Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ACDW38_RS23460 Genome accession   NZ_CP167986
Coordinates   5067672..5068544 (+) Length   290 a.a.
NCBI ID   WP_017148550.1    Uniprot ID   -
Organism   Pseudomonas aeruginosa strain 0805d0     
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 5051543..5075152 5067672..5068544 within 0


Gene organization within MGE regions


Location: 5051543..5075152
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ACDW38_RS23370 (ACDW38_23370) - 5051543..5052727 (+) 1185 WP_174214394.1 tyrosine-type recombinase/integrase -
  ACDW38_RS23375 (ACDW38_23375) - 5053044..5053340 (+) 297 WP_109721881.1 AlpA family transcriptional regulator -
  ACDW38_RS23380 (ACDW38_23380) - 5053344..5055422 (+) 2079 WP_174214395.1 AAA family ATPase -
  ACDW38_RS23385 (ACDW38_23385) - 5055869..5056387 (+) 519 WP_174214396.1 hypothetical protein -
  ACDW38_RS23390 (ACDW38_23390) - 5056380..5056625 (+) 246 WP_174214397.1 hypothetical protein -
  ACDW38_RS23395 (ACDW38_23395) - 5057275..5058000 (+) 726 WP_174214398.1 hypothetical protein -
  ACDW38_RS23400 (ACDW38_23400) - 5057993..5058274 (+) 282 WP_217438146.1 hypothetical protein -
  ACDW38_RS23405 (ACDW38_23405) - 5058497..5059006 (+) 510 WP_174214399.1 hypothetical protein -
  ACDW38_RS23410 (ACDW38_23410) - 5059009..5060121 (-) 1113 WP_174214400.1 restriction endonuclease, SacI family -
  ACDW38_RS23415 (ACDW38_23415) - 5060229..5061326 (+) 1098 WP_174214401.1 DNA cytosine methyltransferase -
  ACDW38_RS23420 (ACDW38_23420) - 5061530..5061994 (+) 465 WP_174214402.1 hypothetical protein -
  ACDW38_RS23425 (ACDW38_23425) - 5062008..5062277 (+) 270 WP_174214403.1 hypothetical protein -
  ACDW38_RS23430 (ACDW38_23430) - 5062290..5062802 (+) 513 WP_174214404.1 hypothetical protein -
  ACDW38_RS23440 (ACDW38_23440) tfpZ 5063181..5063918 (-) 738 WP_023110409.1 TfpX/TfpZ family type IV pilin accessory protein -
  ACDW38_RS23445 (ACDW38_23445) pilE 5063983..5064519 (-) 537 WP_025921208.1 pilin Machinery gene
  ACDW38_RS23450 (ACDW38_23450) pilB 5064746..5066449 (+) 1704 WP_023100230.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ACDW38_RS23455 (ACDW38_23455) - 5066453..5067669 (+) 1217 Protein_4635 type II secretion system F family protein -
  ACDW38_RS23460 (ACDW38_23460) pilD 5067672..5068544 (+) 873 WP_017148550.1 type IV prepilin peptidase/methyltransferase PilD Machinery gene
  ACDW38_RS23465 (ACDW38_23465) coaE 5068541..5069152 (+) 612 WP_003094654.1 dephospho-CoA kinase -
  ACDW38_RS23470 (ACDW38_23470) yacG 5069149..5069349 (+) 201 WP_017148551.1 DNA gyrase inhibitor YacG -
  ACDW38_RS23475 (ACDW38_23475) - 5069386..5069595 (-) 210 WP_003094660.1 hypothetical protein -
  ACDW38_RS23480 (ACDW38_23480) - 5069701..5070390 (-) 690 WP_003094662.1 energy-coupling factor ABC transporter permease -
  ACDW38_RS23485 (ACDW38_23485) - 5070387..5070857 (-) 471 WP_023103507.1 hypothetical protein -
  ACDW38_RS23490 (ACDW38_23490) - 5070854..5071279 (-) 426 WP_016562341.1 GNAT family N-acetyltransferase -
  ACDW38_RS23495 (ACDW38_23495) - 5071412..5072041 (+) 630 WP_003094668.1 DUF1780 domain-containing protein -
  ACDW38_RS23500 (ACDW38_23500) - 5072038..5072487 (+) 450 WP_003161439.1 MOSC domain-containing protein -
  ACDW38_RS23505 (ACDW38_23505) - 5072513..5072683 (+) 171 WP_003094672.1 DUF3094 family protein -
  ACDW38_RS23510 (ACDW38_23510) - 5072747..5074054 (+) 1308 WP_003112837.1 NAD(P)/FAD-dependent oxidoreductase -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31888.88 Da        Isoelectric Point: 7.7068

