Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   LRK55_RS03720 Genome accession   NZ_CP088925
Coordinates   787159..788430 (+) Length   423 a.a.
NCBI ID   WP_008438585.1    Uniprot ID   -
Organism   Rhodanobacter denitrificans strain FW104-MT042     
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 764350..788977 787159..788430 within 0


Gene organization within MGE regions


Location: 764350..788977
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LRK55_RS03625 (LRK55_03625) - 764350..766356 (+) 2007 WP_008438608.1 acyltransferase family protein -
  LRK55_RS03630 (LRK55_03630) - 766569..767012 (+) 444 WP_008438606.1 pilin -
  LRK55_RS03635 (LRK55_03635) pilE 767355..767795 (+) 441 WP_008438605.1 pilin Machinery gene
  LRK55_RS03640 (LRK55_03640) - 767860..769872 (+) 2013 WP_039954252.1 hypothetical protein -
  LRK55_RS03645 (LRK55_03645) - 769869..771863 (+) 1995 WP_008438601.1 hypothetical protein -
  LRK55_RS03650 (LRK55_03650) gmd 771942..773051 (+) 1110 WP_008438600.1 GDP-mannose 4,6-dehydratase -
  LRK55_RS03655 (LRK55_03655) - 773048..774010 (+) 963 WP_008438599.1 GDP-L-fucose synthase -
  LRK55_RS03660 (LRK55_03660) - 774007..774918 (+) 912 WP_008438598.1 hypothetical protein -
  LRK55_RS03665 (LRK55_03665) - 774918..776282 (+) 1365 WP_008438597.1 polysaccharide biosynthesis protein -
  LRK55_RS03670 (LRK55_03670) - 776306..777316 (-) 1011 WP_008438596.1 GDP-mannose 4,6-dehydratase -
  LRK55_RS03675 (LRK55_03675) - 777316..778578 (-) 1263 WP_008438595.1 class I SAM-dependent methyltransferase -
  LRK55_RS03680 (LRK55_03680) - 778575..779603 (-) 1029 WP_008438594.1 glycosyltransferase family 2 protein -
  LRK55_RS03685 (LRK55_03685) - 779851..780882 (+) 1032 WP_008438593.1 glycosyltransferase -
  LRK55_RS03690 (LRK55_03690) - 780902..781636 (-) 735 WP_008438592.1 class I SAM-dependent methyltransferase -
  LRK55_RS03695 (LRK55_03695) - 781633..782886 (-) 1254 WP_008438590.1 glycosyltransferase family 4 protein -
  LRK55_RS03700 (LRK55_03700) - 782879..783733 (-) 855 WP_008438588.1 glycosyltransferase family 2 protein -
  LRK55_RS03705 (LRK55_03705) - 784024..784419 (-) 396 WP_007513922.1 type II toxin-antitoxin system VapC family toxin -
  LRK55_RS03710 (LRK55_03710) - 784416..784658 (-) 243 WP_007513924.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  LRK55_RS03715 (LRK55_03715) pilB 785292..787016 (+) 1725 WP_007513926.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LRK55_RS03720 (LRK55_03720) pilC 787159..788430 (+) 1272 WP_008438585.1 type II secretion system F family protein Machinery gene
  LRK55_RS03725 (LRK55_03725) - 788579..788977 (+) 399 WP_008438584.1 endonuclease domain-containing protein -

Sequence

Protein


Download         Length: 423 a.a.        Molecular weight: 46000.23 Da        Isoelectric Point: 9.8580

>NTDB_id=634029 LRK55_RS03720 WP_008438585.1 787159..788430(+) (pilC) [Rhodanobacter denitrificans strain FW104-MT042]
MATATATNINKARELGAQRAEVSKLTTYEWVALDKRGKRMKGDMPAKNASLVKAELRRQGMNPQTVRERAKPLFGATGST
VKPGDVAVFSRQIATMMASGVPMVQSFDIIADGQKNIRFKNILLDVKQNIEGGAALHEALARYPVQFDELYCNLVHAGET
SGVLDTVLDTVATYKERTEAIKKKIKKALFYPMMVLVVVFLVCLIMLLFVVPVFAKTFQDAGAQLPAPTQLLVSASEFMQ
SYWLLVVGVTVGGVVALVVAKKRSVKFAHFLDRMALKMPVMGNIVRNSAIARFARTLGVTFRAGVPLVEALDAVAGATGS
VVYGDAVKQMREDISVGHQLQLAMKQTNLFPNMVVQMTAIGEESGALDNMLFKVAEFYEEEVSNAVDTLSTLLEPIIMVV
LGTLVGGMVIALYLPIFKLAGTF

