Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ACN0NO_RS14835 Genome accession   NZ_CP183298
Coordinates   3232487..3233350 (+) Length   287 a.a.
NCBI ID   WP_068853817.1    Uniprot ID   A0AAP6GZC8
Organism   Stenotrophomonas rhizophila strain SJ-3     
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 3210350..3239910 3232487..3233350 within 0


Gene organization within MGE regions


Location: 3210350..3239910
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ACN0NO_RS14770 (ACN0NO_14770) - 3210350..3210898 (+) 549 WP_419403255.1 SymE family type I addiction module toxin -
  ACN0NO_RS14775 (ACN0NO_14775) - 3211022..3211504 (-) 483 WP_419403256.1 hypothetical protein -
  ACN0NO_RS14780 (ACN0NO_14780) - 3211712..3212074 (-) 363 WP_419403257.1 hypothetical protein -
  ACN0NO_RS14785 (ACN0NO_14785) - 3212270..3212962 (-) 693 WP_419403258.1 hypothetical protein -
  ACN0NO_RS14790 (ACN0NO_14790) - 3213664..3213843 (-) 180 WP_419403259.1 hypothetical protein -
  ACN0NO_RS14795 (ACN0NO_14795) - 3214162..3219000 (-) 4839 WP_419403260.1 RHS repeat-associated core domain-containing protein -
  ACN0NO_RS14800 (ACN0NO_14800) - 3219401..3219844 (-) 444 WP_419403261.1 hypothetical protein -
  ACN0NO_RS14805 (ACN0NO_14805) - 3219867..3224531 (-) 4665 WP_419403262.1 RHS repeat-associated core domain-containing protein -
  ACN0NO_RS14810 (ACN0NO_14810) - 3224849..3227896 (-) 3048 WP_419403263.1 spermine synthase -
  ACN0NO_RS14815 (ACN0NO_14815) pilB 3228172..3229899 (-) 1728 WP_095363637.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ACN0NO_RS14820 (ACN0NO_14820) pilA 3229953..3230360 (-) 408 WP_419403264.1 pilin Machinery gene
  ACN0NO_RS14825 (ACN0NO_14825) pilA 3230460..3230867 (-) 408 WP_095363635.1 pilin Machinery gene
  ACN0NO_RS14830 (ACN0NO_14830) pilC 3231224..3232480 (+) 1257 WP_419403265.1 type II secretion system F family protein Machinery gene
  ACN0NO_RS14835 (ACN0NO_14835) pilD 3232487..3233350 (+) 864 WP_068853817.1 prepilin peptidase Machinery gene
  ACN0NO_RS14840 (ACN0NO_14840) coaE 3233358..3233966 (+) 609 WP_419403266.1 dephospho-CoA kinase -
  ACN0NO_RS14845 (ACN0NO_14845) - 3234056..3235420 (-) 1365 WP_095363631.1 sensor histidine kinase -
  ACN0NO_RS14850 (ACN0NO_14850) - 3235383..3236060 (-) 678 WP_017356179.1 response regulator transcription factor -
  ACN0NO_RS14855 (ACN0NO_14855) - 3236068..3236538 (-) 471 WP_095363630.1 hypothetical protein -
  ACN0NO_RS14860 (ACN0NO_14860) rimK 3236771..3237676 (-) 906 WP_249833010.1 30S ribosomal protein S6--L-glutamate ligase -
  ACN0NO_RS14865 (ACN0NO_14865) - 3237895..3238674 (+) 780 WP_095363628.1 histidine phosphatase family protein -
  ACN0NO_RS14870 (ACN0NO_14870) - 3238676..3239548 (+) 873 WP_093533699.1 NAD(P)H-hydrate dehydratase -
  ACN0NO_RS14875 (ACN0NO_14875) - 3239551..3239910 (-) 360 WP_210130949.1 nuclear transport factor 2 family protein -

Sequence

Protein


Download         Length: 287 a.a.        Molecular weight: 31733.82 Da        Isoelectric Point: 8.4749

>NTDB_id=1105157 ACN0NO_RS14835 WP_068853817.1 3232487..3233350(+) (pilD) [Stenotrophomonas rhizophila strain SJ-3]
MAFLDQHPGLGYPAAAALGLLIGSFLNVVILRLPKRLEWQWKRDAREVLELPDIYEPPPPGIVVEPSHCPHCKHKLSWYE
NIPLFSWLVLGGKCRHCHAPISIQYPLVELLTGLLVVASVWQFGFGWQGFGAIVLSCFLVALSGIDLRTQLLPDQLTLPL
MWLGLIGSIDNLYMPAKPALLGAIAGYLLLWSVWWLFKQITGKEGIGHGDFKLLAALGAWCGLKGILPIILLSSVLGAII
GSIWLYSRGRDRATPIPFGPYLALAGWIVFMWGEPLINAYLRVSGLR

Nucleotide


Download         Length: 864 bp        

>NTDB_id=1105157 ACN0NO_RS14835 WP_068853817.1 3232487..3233350(+) (pilD) [Stenotrophomonas rhizophila strain SJ-3]
ATGGCATTTCTCGACCAGCATCCCGGCCTCGGCTATCCGGCCGCGGCCGCACTGGGGTTGCTGATTGGCAGCTTCCTCAA
TGTGGTGATCCTGCGCCTGCCCAAGCGGCTGGAGTGGCAGTGGAAGCGCGACGCCCGCGAGGTGCTCGAGCTTCCGGACA
TCTACGAACCACCCCCGCCCGGGATCGTGGTCGAGCCGTCGCACTGCCCGCACTGCAAGCACAAGCTGTCCTGGTACGAG
AACATTCCGCTGTTCAGCTGGCTGGTCCTGGGCGGCAAGTGCCGCCACTGCCATGCGCCGATCTCCATCCAGTACCCGCT
GGTCGAGCTGTTGACCGGCCTGCTGGTGGTGGCCAGCGTCTGGCAGTTCGGCTTCGGCTGGCAGGGCTTTGGCGCCATCG
TGCTGAGCTGCTTCCTGGTGGCCTTGTCCGGTATCGACCTGCGCACCCAGCTGCTACCGGACCAGTTGACCCTGCCGCTG
ATGTGGCTGGGGCTGATAGGCAGCATCGACAACCTGTACATGCCGGCCAAGCCCGCCCTGCTGGGCGCCATTGCCGGCTA
CTTGCTGCTGTGGTCGGTGTGGTGGCTGTTCAAGCAGATCACCGGCAAGGAAGGCATTGGTCACGGCGATTTCAAGCTGC
TGGCCGCGCTGGGCGCCTGGTGTGGGTTGAAGGGCATCCTGCCGATCATCCTGCTCTCGTCGGTGCTTGGGGCGATCATC
GGTTCGATCTGGCTGTACTCGCGCGGACGCGACCGGGCCACGCCGATTCCGTTTGGGCCCTACCTGGCCCTGGCGGGCTG
GATCGTGTTCATGTGGGGCGAGCCGTTGATCAACGCGTATCTGCGGGTGTCCGGCCTGCGCTGA

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

48.264

100

0.484
  pilD Acinetobacter nosocomialis M2

48.41

98.606

0.477
  pilD Vibrio campbellii strain DS40M4

46.479

98.955

0.46
  pilD Vibrio cholerae strain A1552

47.292

96.516

0.456
  pilD Neisseria gonorrhoeae MS11

44.043

96.516

0.425

Multiple sequence alignment