Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   LRK24_RS14965 Genome accession   NZ_CP088919
Coordinates   3245567..3246838 (+) Length   423 a.a.
NCBI ID   WP_007513928.1    Uniprot ID   -
Organism   Rhodanobacter denitrificans strain DSM-24678     
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 3222496..3247378 3245567..3246838 within 0


Gene organization within MGE regions


Location: 3222496..3247378
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LRK24_RS14865 (LRK24_14865) - 3222956..3223312 (+) 357 WP_202946748.1 GtrA family protein -
  LRK24_RS14870 (LRK24_14870) - 3223452..3224822 (+) 1371 WP_007513896.1 glycosyltransferase family 39 protein -
  LRK24_RS14875 (LRK24_14875) - 3224958..3225401 (+) 444 WP_007513899.1 pilin -
  LRK24_RS14880 (LRK24_14880) pilE 3225744..3226175 (+) 432 WP_007513901.1 pilin Machinery gene
  LRK24_RS14885 (LRK24_14885) - 3226246..3228255 (+) 2010 WP_007513903.1 hypothetical protein -
  LRK24_RS14890 (LRK24_14890) - 3228255..3230225 (+) 1971 WP_043292834.1 hypothetical protein -
  LRK24_RS14895 (LRK24_14895) - 3230264..3231385 (+) 1122 WP_007513907.1 glycosyltransferase -
  LRK24_RS14900 (LRK24_14900) - 3231378..3232304 (+) 927 WP_043292835.1 NAD-dependent epimerase/dehydratase family protein -
  LRK24_RS14905 (LRK24_14905) - 3232274..3233320 (+) 1047 WP_007513911.1 glycosyltransferase -
  LRK24_RS14910 (LRK24_14910) - 3233412..3234563 (-) 1152 WP_007513913.1 glycoside hydrolase family 99-like domain-containing protein -
  LRK24_RS14915 (LRK24_14915) - 3234563..3235816 (-) 1254 WP_007513915.1 class I SAM-dependent methyltransferase -
  LRK24_RS14920 (LRK24_14920) - 3235813..3236772 (-) 960 WP_007513916.1 GDP-mannose 4,6-dehydratase -
  LRK24_RS14925 (LRK24_14925) - 3236772..3237797 (-) 1026 WP_007513917.1 glycosyltransferase family 2 protein -
  LRK24_RS14930 (LRK24_14930) - 3237797..3238648 (-) 852 WP_007513918.1 hypothetical protein -
  LRK24_RS14935 (LRK24_14935) - 3238664..3240172 (-) 1509 WP_007513919.1 oligosaccharide flippase family protein -
  LRK24_RS14940 (LRK24_14940) gmd 3240177..3241271 (-) 1095 WP_043292836.1 GDP-mannose 4,6-dehydratase -
  LRK24_RS14945 (LRK24_14945) - 3241315..3242172 (-) 858 WP_007513921.1 glycosyltransferase family 2 protein -
  LRK24_RS14950 (LRK24_14950) - 3242464..3242859 (-) 396 WP_007513922.1 type II toxin-antitoxin system VapC family toxin -
  LRK24_RS14955 (LRK24_14955) - 3242856..3243098 (-) 243 WP_007513924.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  LRK24_RS14960 (LRK24_14960) pilB 3243698..3245422 (+) 1725 WP_007513926.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LRK24_RS14965 (LRK24_14965) pilC 3245567..3246838 (+) 1272 WP_007513928.1 type II secretion system F family protein Machinery gene
  LRK24_RS14970 (LRK24_14970) - 3246986..3247378 (+) 393 WP_007513930.1 DUF559 domain-containing protein -

Sequence

Protein


Download         Length: 423 a.a.        Molecular weight: 45988.18 Da        Isoelectric Point: 9.8580

