Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   QLF99_RS13705 Genome accession   NZ_CP125110
Coordinates   2961407..2962270 (+) Length   287 a.a.
NCBI ID   WP_054667255.1    Uniprot ID   A0A0S1B224
Organism   Stenotrophomonas acidaminiphila strain SPDF1     
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 2948447..2965615 2961407..2962270 within 0


Gene organization within MGE regions


Location: 2948447..2965615
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  QLF99_RS13650 (QLF99_13650) - 2948447..2950366 (-) 1920 WP_282883589.1 hypothetical protein -
  QLF99_RS13655 (QLF99_13655) - 2950491..2952074 (-) 1584 WP_282883590.1 GtrA family protein -
  QLF99_RS13660 (QLF99_13660) - 2952058..2952900 (-) 843 WP_054667241.1 class I SAM-dependent methyltransferase -
  QLF99_RS13665 (QLF99_13665) - 2952897..2953985 (-) 1089 WP_254574356.1 Gfo/Idh/MocA family oxidoreductase -
  QLF99_RS13670 (QLF99_13670) - 2953982..2955160 (-) 1179 WP_054667243.1 glycosyltransferase family 2 protein -
  QLF99_RS13675 (QLF99_13675) - 2955157..2956842 (-) 1686 WP_282883591.1 hypothetical protein -
  QLF99_RS13680 (QLF99_13680) - 2956839..2958383 (-) 1545 WP_054667246.1 NAD(P)/FAD-dependent oxidoreductase -
  QLF99_RS13685 (QLF99_13685) - 2958380..2958811 (-) 432 WP_054667248.1 GtrA family protein -
  QLF99_RS13690 (QLF99_13690) - 2958900..2959235 (-) 336 WP_082394110.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  QLF99_RS17875 - 2959370..2959732 (-) 363 WP_182212758.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  QLF99_RS13700 (QLF99_13700) - 2960140..2961399 (+) 1260 WP_054667253.1 type II secretion system F family protein -
  QLF99_RS13705 (QLF99_13705) pilD 2961407..2962270 (+) 864 WP_054667255.1 A24 family peptidase Machinery gene
  QLF99_RS13710 (QLF99_13710) coaE 2962317..2962940 (+) 624 WP_054667256.1 dephospho-CoA kinase -
  QLF99_RS13715 (QLF99_13715) - 2962971..2964308 (-) 1338 WP_054667259.1 HAMP domain-containing sensor histidine kinase -
  QLF99_RS13720 (QLF99_13720) - 2964301..2964978 (-) 678 WP_054667261.1 response regulator transcription factor -
  QLF99_RS13725 (QLF99_13725) - 2965145..2965615 (-) 471 WP_282883592.1 hypothetical protein -

Sequence

Protein


Download         Length: 287 a.a.        Molecular weight: 31856.83 Da        Isoelectric Point: 8.4746

>NTDB_id=830010 QLF99_RS13705 WP_054667255.1 2961407..2962270(+) (pilD) [Stenotrophomonas acidaminiphila strain SPDF1]
MAFLDQHPGIGYPAAAGLGLLIGSFLNVVILRLPRRMEWQWKRDAREILGEPDIYEPPPPGVVVEPSHCPHCKHKLSWYE
NIPLFSWLLQRGRCRHCQAPISIQYPLVELLTAVLVLASVWQFGFGWQGFGAIVLTCFLIALSGIDLRTQLLPDQLTLPL
MWLGLIGSMDNLYMPTKPALIGAAVGYLSLWTVWWLFKQITGKEGMGHGDFKLLAALGAWCGLKGILPIILLSSLVGAIV
GSVWLYARGRDRATPIPFGPYLAIAGWLVFMWGDPMIAAYRQWAGLA

Nucleotide


Download         Length: 864 bp        

>NTDB_id=830010 QLF99_RS13705 WP_054667255.1 2961407..2962270(+) (pilD) [Stenotrophomonas acidaminiphila strain SPDF1]
ATGGCATTTCTCGACCAGCATCCCGGCATCGGCTACCCGGCCGCTGCCGGATTGGGGTTGCTGATCGGCAGCTTCCTCAA
CGTGGTCATCCTGCGCCTGCCCCGGCGCATGGAGTGGCAATGGAAGCGCGATGCGCGCGAGATCCTCGGTGAGCCGGACA
TCTACGAGCCGCCCCCGCCGGGCGTGGTGGTGGAGCCGTCGCATTGCCCGCACTGCAAGCACAAGCTGAGCTGGTACGAG
AACATCCCGCTGTTCAGCTGGCTGCTGCAGCGGGGACGCTGCCGCCATTGCCAGGCGCCGATCTCCATCCAGTACCCGCT
GGTTGAACTGCTGACCGCCGTACTGGTGCTGGCCAGCGTGTGGCAGTTCGGCTTCGGCTGGCAGGGCTTCGGTGCGATCG
TCCTGACCTGCTTCCTGATCGCGCTGTCCGGCATCGACCTGCGCACCCAGCTGCTGCCCGACCAGCTGACCCTGCCGCTG
ATGTGGCTGGGACTGATCGGCAGCATGGACAACCTGTACATGCCCACCAAACCTGCACTGATCGGTGCCGCGGTGGGCTA
CCTGTCGCTATGGACCGTGTGGTGGCTGTTCAAGCAGATCACCGGCAAGGAAGGCATGGGCCACGGCGATTTCAAGCTGC
TGGCGGCGCTGGGCGCCTGGTGCGGCCTGAAGGGCATCCTGCCGATCATCCTGCTGTCCTCGCTGGTGGGCGCCATCGTC
GGCTCGGTCTGGCTGTACGCACGCGGACGCGACCGCGCCACGCCCATCCCGTTCGGCCCCTACCTGGCCATCGCCGGCTG
GCTGGTCTTCATGTGGGGTGACCCGATGATCGCCGCTTACCGGCAGTGGGCCGGCTTGGCGTGA

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
  AlphaFold DB A0A0S1B224

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 nosocomialis M2

49.822

97.909

0.488
  pilD Acinetobacter baumannii D1279779

49.11

97.909

0.481
  pilD Vibrio cholerae strain A1552

48.921

96.864

0.474
  pilD Vibrio campbellii strain DS40M4

47.703

98.606

0.47
  pilD Neisseria gonorrhoeae MS11

45.775

98.955

0.453