Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   LOY63_RS04355 Genome accession   NZ_CP087202
Coordinates   967255..968124 (-) Length   289 a.a.
NCBI ID   WP_265085287.1    Uniprot ID   -
Organism   Pseudomonas asplenii strain B21-058     
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 950539..985783 967255..968124 within 0


Gene organization within MGE regions


Location: 950539..985783
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LOY63_RS04260 (LOY63_04260) - 950539..951633 (+) 1095 WP_010451855.1 glycosyltransferase family 1 protein -
  LOY63_RS04265 (LOY63_04265) - 951638..952597 (+) 960 WP_265085276.1 GDP-mannose 4,6-dehydratase -
  LOY63_RS04270 (LOY63_04270) gmd 952629..953753 (+) 1125 WP_265085277.1 GDP-mannose 4,6-dehydratase -
  LOY63_RS04275 (LOY63_04275) - 953755..954732 (+) 978 WP_265085278.1 GDP-L-fucose synthase -
  LOY63_RS04280 - 954875..955366 (+) 492 WP_010451863.1 DapH/DapD/GlmU-related protein -
  LOY63_RS04285 (LOY63_04285) - 955363..956547 (+) 1185 WP_010451865.1 glycosyltransferase -
  LOY63_RS04290 (LOY63_04290) - 956544..957710 (+) 1167 WP_265085279.1 glycosyltransferase family 4 protein -
  LOY63_RS04295 (LOY63_04295) - 957707..958831 (+) 1125 WP_265085280.1 glycosyltransferase -
  LOY63_RS04300 (LOY63_04300) - 958832..960241 (+) 1410 WP_265085281.1 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase -
  LOY63_RS04305 (LOY63_04305) - 960251..961018 (+) 768 WP_265085282.1 glycosyltransferase family 2 protein -
  LOY63_RS04310 (LOY63_04310) - 961018..961977 (+) 960 WP_265085283.1 SDR family oxidoreductase -
  LOY63_RS04315 (LOY63_04315) - 962073..962894 (+) 822 WP_080579433.1 class I SAM-dependent methyltransferase -
  LOY63_RS04320 (LOY63_04320) - 962972..964279 (-) 1308 WP_090202196.1 NAD(P)/FAD-dependent oxidoreductase -
  LOY63_RS04325 (LOY63_04325) - 964343..964516 (-) 174 WP_265085284.1 DUF3094 domain-containing protein -
  LOY63_RS04330 (LOY63_04330) - 964690..965319 (-) 630 WP_010451875.1 DUF1780 domain-containing protein -
  LOY63_RS04335 (LOY63_04335) - 965439..966137 (+) 699 WP_265085285.1 energy-coupling factor ABC transporter permease -
  LOY63_RS04340 (LOY63_04340) - 966205..966420 (+) 216 WP_010451878.1 hypothetical protein -
  LOY63_RS04345 (LOY63_04345) yacG 966432..966635 (-) 204 WP_010451880.1 DNA gyrase inhibitor YacG -
  LOY63_RS04350 (LOY63_04350) coaE 966632..967255 (-) 624 WP_265085286.1 dephospho-CoA kinase -
  LOY63_RS04355 (LOY63_04355) pilD 967255..968124 (-) 870 WP_265085287.1 A24 family peptidase Machinery gene
  LOY63_RS04360 (LOY63_04360) pilC 968128..969345 (-) 1218 WP_265085288.1 type II secretion system F family protein Machinery gene
  LOY63_RS04365 (LOY63_04365) pilB 969349..971049 (-) 1701 WP_265085289.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LOY63_RS04370 (LOY63_04370) pilA2 971274..971672 (+) 399 WP_265085290.1 prepilin-type N-terminal cleavage/methylation domain-containing protein Machinery gene
  LOY63_RS04375 (LOY63_04375) - 971793..973439 (+) 1647 WP_265085291.1 tetratricopeptide repeat protein -
  LOY63_RS04380 (LOY63_04380) - 973848..974897 (+) 1050 WP_265085292.1 O-antigen ligase -
  LOY63_RS04390 (LOY63_04390) - 975423..976379 (-) 957 WP_265085293.1 hypothetical protein -
  LOY63_RS04395 (LOY63_04395) - 976421..977605 (-) 1185 WP_265085294.1 amidohydrolase family protein -
  LOY63_RS04400 (LOY63_04400) - 977624..978643 (-) 1020 WP_265085295.1 TauD/TfdA family dioxygenase -
  LOY63_RS04405 (LOY63_04405) - 978796..979998 (-) 1203 WP_265085296.1 MFS transporter -
  LOY63_RS04410 (LOY63_04410) asnB 980059..981909 (-) 1851 WP_265085297.1 asparagine synthase (glutamine-hydrolyzing) -
  LOY63_RS04415 (LOY63_04415) - 981932..982999 (-) 1068 WP_265085298.1 Gfo/Idh/MocA family oxidoreductase -
  LOY63_RS04420 (LOY63_04420) - 982996..983502 (-) 507 WP_265085299.1 GNAT family N-acetyltransferase -
  LOY63_RS04425 (LOY63_04425) hemA 983499..984731 (-) 1233 WP_265085300.1 5-aminolevulinate synthase -
  LOY63_RS04430 (LOY63_04430) - 984878..985783 (+) 906 WP_265085301.1 helix-turn-helix transcriptional regulator -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 31879.97 Da        Isoelectric Point: 8.4892

