Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   LOY34_RS23070 Genome accession   NZ_CP087199
Coordinates   5008933..5010141 (+) Length   402 a.a.
NCBI ID   WP_258664055.1    Uniprot ID   -
Organism   Pseudomonas sp. B21-009     
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 4984437..5007997 5008933..5010141 flank 936


Gene organization within MGE regions


Location: 4984437..5010141
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LOY34_RS22960 (LOY34_22935) - 4984437..4984931 (+) 495 WP_195885015.1 Hcp family type VI secretion system effector -
  LOY34_RS22965 (LOY34_22940) - 4984919..4985632 (+) 714 WP_258664047.1 DUF4225 domain-containing protein -
  LOY34_RS22970 (LOY34_22945) - 4986027..4986374 (-) 348 WP_195885016.1 nucleotidyltransferase family protein -
  LOY34_RS22975 (LOY34_22950) - 4986378..4987154 (-) 777 WP_195885017.1 helix-turn-helix domain-containing protein -
  LOY34_RS22980 (LOY34_22955) - 4987249..4988124 (+) 876 WP_195885018.1 EamA family transporter -
  LOY34_RS22985 (LOY34_22960) - 4988121..4988723 (-) 603 WP_045197126.1 hypothetical protein -
  LOY34_RS22990 (LOY34_22965) - 4989189..4989416 (+) 228 WP_045197124.1 hypothetical protein -
  LOY34_RS22995 (LOY34_22970) - 4989482..4989784 (+) 303 WP_195885019.1 DUF3077 domain-containing protein -
  LOY34_RS23000 (LOY34_22975) - 4989848..4990216 (+) 369 WP_230090897.1 YcgJ family protein -
  LOY34_RS23005 (LOY34_22980) - 4990283..4990813 (-) 531 WP_258664048.1 hypothetical protein -
  LOY34_RS23010 (LOY34_22985) - 4991148..4992230 (+) 1083 WP_258664049.1 Shedu immune nuclease family protein -
  LOY34_RS23015 (LOY34_22990) - 4992905..4999387 (+) 6483 WP_258664050.1 NACHT domain-containing protein -
  LOY34_RS23020 (LOY34_22995) - 4999530..5000408 (-) 879 WP_258664051.1 hypothetical protein -
  LOY34_RS23025 (LOY34_23000) - 5000497..5003397 (-) 2901 WP_258664052.1 DUF927 domain-containing protein -
  LOY34_RS23030 (LOY34_23005) - 5003394..5003678 (-) 285 WP_100782495.1 DUF3077 domain-containing protein -
  LOY34_RS23035 (LOY34_23010) - 5003629..5003958 (-) 330 WP_258664053.1 hypothetical protein -
  LOY34_RS23040 (LOY34_23015) - 5004507..5005100 (-) 594 WP_100782493.1 hypothetical protein -
  LOY34_RS23045 (LOY34_23020) - 5005097..5005360 (-) 264 WP_100782492.1 AlpA family transcriptional regulator -
  LOY34_RS23050 (LOY34_23025) - 5005432..5006355 (-) 924 WP_100782491.1 hypothetical protein -
  LOY34_RS23055 (LOY34_23030) - 5006681..5007997 (-) 1317 WP_258664054.1 phage integrase central domain-containing protein -
  LOY34_RS23065 (LOY34_23040) - 5008305..5008715 (-) 411 WP_195885039.1 pilin -
  LOY34_RS23070 (LOY34_23045) pilC 5008933..5010141 (+) 1209 WP_258664055.1 type II secretion system F family protein Machinery gene

Sequence

Protein


Download         Length: 402 a.a.        Molecular weight: 43156.65 Da        Isoelectric Point: 10.4634

>NTDB_id=627963 LOY34_RS23070 WP_258664055.1 5008933..5010141(+) (pilC) [Pseudomonas sp. B21-009]
MTESNRMYSWQGTNAQGALISGQSAARSPALIRAQLRQRGIRPGRIASVRPPLWQWRRPPDGKALSQFSRQLATLVKAGV
ALLQALDVVAQSSTNPALASLLGAIKADIAAGSSLATALRRHPQYFDRLYCNLVDAGEQSGSLETVLAQVAALQEQRQAL
RMRLKKAMTYPVLVLLVGFGVSALLLLEVVPRFQSLFGGFGAELPAFTQQVINLSQWLGAHLGWLLITFGGACSALVWTY
RHKPGVRLWLVRVALRLPVLGSLLRHAALARFARTLSTSFAAGVPLVEALGPVAGACGNSLYEQAVHKVRDDLASGLALN
VALRASGLFPPLVVQMCAIGETAGTLDDMLARIASHYEQAIDHLLDTLTAMLEPLIVLILGLLVGSLVIAMYLPIFQLGN
VI