>NTDB_id=633931 LRK24_RS14965 WP_007513928.1 3245567..3246838(+) (pilC) [Rhodanobacter denitrificans strain DSM-24678]
MATATATNINKARELGAQRAEVSKLTTYEWVALDKRGKRMKGDMPAKNASLVKAELRRQGMNPQTVRERAKPLFGATGST
IKPGDVAVFSRQIATMMASGVPMVQSFDIIADGQKNIRFKNVLLDVKQNIEGGAALHEALARYPVQFDELYCNLVHAGET
SGVLDTVLDTVATYKERTEAIKKKIKKALFYPMMVLAVVFLVCLIMLLFVVPVFAKTFQDAGAQLPAPTQLLVSASEFMQ
SYWLLVVGVTVGGVVALVVAKKRSVKFAHFLDRMALKMPVMGNIVRNSAIARFARTLGVTFRAGVPLVEALDAVAGATGS
VVYGDAVKQMREDISVGHQLQLAMKQTNLFPNMVVQMTAIGEESGSLDNMLFKVAEFYEEEVSNAVDTLSTLLEPIIMVV
LGTLVGGMVIALYLPIFKLAGTF

Nucleotide


Download         Length: 1272 bp        

>NTDB_id=633931 LRK24_RS14965 WP_007513928.1 3245567..3246838(+) (pilC) [Rhodanobacter denitrificans strain DSM-24678]
ATGGCCACGGCTACCGCAACGAACATCAACAAGGCGCGCGAGCTCGGGGCCCAGCGCGCCGAAGTCAGCAAGCTGACCAC
CTACGAGTGGGTGGCGCTGGACAAGCGCGGCAAGCGCATGAAAGGCGACATGCCGGCGAAGAACGCCTCGCTGGTCAAGG
CCGAATTGCGCCGCCAGGGCATGAACCCGCAGACCGTGCGCGAGCGTGCCAAGCCGCTGTTCGGCGCCACCGGCAGCACG
ATCAAGCCGGGCGACGTGGCCGTGTTCAGCCGCCAGATCGCCACCATGATGGCGTCGGGCGTGCCGATGGTGCAGTCCTT
CGACATCATCGCCGACGGCCAGAAGAACATCCGCTTCAAGAACGTCCTGCTCGACGTGAAGCAGAACATCGAAGGCGGTG
CGGCGCTGCACGAGGCGCTGGCGCGCTACCCGGTGCAGTTCGACGAGCTGTACTGCAACCTGGTGCATGCCGGCGAGACC
TCCGGCGTGCTGGATACCGTGCTGGACACCGTGGCGACCTACAAGGAGCGCACGGAGGCGATCAAGAAGAAGATCAAGAA
GGCGCTGTTCTACCCGATGATGGTGCTGGCCGTGGTGTTCCTGGTCTGCCTGATCATGCTGTTGTTCGTGGTGCCGGTGT
TCGCCAAGACCTTCCAGGACGCCGGCGCGCAGTTGCCGGCGCCGACCCAGTTGCTGGTCAGTGCCTCGGAGTTCATGCAG
AGCTACTGGCTGTTGGTGGTCGGCGTGACCGTGGGCGGCGTGGTCGCGCTGGTCGTCGCCAAGAAGCGCTCGGTGAAGTT
CGCCCACTTCCTCGACCGCATGGCGCTGAAGATGCCGGTGATGGGCAATATCGTGCGCAACTCGGCGATCGCCCGCTTCG
CCCGCACCCTGGGCGTGACGTTCCGCGCCGGCGTGCCGCTGGTCGAGGCACTGGACGCGGTGGCCGGCGCCACCGGCAGC
GTGGTCTACGGCGATGCCGTGAAGCAGATGCGCGAGGACATCTCGGTCGGCCACCAGCTGCAGCTGGCGATGAAACAGAC
CAACCTGTTCCCGAACATGGTGGTGCAGATGACCGCGATCGGCGAAGAATCCGGCTCGCTGGACAACATGTTGTTCAAGG
TCGCCGAGTTCTACGAGGAGGAAGTCAGCAACGCCGTCGACACCCTGTCCACGTTGCTCGAACCGATCATCATGGTGGTG
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

52.273

93.617

0.489
  pilC Acinetobacter baylyi ADP1

48.276

95.981

0.463
  pilC Acinetobacter baumannii D1279779

48.615

93.853

0.456
  pilG Neisseria gonorrhoeae MS11

42.377

91.489

0.388
  pilG Neisseria meningitidis 44/76-A

41.667

90.78

0.378