Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   L2Y01_RS03450 Genome accession   NZ_CP091147
Coordinates   719457..720329 (+) Length   290 a.a.
NCBI ID   WP_024420998.1    Uniprot ID   -
Organism   Pseudomonas avellanae strain NCPPB 4222     
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)
IScluster/Tn 720978..723967 719457..720329 flank 649


Gene organization within MGE regions


Location: 719457..723967
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  L2Y01_RS03450 (L2Y01_03450) pilD 719457..720329 (+) 873 WP_024420998.1 A24 family peptidase Machinery gene
  L2Y01_RS03455 (L2Y01_03455) coaE 720326..720943 (+) 618 WP_005614790.1 dephospho-CoA kinase -
  L2Y01_RS03460 (L2Y01_03460) - 720978..721994 (+) 1017 WP_005614760.1 IS30-like element ISPsy38 family transposase -
  L2Y01_RS03465 (L2Y01_03465) yacG 722049..722258 (+) 210 WP_003381207.1 DNA gyrase inhibitor YacG -
  L2Y01_RS03470 (L2Y01_03470) - 722469..722765 (-) 297 WP_249741631.1 hypothetical protein -
  L2Y01_RS03475 (L2Y01_03475) - 722805..723967 (+) 1163 WP_099265290.1 IS3 family transposase -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 32027.27 Da        Isoelectric Point: 8.1553

>NTDB_id=648032 L2Y01_RS03450 WP_024420998.1 719457..720329(+) (pilD) [Pseudomonas avellanae strain NCPPB 4222]
MPLLDLLASSPLAFVTTCCLLGLIVGSFLNVVVYRLPKMMERDWKAQSREMLGLPAEPDQPVFNLILPHSSCPHCAHKIR
PWENLPIISYLLLRGKCSQCKAPISKRYPVVELTCAVLSAYVAWHFGFGWQAAAMLVLSWGLLAMSLIDADHQLLPDSLV
LPLLWLGLIVNAFGLFTSLNDALWGAVAGYLTLWSVFWLFKLMTGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AVLGVIMMRVRRVESGTPIPFGPYLAIAGWIALLWGGQITDSYMQFAGFR

Nucleotide


Download         Length: 873 bp        

>NTDB_id=648032 L2Y01_RS03450 WP_024420998.1 719457..720329(+) (pilD) [Pseudomonas avellanae strain NCPPB 4222]
ATGCCCCTCCTCGACCTCCTGGCCAGCTCCCCCCTGGCCTTCGTCACCACATGCTGCCTGCTCGGCCTAATCGTCGGAAG
CTTCCTCAACGTAGTCGTCTACCGCCTCCCAAAAATGATGGAGCGCGACTGGAAAGCGCAATCACGGGAAATGCTCGGCC
TCCCTGCCGAACCGGACCAACCCGTCTTCAACCTGATCCTGCCGCACTCCAGTTGCCCGCACTGCGCGCACAAGATCCGC
CCATGGGAAAATCTGCCGATCATCAGTTACCTGTTGCTGCGCGGCAAATGCTCGCAATGCAAAGCACCGATCAGCAAGCG
CTACCCAGTGGTGGAGCTGACCTGCGCAGTGTTATCGGCCTACGTCGCCTGGCACTTCGGTTTCGGCTGGCAGGCGGCTG
CGATGCTGGTGTTGAGTTGGGGTTTGCTGGCGATGAGCCTGATCGATGCCGATCATCAGCTGTTGCCTGACTCTCTGGTG
CTGCCACTGCTGTGGCTGGGCCTGATCGTTAACGCCTTTGGGCTGTTCACCTCGCTGAATGATGCGCTGTGGGGTGCGGT
GGCCGGTTATCTGACGCTGTGGTCAGTGTTCTGGCTGTTCAAGTTGATGACGGGCAAGGAAGGCATGGGCTATGGCGACT
TCAAATTGCTGGCCATGCTTGGCGCGTGGGGTGGCTGGCAGATTCTGCCGTTGACCATTCTGTTGTCGTCGCTGGTGGGC
GCGGTGCTTGGGGTGATCATGATGCGCGTGCGCAGGGTCGAAAGCGGTACGCCGATCCCCTTTGGTCCTTATCTGGCCAT
TGCGGGGTGGATCGCTTTGCTCTGGGGTGGTCAAATAACCGACTCTTATATGCAGTTTGCCGGTTTCAGATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(136-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)


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
  pilD Vibrio cholerae strain A1552

54.064

97.586

0.528
  pilD Vibrio campbellii strain DS40M4

51.59

97.586

0.503
  pilD Acinetobacter baumannii D1279779

52.555

94.483

0.497
  pilD Acinetobacter nosocomialis M2

52.19

94.483

0.493
  pilD Neisseria gonorrhoeae MS11

51.866

92.414

0.479