Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   AAG092_RS07485 Genome accession   NZ_CP154874
Coordinates   1542685..1543557 (+) Length   290 a.a.
NCBI ID   WP_373389178.1    Uniprot ID   -
Organism   Pseudomonas alcaligenes strain Med1     
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 1536269..1545789 1542685..1543557 within 0


Gene organization within MGE regions


Location: 1536269..1545789
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AAG092_RS07450 (AAG092_07400) - 1536269..1537162 (-) 894 WP_373389177.1 ABC transporter ATP-binding protein -
  AAG092_RS07455 (AAG092_07405) - 1537159..1537995 (-) 837 WP_110680826.1 hypothetical protein -
  AAG092_RS07460 (AAG092_07410) - 1537992..1538789 (-) 798 WP_110680825.1 ABC transporter permease subunit -
  AAG092_RS07465 (AAG092_07415) - 1538861..1539301 (-) 441 WP_110680824.1 hypothetical protein -
  AAG092_RS07470 (AAG092_07420) pilA 1539321..1539503 (-) 183 WP_110680823.1 type IV pilin protein Machinery gene
  AAG092_RS07475 (AAG092_07425) pilB 1539749..1541455 (+) 1707 WP_373389568.1 type IV-A pilus assembly ATPase PilB Machinery gene
  AAG092_RS07480 (AAG092_07430) pilC 1541462..1542685 (+) 1224 WP_110680822.1 type II secretion system F family protein Machinery gene
  AAG092_RS07485 (AAG092_07435) pilD 1542685..1543557 (+) 873 WP_373389178.1 A24 family peptidase Machinery gene
  AAG092_RS07490 (AAG092_07440) coaE 1543554..1544165 (+) 612 WP_373389179.1 dephospho-CoA kinase -
  AAG092_RS07495 (AAG092_07445) yacG 1544162..1544356 (+) 195 WP_110680819.1 DNA gyrase inhibitor YacG -
  AAG092_RS07500 (AAG092_07450) - 1544360..1544575 (-) 216 WP_373389180.1 hypothetical protein -
  AAG092_RS07505 (AAG092_07455) - 1544681..1545367 (-) 687 WP_373389181.1 energy-coupling factor ABC transporter permease -
  AAG092_RS07510 (AAG092_07460) - 1545364..1545789 (-) 426 WP_373389182.1 GNAT family N-acetyltransferase -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31820.73 Da        Isoelectric Point: 6.9209

>NTDB_id=994321 AAG092_RS07485 WP_373389178.1 1542685..1543557(+) (pilD) [Pseudomonas alcaligenes strain Med1]
MSLPSFLAGNLPAFVLSVTLLGLIIGSFLNVVIYRLPVMMQRDWRQQAREILELPEEPAQGTFNLLLPNSCCPHCGHQIR
AWENIPLLSYLALRGKCAGCKAPISPRYPLVELACGLLSGYVAFHYGFGWQAAGVLVLTWGLLAMSLIDCDHQLLPDSLV
LPLLWLGLIANHFGLFASLEDALWGAIGGYLSLWSVYWLFKLVTGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AVLGVMLLRLRNQETSTPIPFGPYLAIAGWIALLWGDQITGTYLQFAGFK

Nucleotide


Download         Length: 873 bp        

>NTDB_id=994321 AAG092_RS07485 WP_373389178.1 1542685..1543557(+) (pilD) [Pseudomonas alcaligenes strain Med1]
ATGTCGCTACCTTCCTTCCTGGCCGGCAATCTGCCGGCCTTTGTTTTATCCGTCACCCTGCTCGGCCTGATCATCGGCAG
CTTCCTCAACGTGGTGATCTATCGCCTGCCGGTGATGATGCAGCGCGATTGGCGCCAGCAGGCGCGCGAGATCCTGGAAC
TGCCGGAAGAGCCGGCGCAGGGCACCTTCAACCTGCTCCTGCCGAACTCCTGCTGCCCCCACTGCGGCCACCAGATCCGC
GCCTGGGAGAACATCCCGCTGCTCAGCTACCTGGCACTGCGCGGCAAGTGCGCAGGCTGCAAGGCGCCGATTAGCCCGCG
CTACCCGCTGGTCGAGCTGGCCTGCGGGCTGCTGTCCGGCTATGTCGCCTTCCACTACGGTTTCGGCTGGCAGGCGGCCG
GGGTGCTGGTGCTGACCTGGGGCCTGTTGGCGATGAGCCTGATCGACTGCGATCACCAGCTGCTGCCGGACTCCCTGGTG
CTGCCGCTGCTCTGGCTGGGGCTGATCGCCAACCACTTCGGCCTGTTCGCCAGCCTGGAAGACGCCCTGTGGGGTGCCAT
CGGCGGTTATCTGAGCCTGTGGTCGGTGTACTGGCTGTTCAAGCTGGTGACCGGCAAGGAAGGCATGGGCTATGGCGACT
TCAAGCTGCTGGCCATGCTCGGCGCCTGGGGGGGCTGGCAGATTCTGCCGCTGACCATCCTGCTGTCGTCGCTGGTCGGC
GCCGTGCTCGGGGTGATGCTGCTGCGCCTGCGCAACCAGGAGACCAGCACGCCCATCCCCTTCGGCCCCTACCTGGCCAT
CGCCGGCTGGATCGCATTGCTCTGGGGTGATCAAATAACCGGGACCTATCTGCAGTTCGCCGGTTTCAAATGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)

Type IV leader peptidase family (Peptidase_A24)

(136-245)


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

56.569

94.483

0.534
  pilD Acinetobacter nosocomialis M2

53.901

97.241

0.524
  pilD Acinetobacter baumannii D1279779

53.546

97.241

0.521
  pilD Vibrio campbellii strain DS40M4

54.945

94.138

0.517
  pilD Neisseria gonorrhoeae MS11

51.724

90

0.466

Multiple sequence alignment