Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ACN429_RS04890 Genome accession   NZ_CP183397
Coordinates   1052788..1053660 (+) Length   290 a.a.
NCBI ID   WP_197851792.1    Uniprot ID   -
Organism   Pseudomonas oryzihabitans strain CCSM P719     
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 1033016..1054462 1052788..1053660 within 0


Gene organization within MGE regions


Location: 1033016..1054462
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ACN429_RS04810 (ACN429_04810) - 1033584..1034381 (+) 798 WP_278894072.1 PilW family protein -
  ACN429_RS04815 (ACN429_04815) - 1034378..1034992 (+) 615 WP_278894074.1 pilus assembly PilX family protein -
  ACN429_RS04820 (ACN429_04820) - 1034989..1038918 (+) 3930 WP_244950633.1 pilus assembly protein -
  ACN429_RS04825 (ACN429_04825) cyoE 1038989..1039876 (-) 888 WP_260982922.1 heme o synthase -
  ACN429_RS04830 (ACN429_04830) cyoD 1039888..1040226 (-) 339 WP_007160921.1 cytochrome o ubiquinol oxidase subunit IV -
  ACN429_RS04835 (ACN429_04835) - 1040226..1040840 (-) 615 WP_027600197.1 cytochrome o ubiquinol oxidase subunit III -
  ACN429_RS04840 (ACN429_04840) cyoB 1040845..1042833 (-) 1989 WP_007160923.1 cytochrome o ubiquinol oxidase subunit I -
  ACN429_RS04845 (ACN429_04845) cyoA 1042837..1043760 (-) 924 WP_007160924.1 ubiquinol oxidase subunit II -
  ACN429_RS04855 (ACN429_04855) - 1044533..1045531 (+) 999 WP_377709506.1 SDR family oxidoreductase -
  ACN429_RS04860 (ACN429_04860) - 1045593..1046522 (-) 930 WP_084222132.1 glycosyltransferase -
  ACN429_RS04865 (ACN429_04865) - 1046491..1047384 (-) 894 WP_084222133.1 glycosyltransferase family 2 protein -
  ACN429_RS04870 (ACN429_04870) - 1047386..1049005 (-) 1620 WP_377709503.1 O-antigen ligase family protein -
  ACN429_RS04875 (ACN429_04875) pilE 1048983..1049453 (-) 471 WP_027600199.1 pilin Machinery gene
  ACN429_RS04880 (ACN429_04880) pilB 1049666..1051360 (+) 1695 WP_377709501.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ACN429_RS04885 (ACN429_04885) pilC 1051571..1052788 (+) 1218 WP_027600839.1 type II secretion system F family protein Machinery gene
  ACN429_RS04890 (ACN429_04890) pilD 1052788..1053660 (+) 873 WP_197851792.1 prepilin peptidase Machinery gene
  ACN429_RS04895 (ACN429_04895) coaE 1053657..1054268 (+) 612 WP_377709498.1 dephospho-CoA kinase -
  ACN429_RS04900 (ACN429_04900) yacG 1054265..1054462 (+) 198 WP_007160931.1 DNA gyrase inhibitor YacG -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31554.58 Da        Isoelectric Point: 8.4838

>NTDB_id=1105533 ACN429_RS04890 WP_197851792.1 1052788..1053660(+) (pilD) [Pseudomonas oryzihabitans strain CCSM P719]
MALLEFLAGAPLAATLCALVLGLLVGSFLNVVVYRLPVMLRRAWQAEAREVLELPAEPAGAPFNLARPASRCSHCQRGVR
PWENVPVLSYLLLRGRCKGCQATISLRYPLVELACGLLSAWVIWHLGVTWQGGAFLLLTWGLLAASLIDADHQLLPDVIV
LPLLWLGLIVNQFGLFTNLGDAVWGAVAGYLSLWLVFQLFRLVTGKEGMGYGDFKLLALLGAWGGWQILPLTILLSSLVG
AILGVITLRLRRAESSTPLPFGPYLAVAGWIALLWGDQITGLYLNFAGFR

Nucleotide


Download         Length: 873 bp        

>NTDB_id=1105533 ACN429_RS04890 WP_197851792.1 1052788..1053660(+) (pilD) [Pseudomonas oryzihabitans strain CCSM P719]
ATGGCGCTGTTGGAGTTTCTGGCCGGCGCTCCGCTGGCCGCAACGCTGTGCGCGCTGGTCCTGGGGCTGCTGGTGGGCAG
CTTTCTCAATGTGGTGGTCTATCGCCTGCCGGTGATGCTGAGGCGGGCTTGGCAGGCGGAGGCGCGTGAAGTACTGGAGC
TGCCGGCCGAGCCGGCAGGCGCCCCCTTCAACCTGGCGCGACCTGCTTCCCGCTGCTCCCACTGCCAGCGCGGCGTAAGG
CCCTGGGAAAACGTGCCGGTGCTGAGTTATCTGCTCCTGCGCGGGCGTTGCAAGGGCTGCCAGGCAACCATCAGCCTGCG
TTATCCGCTGGTGGAGCTGGCCTGTGGACTGCTGTCGGCCTGGGTCATCTGGCACCTGGGCGTGACCTGGCAGGGCGGGG
CCTTCCTGTTGCTGACCTGGGGCTTGCTTGCGGCCAGTCTGATCGATGCCGATCACCAACTGTTGCCGGACGTCATCGTC
CTGCCGCTGCTGTGGCTGGGGCTGATCGTCAACCAGTTCGGCCTGTTCACCAATCTGGGTGATGCCGTCTGGGGCGCGGT
GGCGGGGTATCTGAGTCTTTGGCTGGTATTTCAACTGTTCCGTCTGGTGACCGGCAAGGAAGGCATGGGCTATGGCGACT
TCAAGCTGCTGGCGCTGCTCGGCGCCTGGGGTGGTTGGCAGATCCTGCCATTGACCATCCTGCTGTCGTCGCTGGTGGGC
GCTATTCTGGGCGTCATCACCCTGCGGCTGCGGCGGGCGGAAAGCAGCACGCCCTTGCCCTTCGGTCCCTATCTCGCCGT
GGCGGGGTGGATTGCCTTGCTCTGGGGTGATCAAATAACCGGCCTGTACCTGAACTTCGCCGGATTCCGATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(137-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-125)


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

49.648

97.931

0.486
  pilD Acinetobacter baumannii D1279779

51.311

92.069

0.472
  pilD Vibrio campbellii strain DS40M4

48.239

97.931

0.472
  pilD Acinetobacter nosocomialis M2

50.562

92.069

0.466
  pilD Neisseria gonorrhoeae MS11

49.815

93.448

0.466

Multiple sequence alignment