Nucleotide


Download         Length: 1209 bp        

>NTDB_id=627963 LOY34_RS23070 WP_258664055.1 5008933..5010141(+) (pilC) [Pseudomonas sp. B21-009]
ATGACCGAAAGCAACCGGATGTACAGCTGGCAAGGCACCAACGCCCAAGGTGCCTTGATCAGCGGCCAGAGTGCGGCGCG
CAGCCCGGCGTTGATCAGGGCGCAGTTGCGCCAGCGCGGGATTCGCCCGGGGCGTATCGCCAGTGTGCGCCCGCCGTTGT
GGCAATGGCGGCGGCCACCGGATGGCAAGGCGCTGAGCCAGTTCAGCCGCCAGCTGGCCACCTTGGTCAAGGCCGGGGTG
GCGCTGTTGCAGGCGTTGGATGTAGTCGCCCAGAGCAGCACCAACCCGGCGCTGGCCAGCCTGCTGGGGGCGATCAAGGC
CGATATCGCCGCTGGTAGCAGCCTGGCCACTGCGCTGCGCCGCCACCCGCAGTACTTCGATCGGCTGTACTGCAACCTGG
TGGACGCCGGTGAGCAGTCCGGCAGCCTGGAGACGGTGCTGGCCCAGGTGGCGGCGCTGCAGGAGCAACGCCAGGCCCTG
CGCATGCGGCTGAAAAAAGCCATGACCTATCCTGTGCTGGTGTTGCTGGTGGGCTTTGGAGTGTCGGCGTTGTTATTGCT
GGAGGTGGTGCCGCGCTTTCAGTCGTTGTTCGGCGGTTTTGGTGCCGAGCTGCCGGCGTTTACTCAACAGGTGATCAATT
TGTCGCAGTGGTTGGGCGCGCACCTTGGGTGGCTGTTGATAACCTTTGGCGGCGCTTGTAGTGCGCTGGTTTGGACTTAT
CGGCACAAGCCTGGGGTGCGTTTGTGGCTGGTGCGCGTGGCGCTGCGCTTGCCGGTGCTGGGCAGCCTGCTCCGGCACGC
CGCCCTCGCCCGCTTTGCCCGCACCCTGTCGACCTCGTTTGCCGCCGGGGTGCCGCTGGTGGAGGCGCTGGGGCCGGTTG
CCGGGGCCTGCGGCAATTCGTTGTATGAGCAGGCGGTGCACAAGGTGCGCGACGACCTTGCCAGTGGCCTGGCCTTGAAC
GTGGCACTGCGCGCCAGCGGGTTGTTCCCACCGTTGGTGGTGCAGATGTGCGCCATTGGCGAGACAGCCGGCACGCTGGA
CGATATGCTCGCCAGGATCGCCAGCCACTATGAACAGGCCATCGACCACCTGCTCGACACCCTCACGGCCATGCTCGAGC
CGTTGATCGTGCTGATCCTGGGGTTGCTGGTGGGCAGCCTGGTGATCGCCATGTACCTGCCAATCTTCCAGCTGGGCAAT
GTGATCTGA

Domains

Predicted by InterproScan.

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

(68-191)

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

(272-394)


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

48.622

99.254

0.483
  pilC Legionella pneumophila strain ERS1305867

45.477

99.005

0.45
  pilC Acinetobacter baylyi ADP1

44.724

99.005

0.443
  pilC Acinetobacter baumannii D1279779

44.332

98.756

0.438
  pilG Neisseria meningitidis 44/76-A

39.801

100

0.398
  pilC Vibrio cholerae strain A1552

39.95

99.005

0.396
  pilG Neisseria gonorrhoeae MS11

39.552

100

0.396
  pilC Vibrio campbellii strain DS40M4

39.012

100

0.393
  pilC Thermus thermophilus HB27

38.155

99.751

0.381