Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   ABFU65_RS05035 Genome accession   NZ_CP155964
Coordinates   1194962..1196221 (-) Length   419 a.a.
NCBI ID   WP_323549480.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. raphani strain BR25     
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 1193455..1212566 1194962..1196221 within 0


Gene organization within MGE regions


Location: 1193455..1212566
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFU65_RS05025 (ABFU65_05025) coaE 1193455..1194078 (-) 624 WP_323549481.1 dephospho-CoA kinase -
  ABFU65_RS05030 (ABFU65_05030) - 1194092..1194955 (-) 864 WP_011038216.1 A24 family peptidase -
  ABFU65_RS05035 (ABFU65_05035) pilC 1194962..1196221 (-) 1260 WP_323549480.1 type II secretion system F family protein Machinery gene
  ABFU65_RS05040 (ABFU65_05040) pilA2 1196576..1196995 (+) 420 WP_323549479.1 pilin Machinery gene
  ABFU65_RS05045 (ABFU65_05045) - 1197077..1198978 (+) 1902 WP_323549478.1 hypothetical protein -
  ABFU65_RS05050 (ABFU65_05050) - 1198975..1199433 (+) 459 WP_323549477.1 GtrA family protein -
  ABFU65_RS05055 (ABFU65_05055) - 1199439..1200983 (+) 1545 WP_323552249.1 NAD(P)/FAD-dependent oxidoreductase -
  ABFU65_RS05060 (ABFU65_05060) galE 1201079..1202056 (+) 978 WP_323550507.1 UDP-glucose 4-epimerase GalE -
  ABFU65_RS05065 (ABFU65_05065) pilB 1202199..1203905 (+) 1707 WP_323550509.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFU65_RS05070 (ABFU65_05070) - 1204088..1204717 (-) 630 WP_407472217.1 toxin -
  ABFU65_RS05075 (ABFU65_05075) - 1204816..1205614 (+) 799 WP_087941972.1 IS5 family transposase -
  ABFU65_RS05080 (ABFU65_05080) - 1205676..1206038 (-) 363 WP_148263072.1 hypothetical protein -
  ABFU65_RS05085 (ABFU65_05085) pilR 1206230..1207624 (-) 1395 WP_043921909.1 sigma-54 dependent transcriptional regulator Regulator
  ABFU65_RS05090 (ABFU65_05090) - 1207833..1209443 (-) 1611 WP_014508702.1 PAS domain-containing sensor histidine kinase -
  ABFU65_RS05095 (ABFU65_05095) sucC 1209677..1210846 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ABFU65_RS05100 (ABFU65_05100) sucD 1210871..1211746 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  ABFU65_RS05105 (ABFU65_05105) - 1211850..1212260 (+) 411 WP_029628876.1 CopG family ribbon-helix-helix protein -
  ABFU65_RS05110 (ABFU65_05110) - 1212264..1212566 (+) 303 WP_323475834.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 419 a.a.        Molecular weight: 45968.45 Da        Isoelectric Point: 10.2875

>NTDB_id=1000369 ABFU65_RS05035 WP_323549480.1 1194962..1196221(-) (pilC) [Xanthomonas campestris pv. raphani strain BR25]
MSVARSAIKKQPVDRNTSMLQTFVWEGADKRGVKMKGEQTARNANMLRAELRRQGIVPSMVKQKPKPLFGAAGKKITAKD
IAFFSRQMATMMKSGVPIVSSLEIIGEGHKNPRMKKMVGQVRTDIEGGSSLYESISKHPVQFDELYRNLVRAGEGAGVLE
TVLDTVATYKENIEALKGKIKKAMFYPAMVVAVAIIVSAILLIFVVPQFEEVFKNFGAELPAFTQLLVNASRFMVSYWWL
MLVVTVGSIVGFIFAYKRSPRMQHALDRLILKVPVIGQIMHNSAIARFARTTAVTFKAGVPLVEALGIVAGATGNKVYEE
AVLRMRDDVSVGYPVNMAMKQVNLLPHMVVQMTAIGEEAGALDTMLFKVADYFEQEVNNAVDALSSLLEPLIMVFIGTIV
GGMVIGMYLPIFKLGAVVG

