii D1279779

50.369

96.905

0.488
  pilG Neisseria gonorrhoeae MS11

42.857

98.333

0.421
  pilG Neisseria meningitidis 44/76-A

42.271

98.571

0.417
  pilC Vibrio cholerae strain A1552

41.562

94.524

0.393
  pilC Vibrio campbellii strain DS40M4

39.9

95.476

0.381