Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   A237_RS04340 Genome accession   NZ_CP081457
Coordinates   940285..941157 (-) Length   290 a.a.
NCBI ID   WP_017700942.1    Uniprot ID   A0AAT9SKA1
Organism   Pseudomonas syringae pv. actinidifoliorum ICMP 18803     
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 922076..948714 940285..941157 within 0


Gene organization within MGE regions


Location: 922076..948714
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  A237_RS04275 (A237_004255) - 922076..922687 (+) 612 WP_017700649.1 hypothetical protein -
  A237_RS04280 (A237_004260) - 922883..924283 (+) 1401 WP_017700650.1 TolC family outer membrane protein -
  A237_RS04285 (A237_004265) - 924430..926592 (+) 2163 WP_017700651.1 type I secretion system permease/ATPase -
  A237_RS04290 (A237_004270) - 926585..928006 (+) 1422 WP_017700652.1 HlyD family type I secretion periplasmic adaptor subunit -
  A237_RS04295 (A237_004275) - 928068..929573 (+) 1506 WP_017700653.1 tetratricopeptide repeat protein -
  A237_RS04300 (A237_004280) - 929809..934365 (+) 4557 WP_264297527.1 calcium-binding protein -
  A237_RS04305 (A237_004285) - 934316..934855 (+) 540 WP_264297528.1 calcium-binding protein -
  A237_RS04310 (A237_004290) - 934806..935312 (+) 507 WP_264297529.1 calcium-binding protein -
  A237_RS04315 - 935297..936940 (+) 1644 WP_264297530.1 calcium-binding protein -
  A237_RS04320 (A237_004310) tnpB 937063..937422 (+) 360 WP_005621010.1 IS66 family insertion sequence element accessory protein TnpB -
  A237_RS04325 (A237_004315) tnpC 937440..938972 (+) 1533 WP_032607211.1 IS66 family transposase -
  A237_RS04330 (A237_004320) yacG 939459..939668 (-) 210 WP_017700940.1 DNA gyrase inhibitor YacG -
  A237_RS04335 (A237_004325) coaE 939665..940288 (-) 624 WP_017700941.1 dephospho-CoA kinase -
  A237_RS04340 (A237_004330) pilD 940285..941157 (-) 873 WP_017700942.1 A24 family peptidase Machinery gene
  A237_RS04345 (A237_004335) pilC 941159..942376 (-) 1218 WP_005614794.1 type II secretion system F family protein Machinery gene
  A237_RS04350 (A237_004340) pilB 942379..944073 (-) 1695 WP_017700943.1 type IV-A pilus assembly ATPase PilB Machinery gene
  A237_RS04355 (A237_004345) - 944299..944685 (+) 387 WP_020320879.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  A237_RS04360 (A237_004350) - 945171..946358 (+) 1188 WP_375233760.1 O-antigen ligase family protein -
  A237_RS04365 (A237_004355) - 946467..947753 (+) 1287 WP_017700945.1 polysaccharide biosynthesis C-terminal domain-containing protein -
  A237_RS28115 (A237_004360) - 947679..947858 (-) 180 WP_077528389.1 DUF1523 family protein -
  A237_RS04375 (A237_004365) - 948127..948714 (+) 588 WP_017700946.1 hypothetical protein -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31996.16 Da        Isoelectric Point: 7.6006

>NTDB_id=596442 A237_RS04340 WP_017700942.1 940285..941157(-) (pilD) [Pseudomonas syringae pv. actinidifoliorum ICMP 18803]
MPLLDLLASSPLAFVTTCCLLGLIVGSFLNVVVYRLPKMMERDWEAQSREMLGLPAEPDQPVFNLILPHSSCPHCAHKIR
PWENLPIISYVLLRGKCSQCKAPISKRYPLVELTCAVLSAYVAWHFGFGWQAAAMLVLSWGLLAMSLIDADHQLLPDSLV
LPLLWLGLIVNAFGLFTSLNDALWGAVAGYLTLWSVFWLFKLVTGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AVLGVIMMRVRRVESGTPIPFGPYLAIAGWIALLWGGQITDSYMQFAGFR

Nucleotide


Download         Length: 873 bp        

>NTDB_id=596442 A237_RS04340 WP_017700942.1 940285..941157(-) (pilD) [Pseudomonas syringae pv. actinidifoliorum ICMP 18803]
ATGCCCCTCCTCGACCTCCTGGCCAGCTCTCCCCTGGCCTTCGTAACCACATGCTGCCTACTCGGCCTCATCGTCGGAAG
CTTCCTTAACGTAGTCGTCTACCGCCTCCCAAAAATGATGGAGCGCGACTGGGAAGCGCAATCACGGGAAATGCTCGGCC
TCCCTGCCGAACCGGACCAACCCGTCTTCAACCTGATCCTGCCGCACTCAAGCTGCCCGCACTGCGCGCACAAGATCCGC
CCGTGGGAAAATCTGCCGATCATCAGTTACGTGTTGCTGCGCGGTAAATGCTCGCAATGCAAAGCCCCGATCAGCAAGCG
CTACCCATTGGTGGAGCTGACCTGCGCAGTGTTGTCGGCCTACGTCGCCTGGCACTTCGGCTTTGGCTGGCAGGCGGCTG
CGATGCTGGTGTTGAGCTGGGGGTTGCTGGCGATGAGTCTGATCGATGCCGATCATCAGCTGTTGCCTGACTCTCTGGTA
CTTCCACTGCTGTGGCTGGGCCTGATCGTTAACGCCTTTGGGCTGTTCACCTCGCTGAATGATGCGCTGTGGGGCGCAGT
GGCCGGTTATCTGACGCTGTGGTCGGTGTTCTGGCTGTTCAAGCTGGTGACGGGCAAGGAAGGCATGGGCTATGGCGACT
TCAAGTTGCTGGCCATGCTTGGCGCGTGGGGTGGCTGGCAGATTCTGCCGTTGACCATCCTGTTGTCGTCGCTGGTGGGT
GCGGTACTTGGGGTGATCATGATGCGCGTGCGCAGGGTCGAAAGCGGTACGCCGATCCCCTTTGGTCCTTATCTGGCCAT
TGCGGGGTGGATCGCTTTGCTCTGGGGTGGTCAAATAACCGACTCTTACATGCAGTTTGCCGGTTTCAGATGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)

Type IV leader peptidase family (Peptidase_A24)

(136-245)


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

52.19

94.483

0.493
  pilD Acinetobacter nosocomialis M2

51.825

94.483

0.49
  pilD Neisseria gonorrhoeae MS11

51.866

92.414

0.479