>NTDB_id=628028 LOY63_RS04355 WP_265085287.1 967255..968124(-) (pilD) [Pseudomonas asplenii strain B21-058]
MPLPDFLASYPLAFVFCALILGLIVGSFLNVVVWRLPKMLERDWRAQAHDVLGLPPPEPTSTYNLLLPHSHCPHCNHRIR
ARENLPLLSYALLRGRCSSCKAPISKRYPLTELACGLLSAFIAWHFGFGWPAGLMLVLTWGLLAMSLIDADHQILPDVLV
LPLLWLGLIANHFAMFTSLNDALWGAVAGYLSLWSVYWVFKLLTGKEGMGHGDFKLLAMLGAWGGWQILPLTILLSSLVG
AILGLILLRLRNAQTSTPIPFGPYLAIAGWIALLWGGQITASYLQFAGF

Nucleotide


Download         Length: 870 bp        

>NTDB_id=628028 LOY63_RS04355 WP_265085287.1 967255..968124(-) (pilD) [Pseudomonas asplenii strain B21-058]
ATGCCCCTACCCGATTTCCTGGCCAGCTACCCGCTGGCCTTTGTTTTTTGCGCACTCATTCTCGGCCTGATCGTCGGCAG
CTTCCTCAACGTCGTCGTCTGGCGACTGCCGAAAATGCTCGAGCGCGACTGGCGCGCCCAGGCCCACGATGTACTCGGCC
TGCCGCCCCCCGAACCCACTTCGACCTATAACCTGCTGCTGCCGCATTCGCATTGTCCGCACTGCAACCATCGCATCCGA
GCCAGGGAAAACCTGCCACTGCTCAGTTACGCCCTGCTACGCGGCAGATGCTCAAGCTGCAAGGCCCCGATCAGCAAGCG
CTACCCGCTGACCGAACTGGCCTGCGGCCTGCTCTCGGCATTTATTGCCTGGCACTTCGGCTTCGGCTGGCCTGCCGGCT
TGATGCTGGTGCTGACCTGGGGGCTGCTGGCCATGAGCCTGATCGATGCCGACCACCAGATACTCCCCGACGTCCTGGTA
CTGCCCCTGCTCTGGCTGGGCCTGATCGCCAACCACTTCGCGATGTTCACCTCACTGAACGATGCGCTGTGGGGCGCCGT
CGCCGGTTATCTGAGCCTGTGGTCGGTGTATTGGGTATTCAAGCTGTTGACCGGCAAGGAAGGCATGGGCCATGGCGACT
TCAAGCTGCTGGCGATGCTCGGCGCCTGGGGCGGCTGGCAAATACTGCCGCTGACCATCCTGCTGTCGTCGCTGGTAGGC
GCGATACTCGGGCTGATTCTGCTGCGCCTGCGTAACGCCCAGACCTCGACGCCGATCCCCTTTGGCCCTTATCTGGCGAT
TGCCGGCTGGATTGCATTGCTCTGGGGTGGTCAAATAACCGCCTCCTATCTGCAATTTGCCGGCTTCTAA

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

57.5

96.886

0.557
  pilD Vibrio campbellii strain DS40M4

54.035

98.616

0.533
  pilD Acinetobacter baumannii D1279779

49.645

97.578

0.484
  pilD Acinetobacter nosocomialis M2

49.645

97.578

0.484
  pilD Neisseria gonorrhoeae MS11

50.196

88.235

0.443