Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   PHA56_RS20725 Genome accession   NZ_CP116214
Coordinates   4375721..4376563 (-) Length   280 a.a.
NCBI ID   WP_119834446.1    Uniprot ID   A0AB35Q1H5
Organism   Klebsiella michiganensis strain 2563     
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 4376625..4393239 4375721..4376563 flank 62


Gene organization within MGE regions


Location: 4375721..4393239
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PHA56_RS20725 (PHA56_20725) pilD 4375721..4376563 (-) 843 WP_119834446.1 prepilin peptidase Machinery gene
  PHA56_RS20730 (PHA56_20730) - 4376625..4377365 (-) 741 WP_119834447.1 type II secretion system protein N -
  PHA56_RS20735 (PHA56_20735) gspM 4377355..4377849 (-) 495 WP_014228304.1 type II secretion system protein GspM -
  PHA56_RS20740 (PHA56_20740) gspL 4377836..4379041 (-) 1206 WP_119834448.1 type II secretion system protein GspL -
  PHA56_RS20745 (PHA56_20745) gspK 4379041..4380027 (-) 987 WP_042944535.1 type II secretion system minor pseudopilin GspK -
  PHA56_RS20750 (PHA56_20750) gspJ 4380024..4380623 (-) 600 WP_014228301.1 type II secretion system minor pseudopilin GspJ -
  PHA56_RS20755 (PHA56_20755) gspI 4380620..4380985 (-) 366 WP_119834449.1 type II secretion system minor pseudopilin GspI -
  PHA56_RS20760 (PHA56_20760) gspH 4380982..4381533 (-) 552 WP_119834450.1 type II secretion system minor pseudopilin GspH -
  PHA56_RS20765 (PHA56_20765) gspG 4381533..4381961 (-) 429 WP_042944533.1 type II secretion system major pseudopilin GspG -
  PHA56_RS20770 (PHA56_20770) gspF 4381991..4383211 (-) 1221 WP_119834451.1 type II secretion system inner membrane protein GspF -
  PHA56_RS20775 (PHA56_20775) gspE 4383216..4384721 (-) 1506 WP_014228296.1 type II secretion system ATPase GspE -
  PHA56_RS20780 (PHA56_20780) gspD 4384721..4386685 (-) 1965 WP_370429303.1 type II secretion system secretin GspD -
  PHA56_RS20785 (PHA56_20785) gspC 4386701..4387558 (-) 858 WP_119834453.1 type II secretion system protein GspC -
  PHA56_RS20790 (PHA56_20790) - 4387839..4390526 (-) 2688 WP_119834454.1 glycoside hydrolase family 32 protein -
  PHA56_RS20795 (PHA56_20795) - 4390658..4391506 (-) 849 WP_014228291.1 mannose/fructose/sorbose PTS transporter subunit IID -
  PHA56_RS20800 (PHA56_20800) - 4391518..4392318 (-) 801 WP_014228290.1 PTS mannose/fructose/sorbose transporter subunit IIC -
  PHA56_RS32365 - 4392330..4392806 (-) 477 WP_014228289.1 PTS system mannose/fructose/N-acetylgalactosamine-transporter subunit IIB -
  PHA56_RS32370 - 4392808..4393239 (-) 432 WP_038424192.1 mannose/fructose/sorbose PTS transporter subunit IIA -

Sequence

Protein


Download         Length: 280 a.a.        Molecular weight: 30587.69 Da        Isoelectric Point: 8.8641

>NTDB_id=776186 PHA56_RS20725 WP_119834446.1 4375721..4376563(-) (pilD) [Klebsiella michiganensis strain 2563]
MTLLVAFSSTYPIIWWFGLGATGAIVGSFLNVVICRLPVMLEKHWQREALLQLSLPSPEPTARFNLVLPHSRCPYCHTPV
AARDNIPLLSFLLLKGKTRCCGAPISAQYPLVEAATAALFVLTARVFPPGLALCGAWVFVSFLLILAVIDYHRQLLPDLL
TLPLLWIGLLFNLQSYFVSLPQATIGAVAGYLCLWCLFWLFKLLTGKDALGYGDFKLLAALGAWLGWQALPHVVLLAALS
GLLFAFVQRGGAKKDLNQPLAFGPWLALAGVANMLLFQGI

Nucleotide


Download         Length: 843 bp        

>NTDB_id=776186 PHA56_RS20725 WP_119834446.1 4375721..4376563(-) (pilD) [Klebsiella michiganensis strain 2563]
ATGACATTATTAGTGGCTTTTTCATCCACGTATCCCATCATTTGGTGGTTTGGTCTTGGGGCGACAGGCGCTATCGTCGG
GAGTTTTCTGAATGTGGTGATCTGCCGCTTACCCGTAATGCTCGAGAAACACTGGCAGCGTGAGGCGTTGCTGCAGCTGT
CACTGCCTTCACCTGAACCCACGGCGCGCTTTAATCTGGTATTGCCGCACTCTCGTTGCCCATATTGTCATACTCCTGTT
GCCGCAAGGGATAATATACCTCTGCTGAGTTTCCTGTTGTTAAAGGGCAAGACTCGCTGTTGCGGCGCGCCTATTTCCGC
GCAGTATCCGCTGGTTGAGGCGGCCACCGCTGCGCTGTTTGTCTTAACCGCACGTGTATTTCCGCCGGGGCTGGCGCTGT
GTGGCGCCTGGGTATTCGTCTCTTTTTTATTGATCCTGGCCGTTATTGATTATCACCGACAGCTGCTACCCGATCTCCTG
ACGCTGCCCTTATTGTGGATCGGCTTACTGTTTAATCTTCAGTCGTATTTTGTTTCGTTGCCGCAGGCGACGATTGGCGC
AGTGGCAGGATATCTCTGCTTGTGGTGCCTGTTCTGGCTGTTCAAGCTACTGACAGGCAAGGATGCGCTGGGCTATGGCG
ATTTTAAGCTACTGGCCGCGTTGGGAGCCTGGCTAGGCTGGCAAGCATTACCCCATGTGGTTTTACTGGCGGCGTTAAGC
GGATTGCTGTTTGCGTTCGTACAGCGAGGAGGGGCAAAAAAAGATCTCAATCAGCCGCTGGCATTCGGCCCGTGGCTGGC
GTTAGCCGGTGTGGCAAATATGCTGCTATTTCAGGGTATTTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(137-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(22-124)


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

52.06

95.357

0.496
  pilD Vibrio campbellii strain DS40M4

49.077

96.786

0.475
  pilD Neisseria gonorrhoeae MS11

48.193

88.929

0.429
  pilD Acinetobacter nosocomialis M2

43.902

87.857

0.386
  pilD Acinetobacter baumannii D1279779

43.496

87.857

0.382