Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   HIV01_RS09820 Genome accession   NZ_CP071517
Coordinates   2101913..2102776 (+) Length   287 a.a.
NCBI ID   WP_200606766.1    Uniprot ID   -
Organism   Lysobacter arenosi strain R7     
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 2090962..2104331 2101913..2102776 within 0


Gene organization within MGE regions


Location: 2090962..2104331
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  HIV01_RS09775 (HIV01_009775) - 2090962..2091363 (+) 402 WP_200606753.1 pilin -
  HIV01_RS09780 (HIV01_009780) - 2091439..2093343 (+) 1905 WP_200606754.1 hypothetical protein -
  HIV01_RS09785 (HIV01_009785) - 2093370..2094218 (+) 849 WP_200606755.1 hypothetical protein -
  HIV01_RS09790 (HIV01_009790) - 2094220..2095518 (+) 1299 WP_207526915.1 oligosaccharide flippase family protein -
  HIV01_RS09795 (HIV01_009795) - 2095555..2096619 (-) 1065 WP_200606757.1 glycosyltransferase family 4 protein -
  HIV01_RS09800 (HIV01_009800) - 2096623..2097711 (-) 1089 WP_200606758.1 UDP-N-acetylglucosamine 2-epimerase -
  HIV01_RS09805 (HIV01_009805) - 2097708..2098580 (-) 873 WP_200606760.1 glycosyltransferase family 2 protein -
  HIV01_RS09810 (HIV01_009810) pilB 2098753..2100477 (+) 1725 WP_200606762.1 type IV-A pilus assembly ATPase PilB Machinery gene
  HIV01_RS09815 (HIV01_009815) pilC 2100619..2101875 (+) 1257 WP_200606764.1 type II secretion system F family protein Machinery gene
  HIV01_RS09820 (HIV01_009820) pilD 2101913..2102776 (+) 864 WP_200606766.1 A24 family peptidase Machinery gene
  HIV01_RS09825 (HIV01_009825) - 2102805..2103554 (-) 750 WP_200606767.1 class I SAM-dependent methyltransferase -
  HIV01_RS09830 (HIV01_009830) coaE 2103708..2104331 (+) 624 WP_200606768.1 dephospho-CoA kinase -

Sequence

Protein


Download         Length: 287 a.a.        Molecular weight: 31882.83 Da        Isoelectric Point: 9.1775

>NTDB_id=545898 HIV01_RS09820 WP_200606766.1 2101913..2102776(+) (pilD) [Lysobacter arenosi strain R7]
MAFLDQNPAIGFPLAAGLGLLVGSFLNVVILRLPKRLEWQWRRDSREVLGEPETYDPPPPGIVIERSHCPHCKHQLSWYE
NIPVFSYLALRGRCRSCKTPISPQYPLVELLTMLLVVACVWRFGFGWQGFGAIVFTCFLIVLSGIDLRTQLLPDQLTLPL
MWLGLIAASDNLYFPAKPALLGAVAGYLSLWTVWWLFKQLTGKEGMGHGDFKLLAAIGAWTGLKGILPTILLSSLVGAII
GSIWLAMKGRDRATPIPFGPYLAIAGWIAFFWGEQIVGTYMRVSGLR

Nucleotide


Download         Length: 864 bp        

>NTDB_id=545898 HIV01_RS09820 WP_200606766.1 2101913..2102776(+) (pilD) [Lysobacter arenosi strain R7]
ATGGCATTCCTAGATCAGAACCCCGCCATCGGTTTTCCGCTGGCGGCCGGGCTCGGCCTGTTGGTCGGCAGCTTCCTCAA
CGTGGTGATCCTGCGGCTGCCCAAGCGGCTGGAGTGGCAGTGGCGGCGTGACAGCCGCGAGGTCCTCGGCGAGCCGGAGA
CCTACGATCCGCCACCGCCAGGCATCGTGATCGAGAGATCGCACTGCCCGCATTGCAAGCACCAGCTGTCCTGGTACGAG
AACATTCCGGTGTTCAGCTACCTGGCGCTGCGCGGCCGTTGCCGCAGCTGCAAGACGCCGATCTCGCCGCAGTACCCGCT
GGTCGAGTTGCTGACCATGCTGCTGGTGGTCGCCTGCGTCTGGCGTTTCGGCTTCGGCTGGCAGGGCTTCGGTGCAATCG
TCTTCACCTGCTTCCTGATCGTGCTGTCGGGCATCGACCTGCGCACGCAGCTATTGCCCGACCAGCTGACATTGCCGTTG
ATGTGGCTGGGGTTGATAGCCGCTTCGGACAATCTCTATTTCCCCGCCAAGCCGGCCCTGCTCGGCGCGGTTGCGGGCTA
CCTGAGCCTTTGGACCGTCTGGTGGCTGTTCAAGCAGCTCACCGGCAAGGAAGGCATGGGCCACGGCGACTTCAAGCTGC
TGGCCGCCATTGGTGCCTGGACCGGCCTCAAGGGCATCCTGCCGACCATCCTGCTCTCATCGCTGGTTGGCGCGATCATC
GGCTCGATCTGGCTGGCGATGAAGGGGCGCGATCGCGCCACGCCGATTCCGTTCGGCCCCTACCTGGCCATTGCCGGCTG
GATCGCCTTCTTCTGGGGCGAGCAGATCGTCGGGACCTACATGCGGGTTTCAGGCCTCCGCTAG

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(133-241)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(18-123)


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 Acinetobacter baumannii D1279779

47.917

100

0.481
  pilD Vibrio cholerae strain A1552

49.818

95.819

0.477
  pilD Vibrio campbellii strain DS40M4

48.057

98.606

0.474
  pilD Acinetobacter nosocomialis M2

47.163

98.258

0.463
  pilD Neisseria gonorrhoeae MS11

47.925

92.334

0.443