Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   LRK54_RS03950 Genome accession   NZ_CP088922
Coordinates   833075..834346 (+) Length   423 a.a.
NCBI ID   WP_027490752.1    Uniprot ID   -
Organism   Rhodanobacter denitrificans strain FW104-10B01     
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 817384..834893 833075..834346 within 0


Gene organization within MGE regions


Location: 817384..834893
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LRK54_RS03885 (LRK54_03885) - 817384..819396 (+) 2013 WP_027490744.1 hypothetical protein -
  LRK54_RS03890 (LRK54_03890) - 819396..821360 (+) 1965 WP_027490745.1 hypothetical protein -
  LRK54_RS03895 (LRK54_03895) - 821760..823007 (+) 1248 WP_027490746.1 lipopolysaccharide biosynthesis protein -
  LRK54_RS03900 (LRK54_03900) - 823504..824361 (+) 858 WP_196802027.1 class I SAM-dependent methyltransferase -
  LRK54_RS03905 (LRK54_03905) - 824358..825365 (+) 1008 WP_196802028.1 glycosyltransferase -
  LRK54_RS03910 (LRK54_03910) - 825425..826324 (-) 900 WP_196802029.1 glycosyltransferase -
  LRK54_RS03915 (LRK54_03915) - 826308..827258 (-) 951 WP_027490747.1 glycosyltransferase family 2 protein -
  LRK54_RS03920 (LRK54_03920) - 827255..827551 (-) 297 WP_027490748.1 hypothetical protein -
  LRK54_RS03925 (LRK54_03925) - 827548..828801 (-) 1254 WP_027490749.1 glycosyltransferase family 4 protein -
  LRK54_RS03930 (LRK54_03930) - 828794..829648 (-) 855 WP_027490750.1 glycosyltransferase family 2 protein -
  LRK54_RS03935 (LRK54_03935) - 829940..830335 (-) 396 WP_007513922.1 type II toxin-antitoxin system VapC family toxin -
  LRK54_RS03940 (LRK54_03940) - 830332..830574 (-) 243 WP_007513924.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  LRK54_RS03945 (LRK54_03945) pilB 831208..832932 (+) 1725 WP_027490751.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LRK54_RS03950 (LRK54_03950) pilC 833075..834346 (+) 1272 WP_027490752.1 type II secretion system F family protein Machinery gene
  LRK54_RS03955 (LRK54_03955) - 834495..834893 (+) 399 WP_008438584.1 endonuclease domain-containing protein -

Sequence

Protein


Download         Length: 423 a.a.        Molecular weight: 46016.23 Da        Isoelectric Point: 9.8580

>NTDB_id=633985 LRK54_RS03950 WP_027490752.1 833075..834346(+) (pilC) [Rhodanobacter denitrificans strain FW104-10B01]
MATATATNINKARELGAQRAEVSKLTTYEWVALDKRGKRMKGDMPAKNASLVKAELRRQGMNPQTVRERAKPLFGATGST
VKPGDVAVFSRQIATMMASGVPMVQSFDIIADGQKNIRFKNILLDVKQNIEGGAALHEALARYPVQFDELYCNLVHAGET
SGVLDTVLDTVATYKERTEAIKKKIKKALFYPMMVLVVVFLVCLIMLLFVVPVFAKTFQDAGAQLPAPTQLLVSASEFMQ
SYWLLVVGVTVGGVVALVVAKKRSVKFAHFLDRMALKMPVMGNIVRNSAIARFARTLGVTFRAGVPLVEALDAVAGATGS
VVYGDAVKQMREDISVGHQLQLAMKQTNLFPNMVVQMTAIGEESGSLDNMLFKVAEFYEEEVSNAVDTLSTLLEPIIMVV
LGTLVGGMVIALYLPIFKLAGTF

Nucleotide


Download         Length: 1272 bp        

>NTDB_id=633985 LRK54_RS03950 WP_027490752.1 833075..834346(+) (pilC) [Rhodanobacter denitrificans strain FW104-10B01]
ATGGCCACGGCTACCGCAACGAACATCAACAAGGCGCGCGAGCTCGGGGCCCAGCGCGCCGAAGTCAGCAAGCTGACCAC
CTACGAGTGGGTGGCGCTGGACAAGCGCGGCAAGCGCATGAAAGGCGACATGCCGGCGAAGAACGCCTCGCTGGTCAAGG
CCGAACTGCGCCGCCAGGGCATGAACCCGCAGACCGTGCGCGAGCGCGCCAAGCCGCTGTTCGGCGCCACCGGCAGCACG
GTCAAGCCGGGCGACGTGGCCGTGTTCAGCCGCCAGATCGCCACCATGATGGCCTCCGGCGTGCCGATGGTGCAGTCCTT
CGACATCATCGCCGACGGCCAGAAGAACATCCGTTTCAAGAACATCCTGCTCGACGTGAAGCAGAACATCGAGGGCGGCG
CGGCGCTGCACGAGGCGCTGGCGCGCTACCCGGTGCAGTTCGACGAGCTGTATTGCAACCTGGTGCACGCCGGCGAGACC
TCCGGCGTGCTGGATACCGTGCTGGACACCGTGGCCACCTACAAGGAGCGCACGGAAGCGATCAAGAAGAAGATCAAGAA
GGCGCTGTTCTACCCGATGATGGTGCTGGTGGTGGTGTTCCTGGTCTGCCTGATCATGCTGTTGTTCGTGGTGCCGGTGT
TCGCCAAGACCTTCCAGGATGCCGGCGCGCAGCTGCCGGCGCCGACCCAGTTGCTGGTCAGTGCCTCGGAGTTCATGCAG
AGCTACTGGCTGTTGGTGGTCGGCGTGACCGTGGGCGGCGTGGTCGCGCTGGTCGTCGCCAAGAAGCGCTCGGTGAAGTT
CGCCCACTTCCTCGACCGCATGGCGCTGAAGATGCCGGTGATGGGCAACATCGTGCGCAACTCGGCGATCGCCCGCTTCG
CCCGCACCCTGGGCGTGACGTTCCGCGCCGGCGTGCCGCTGGTCGAGGCGCTGGACGCGGTGGCCGGCGCCACCGGCAGC
GTGGTCTACGGCGATGCCGTGAAGCAGATGCGCGAGGACATCTCGGTCGGCCACCAGCTGCAGCTGGCGATGAAACAGAC
CAACCTGTTCCCGAACATGGTGGTGCAGATGACCGCGATCGGCGAAGAATCCGGCTCGCTGGACAACATGTTGTTCAAGG
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

53.924

93.381

0.504
  pilC Pseudomonas stutzeri DSM 10701

51.889

93.853

0.487
  pilC Acinetobacter baylyi ADP1

48.522

95.981

0.466
  pilC Acinetobacter baumannii D1279779

48.866

93.853

0.459
  pilG Neisseria gonorrhoeae MS11

41.86

91.489

0.383
  pilG Neisseria meningitidis 44/76-A

41.146

90.78

0.374