Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   QQA12_RS12300 Genome accession   NZ_CP128405
Coordinates   2723236..2724099 (+) Length   287 a.a.
NCBI ID   WP_054667255.1    Uniprot ID   A0A0S1B224
Organism   Stenotrophomonas sp. 17(2023)     
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 2706889..2727401 2723236..2724099 within 0


Gene organization within MGE regions


Location: 2706889..2727401
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  QQA12_RS12220 - 2706889..2708022 (+) 1134 WP_226049446.1 glycosyltransferase family 4 protein -
  QQA12_RS12225 - 2708183..2709259 (-) 1077 WP_233324880.1 glycosyltransferase family 4 protein -
  QQA12_RS12230 - 2709256..2710254 (-) 999 WP_226049448.1 hypothetical protein -
  QQA12_RS12235 - 2710251..2711372 (-) 1122 WP_226049449.1 DegT/DnrJ/EryC1/StrS family aminotransferase -
  QQA12_RS12240 - 2711374..2712357 (-) 984 WP_226049450.1 NAD-dependent epimerase/dehydratase family protein -
  QQA12_RS12245 - 2712354..2713046 (-) 693 WP_226049451.1 methyltransferase domain-containing protein -
  QQA12_RS12250 - 2713052..2713858 (-) 807 WP_226049452.1 methyltransferase, TIGR04325 family -
  QQA12_RS12255 - 2713877..2714599 (-) 723 WP_226049453.1 hypothetical protein -
  QQA12_RS12260 - 2714596..2715264 (-) 669 WP_226049454.1 class I SAM-dependent methyltransferase -
  QQA12_RS12265 - 2715261..2716622 (-) 1362 WP_226049455.1 flippase -
  QQA12_RS12270 - 2716582..2717511 (-) 930 WP_226049456.1 NAD-dependent epimerase/dehydratase family protein -
  QQA12_RS12275 gmd 2717517..2718635 (-) 1119 WP_226049457.1 GDP-mannose 4,6-dehydratase -
  QQA12_RS12280 - 2718640..2720565 (-) 1926 WP_226049458.1 hypothetical protein -
  QQA12_RS12285 - 2720676..2721002 (-) 327 WP_289211189.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  QQA12_RS12290 - 2721464..2721556 (-) 93 Protein_2390 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  QQA12_RS12295 pilC 2721969..2723228 (+) 1260 WP_226049459.1 type II secretion system F family protein Machinery gene
  QQA12_RS12300 pilD 2723236..2724099 (+) 864 WP_054667255.1 A24 family peptidase Machinery gene
  QQA12_RS12305 coaE 2724146..2724769 (+) 624 WP_182212757.1 dephospho-CoA kinase -
  QQA12_RS12310 - 2724800..2726137 (-) 1338 WP_226049460.1 HAMP domain-containing sensor histidine kinase -
  QQA12_RS12315 - 2726130..2726807 (-) 678 WP_054667261.1 response regulator transcription factor -
  QQA12_RS12320 - 2726937..2727401 (-) 465 WP_226049461.1 hypothetical protein -

Sequence

Protein


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

>NTDB_id=847283 QQA12_RS12300 WP_054667255.1 2723236..2724099(+) (pilD) [Stenotrophomonas sp. 17(2023)]
MAFLDQHPGIGYPAAAGLGLLIGSFLNVVILRLPRRMEWQWKRDAREILGEPDIYEPPPPGVVVEPSHCPHCKHKLSWYE
NIPLFSWLLQRGRCRHCQAPISIQYPLVELLTAVLVLASVWQFGFGWQGFGAIVLTCFLIALSGIDLRTQLLPDQLTLPL
MWLGLIGSMDNLYMPTKPALIGAAVGYLSLWTVWWLFKQITGKEGMGHGDFKLLAALGAWCGLKGILPIILLSSLVGAIV
GSVWLYARGRDRATPIPFGPYLAIAGWLVFMWGDPMIAAYRQWAGLA

Nucleotide


Download         Length: 864 bp        

>NTDB_id=847283 QQA12_RS12300 WP_054667255.1 2723236..2724099(+) (pilD) [Stenotrophomonas sp. 17(2023)]
ATGGCATTTCTCGACCAGCATCCCGGCATCGGCTACCCGGCCGCTGCCGGATTGGGGTTGCTGATCGGCAGCTTCCTCAA
CGTTGTGATCCTGCGCCTGCCCCGGCGCATGGAGTGGCAATGGAAGCGCGATGCGCGCGAGATCCTCGGTGAGCCGGACA
TCTACGAGCCCCCCCCGCCGGGCGTGGTGGTGGAGCCGTCGCATTGCCCGCACTGCAAGCACAAGCTGAGCTGGTACGAG
AACATCCCGCTGTTCAGCTGGCTGCTGCAGCGGGGACGCTGCCGCCATTGCCAGGCGCCGATCTCCATCCAGTACCCGCT
GGTTGAACTGCTGACCGCCGTACTGGTGCTGGCCAGCGTCTGGCAGTTCGGCTTCGGCTGGCAGGGCTTCGGTGCGATCG
TGCTGACCTGCTTCCTGATCGCACTGTCCGGCATCGACCTGCGCACCCAGCTGCTGCCCGACCAGCTGACCCTGCCACTG
ATGTGGCTGGGCCTGATCGGCAGCATGGACAACCTGTACATGCCCACCAAACCTGCACTGATCGGTGCCGCGGTGGGCTA
CCTGTCGCTATGGACCGTGTGGTGGCTGTTCAAGCAGATCACAGGCAAGGAAGGCATGGGCCACGGCGATTTCAAGCTGC
TGGCGGCGCTGGGCGCCTGGTGCGGACTGAAGGGCATCCTGCCGATCATCCTGCTGTCCTCGCTGGTGGGCGCCATCGTC
GGCTCGGTCTGGCTGTACGCACGCGGACGCGACCGCGCCACGCCCATCCCGTTCGGCCCCTACCTGGCCATCGCCGGCTG
GCTGGTCTTCATGTGGGGTGACCCGATGATCGCCGCTTACCGGCAGTGGGCCGGCCTGGCGTGA

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