>NTDB_id=1040860 ACDW38_RS23460 WP_017148550.1 5067672..5068544(+) (pilD) [Pseudomonas aeruginosa strain 0805d0]
MQLTDYLASHPLAFVLCTILLGLLVGSFLNVVVHRLPKMMERNWKAEAREALGLEPEPKQATYNLVLPNSACPRCGHEIR
PWENIPLVSYLALGGKCSSCKAAIGKRYPLVELATALLSGYVAWHFGFTWQAGAMLLLTWGLLAMSLIDADHQLLPDVLV
LPLLWLGLIANHFGLFASLDDALFGAVFGYLSLWSVFWLFKLVTGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AILGVIMLRLRNAESGTPIPFGPYLAIAGWIALLWGDQITRTYLQFAGFK

Nucleotide


Download         Length: 873 bp        

>NTDB_id=1040860 ACDW38_RS23460 WP_017148550.1 5067672..5068544(+) (pilD) [Pseudomonas aeruginosa strain 0805d0]
ATGCAACTCACAGACTACCTGGCCAGCCATCCGCTGGCCTTTGTCTTGTGCACCATCCTCCTCGGCCTGCTGGTCGGCAG
CTTCCTCAACGTCGTCGTGCATCGCCTGCCGAAGATGATGGAGCGCAACTGGAAGGCCGAGGCCCGCGAAGCGCTCGGGC
TGGAGCCGGAACCCAAGCAGGCGACCTACAACCTGGTGCTGCCGAATTCGGCGTGCCCGCGCTGCGGCCACGAGATCCGC
CCCTGGGAAAACATCCCGCTGGTCAGCTACCTGGCGCTGGGCGGCAAGTGCTCGTCCTGCAAGGCCGCCATCGGCAAACG
CTACCCCCTGGTGGAACTGGCCACCGCGCTGCTTTCCGGCTACGTCGCCTGGCATTTCGGCTTCACCTGGCAGGCGGGCG
CGATGCTCCTGCTGACCTGGGGTCTGCTGGCGATGAGCCTGATCGATGCCGATCACCAACTGCTGCCGGACGTGCTGGTG
CTGCCGCTGCTCTGGCTGGGCCTGATCGCCAACCATTTCGGCCTCTTCGCCAGCCTCGACGATGCGCTGTTCGGCGCGGT
GTTCGGCTACCTGAGCCTGTGGTCGGTGTTCTGGCTGTTCAAGCTGGTGACCGGCAAGGAGGGCATGGGCTACGGCGACT
TCAAGCTGCTGGCCATGCTCGGTGCCTGGGGCGGCTGGCAGATCCTGCCGCTGACCATCCTGCTGTCGTCGCTGGTCGGG
GCGATCCTCGGGGTGATCATGCTGCGCCTGCGCAACGCCGAAAGCGGCACGCCGATCCCCTTCGGTCCCTATCTGGCTAT
TGCCGGGTGGATTGCTTTGCTCTGGGGTGATCAAATAACCCGGACCTATCTGCAATTCGCCGGATTCAAATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(137-245)

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

55.357

96.552

0.534
  pilD Vibrio campbellii strain DS40M4

53.791

95.517

0.514
  pilD Acinetobacter nosocomialis M2

51.071

96.552

0.493
  pilD Acinetobacter baumannii D1279779

51.071

96.552

0.493
  pilD Neisseria gonorrhoeae MS11

48.571

96.552

0.469

Multiple sequence alignment