Nucleotide


Download         Length: 1272 bp        

>NTDB_id=634029 LRK55_RS03720 WP_008438585.1 787159..788430(+) (pilC) [Rhodanobacter denitrificans strain FW104-MT042]
ATGGCCACGGCTACCGCAACGAACATCAACAAGGCGCGCGAGCTCGGGGCCCAGCGCGCCGAAGTCAGCAAGCTGACCAC
CTACGAGTGGGTGGCGCTGGACAAGCGCGGCAAGCGCATGAAAGGCGACATGCCGGCGAAGAACGCCTCGCTGGTCAAGG
CCGAACTGCGCCGCCAGGGCATGAACCCGCAGACCGTGCGCGAGCGCGCCAAGCCGCTGTTCGGCGCCACCGGCAGCACG
GTCAAGCCGGGCGACGTGGCCGTGTTCAGCCGCCAGATCGCCACCATGATGGCCTCCGGCGTGCCGATGGTGCAGTCCTT
CGACATCATCGCCGACGGCCAGAAGAACATCCGTTTCAAGAACATCCTGCTCGACGTGAAGCAGAACATCGAGGGCGGCG
CGGCGCTGCACGAGGCGCTGGCGCGCTACCCGGTGCAGTTCGACGAGCTGTATTGCAACCTGGTGCACGCCGGCGAGACC
TCCGGCGTGCTGGATACCGTGCTGGACACCGTGGCCACCTACAAGGAGCGCACGGAAGCGATCAAGAAGAAGATCAAGAA
GGCGCTGTTCTACCCGATGATGGTGCTGGTGGTGGTGTTCCTGGTCTGCCTGATCATGCTGTTGTTCGTGGTGCCGGTGT
TCGCCAAGACCTTCCAGGATGCCGGCGCGCAGCTGCCGGCGCCGACCCAGTTGCTGGTCAGTGCCTCGGAGTTCATGCAG
AGCTACTGGCTGTTGGTGGTCGGCGTGACCGTGGGCGGCGTGGTCGCGCTGGTCGTCGCCAAGAAGCGCTCGGTGAAGTT
CGCCCACTTCCTCGACCGCATGGCGCTGAAGATGCCGGTGATGGGCAACATCGTGCGCAACTCGGCGATCGCCCGCTTCG
CCCGCACCCTGGGCGTGACCTTCCGCGCCGGCGTGCCGCTGGTCGAGGCGCTGGACGCGGTGGCCGGCGCCACCGGCAGC
GTGGTCTACGGCGATGCCGTGAAGCAGATGCGCGAGGACATCTCGGTCGGCCACCAGCTGCAGCTGGCGATGAAACAGAC
CAACCTGTTCCCGAACATGGTGGTGCAGATGACCGCGATCGGCGAAGAATCCGGCGCGCTGGACAACATGTTGTTCAAGG
TTGCCGAGTTCTACGAGGAGGAAGTCAGCAACGCCGTCGACACCCTGTCCACCCTGCTCGAACCGATCATCATGGTGGTG
CTGGGCACCCTGGTCGGCGGCATGGTGATCGCGCTGTACCTGCCGATCTTCAAGCTCGCCGGCACGTTCTGA

Domains

Predicted by InterproScan.

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

(293-415)

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

(89-212)


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 Legionella pneumophila strain ERS1305867

54.177

93.381

0.506
  pilC Pseudomonas stutzeri DSM 10701

52.141

93.853

0.489
  pilC Acinetobacter baylyi ADP1

48.768

95.981

0.468
  pilC Acinetobacter baumannii D1279779

49.118

93.853

0.461
  pilG Neisseria gonorrhoeae MS11

41.602

91.489

0.381
  pilG Neisseria meningitidis 44/76-A

40.885

90.78

0.371