Nucleotide


Download         Length: 1260 bp        

>NTDB_id=1000369 ABFU65_RS05035 WP_323549480.1 1194962..1196221(-) (pilC) [Xanthomonas campestris pv. raphani strain BR25]
ATGTCAGTCGCGCGTAGCGCCATTAAGAAGCAACCGGTCGACCGGAACACCAGCATGCTGCAGACCTTCGTTTGGGAAGG
GGCTGACAAGCGTGGCGTGAAGATGAAGGGGGAGCAGACAGCCCGCAACGCCAATATGTTGCGAGCAGAGCTGCGCCGTC
AGGGCATCGTGCCCAGCATGGTGAAGCAAAAACCAAAGCCCTTGTTCGGAGCTGCCGGCAAGAAGATTACTGCCAAAGAC
ATTGCGTTCTTCAGCCGTCAGATGGCGACGATGATGAAGTCGGGCGTGCCTATTGTCAGTTCGCTGGAGATCATCGGCGA
GGGTCACAAAAATCCACGCATGAAGAAGATGGTGGGCCAGGTCAGGACTGACATTGAGGGCGGTTCGTCGCTCTACGAGT
CCATCAGCAAACATCCCGTCCAGTTTGACGAGCTCTACCGCAACCTCGTCCGCGCGGGCGAAGGTGCCGGCGTACTGGAG
ACTGTCCTAGATACGGTCGCGACGTACAAAGAAAACATTGAAGCCCTGAAGGGCAAGATCAAAAAGGCGATGTTCTACCC
TGCCATGGTGGTTGCCGTGGCAATCATCGTGAGTGCGATCTTGCTTATTTTCGTGGTCCCTCAGTTCGAAGAGGTATTCA
AGAATTTCGGCGCTGAGCTACCGGCATTCACTCAGCTGCTCGTCAACGCCTCGCGCTTCATGGTCAGCTATTGGTGGCTA
ATGCTGGTGGTGACAGTTGGATCTATCGTTGGCTTCATCTTTGCCTACAAACGTTCTCCACGGATGCAACATGCACTTGA
TCGATTGATCCTCAAGGTTCCTGTAATCGGGCAGATCATGCACAACAGTGCGATCGCACGTTTTGCACGGACTACTGCCG
TGACGTTCAAGGCTGGCGTACCTCTTGTCGAGGCACTAGGCATCGTGGCTGGCGCAACCGGTAATAAGGTTTACGAAGAA
GCGGTACTACGCATGCGGGACGATGTATCGGTTGGCTATCCGGTCAACATGGCCATGAAGCAGGTCAACCTGCTCCCTCA
TATGGTGGTGCAGATGACCGCAATCGGCGAGGAAGCAGGCGCCTTGGATACCATGTTGTTCAAGGTGGCCGACTACTTCG
AGCAGGAAGTCAACAACGCCGTGGACGCGCTCAGCAGCCTGCTTGAACCACTGATCATGGTGTTCATCGGCACCATCGTA
GGCGGCATGGTCATCGGCATGTATCTTCCGATCTTCAAACTCGGCGCAGTGGTTGGATAA

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

54.293

94.511

0.513
  pilC Legionella pneumophila strain ERS1305867

52.463

96.897

0.508
  pilC Acinetobacter baylyi ADP1

50.864

96.659

0.492
  pilC Acinetobacter baumannii D1279779

49.877

96.659

0.482
  pilG Neisseria gonorrhoeae MS11

43.108

95.227

0.411
  pilG Neisseria meningitidis 44/76-A

42.607

95.227

0.406
  pilC Vibrio cholerae strain A1552

40

95.465

0.382
  pilC Vibrio campbellii strain DS40M4

38.75

95.465

0.37
  pilC Thermus thermophilus HB27

38.75

95.465

0.37

Multiple sequence alignment