Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   PSYTB_RS04435 Genome accession   NZ_CP042804
Coordinates   905192..906064 (-) Length   290 a.a.
NCBI ID   WP_005782691.1    Uniprot ID   -
Organism   Pseudomonas amygdali pv. tabaci str. ATCC 11528     
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 892901..904575 905192..906064 flank 617


Gene organization within MGE regions


Location: 892901..906064
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PSYTB_RS04360 (PSYTB_04365) - 892901..894556 (-) 1656 WP_005745467.1 methyl-accepting chemotaxis protein -
  PSYTB_RS04365 (PSYTB_04370) - 894587..896689 (-) 2103 WP_016981128.1 chemotaxis protein CheA -
  PSYTB_RS04370 (PSYTB_04375) - 896736..897026 (-) 291 WP_005732323.1 lipid asymmetry maintenance protein MlaB -
  PSYTB_RS04375 (PSYTB_04380) - 897050..897418 (-) 369 WP_002553206.1 response regulator -
  PSYTB_RS04380 (PSYTB_04385) - 897428..898645 (-) 1218 WP_005782675.1 methyl-accepting chemotaxis protein -
  PSYTB_RS04390 (PSYTB_04395) - 899091..900389 (-) 1299 WP_005782677.1 NAD(P)/FAD-dependent oxidoreductase -
  PSYTB_RS29825 - 900486..900722 (-) 237 WP_324606571.1 DUF3094 family protein -
  PSYTB_RS04400 (PSYTB_04405) - 900607..901140 (-) 534 WP_005782679.1 MOSC domain-containing protein -
  PSYTB_RS04405 (PSYTB_04410) - 901137..901766 (-) 630 WP_003430735.1 DUF1780 domain-containing protein -
  PSYTB_RS04410 (PSYTB_04415) - 901881..902195 (+) 315 Protein_799 hypothetical protein -
  PSYTB_RS04415 (PSYTB_04420) - 902192..903664 (+) 1473 WP_010196255.1 tetratricopeptide repeat protein -
  PSYTB_RS04420 (PSYTB_04425) - 903769..904227 (+) 459 WP_005782685.1 hypothetical protein -
  PSYTB_RS04425 (PSYTB_04430) yacG 904366..904575 (-) 210 WP_002552020.1 DNA gyrase inhibitor YacG -
  PSYTB_RS04430 (PSYTB_04435) coaE 904572..905195 (-) 624 WP_005782687.1 dephospho-CoA kinase -
  PSYTB_RS04435 (PSYTB_04440) pilD 905192..906064 (-) 873 WP_005782691.1 A24 family peptidase Machinery gene

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 32017.26 Da        Isoelectric Point: 8.5809

>NTDB_id=378651 PSYTB_RS04435 WP_005782691.1 905192..906064(-) (pilD) [Pseudomonas amygdali pv. tabaci str. ATCC 11528]
MPLLDLLASSPLAFVITCCLLGLIVGSFLNVVVYRLPKMMERDWKAQSREMLGLPAEPDQPAFNLNRPRSSCPHCAHKIR
PRENLPLISYLLLRGKCSQCKAPISMRYPMVELTCAVLSAYVAWHFGFGWQAAAMLVLSWGLLAMSLIDADHQLLPDSLV
LPLLWLGLIVNAFGLFTSLNDALWGAVAGYLALWSVFWLFKLVTGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AVLGVIMMRVRRVESGTPIPFGPYLAIAGWIALLWGGQITDSYMQFAGFR

Nucleotide


Download         Length: 873 bp        

>NTDB_id=378651 PSYTB_RS04435 WP_005782691.1 905192..906064(-) (pilD) [Pseudomonas amygdali pv. tabaci str. ATCC 11528]
ATGCCCCTCCTCGACCTCCTGGCCAGCTCACCGCTGGCCTTCGTCATTACCTGCTGCCTACTCGGCCTCATCGTCGGAAG
CTTCCTCAACGTAGTCGTCTACCGCCTCCCCAAAATGATGGAGCGCGACTGGAAAGCCCAATCCCGTGAAATGCTCGGCC
TGCCCGCCGAACCTGATCAGCCTGCCTTCAACCTGAACCGCCCCCGCTCCAGTTGCCCGCACTGCGCGCACAAGATCCGC
CCGAGGGAAAACCTGCCGCTGATCAGCTATCTGCTGCTGCGCGGTAAATGCTCACAATGCAAAGCCCCCATCAGCATGCG
CTACCCAATGGTCGAGCTGACCTGCGCAGTGTTGTCGGCCTACGTCGCCTGGCATTTCGGCTTCGGCTGGCAGGCAGCGG
CGATGCTGGTGTTGAGCTGGGGCCTGCTGGCGATGAGTCTGATCGACGCCGACCACCAGCTGTTACCTGACTCTCTGGTG
CTGCCACTGCTGTGGCTGGGCCTCATCGTCAACGCTTTCGGGCTGTTCACCTCGCTGAACGATGCGCTGTGGGGCGCGGT
GGCCGGCTATCTGGCGCTGTGGTCGGTGTTCTGGCTATTCAAACTGGTGACCGGCAAGGAAGGCATGGGTTATGGCGACT
TCAAGTTGCTGGCCATGCTTGGCGCATGGGGCGGCTGGCAGATTCTGCCGTTGACCATCCTGCTGTCATCGCTGGTGGGT
GCGGTGCTTGGGGTGATCATGATGCGCGTGCGCAGGGTTGAAAGCGGTACGCCGATCCCCTTTGGTCCTTATCTGGCCAT
TGCGGGGTGGATCGCTTTGCTCTGGGGTGGTCAAATAACCGACTCTTACATGCAGTTTGCCGGTTTCAGATGA

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

54.225

97.931

0.531
  pilD Vibrio campbellii strain DS40M4

52.297

97.586

0.51
  pilD Acinetobacter baumannii D1279779

53.285

94.483

0.503
  pilD Acinetobacter nosocomialis M2

52.92

94.483

0.5
  pilD Neisseria gonorrhoeae MS11

51.119

92.414

0.472

Multiple sequence alignment