Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   WM2015_RS09575 Genome accession   NZ_CP012154
Coordinates   2256521..2257342 (+) Length   273 a.a.
NCBI ID   WP_049727044.1    Uniprot ID   -
Organism   Wenzhouxiangella marina strain KCTC 42284     
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 2244465..2269677 2256521..2257342 within 0


Gene organization within MGE regions


Location: 2244465..2269677
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  WM2015_RS09530 (WM2015_1879) - 2244465..2246438 (-) 1974 WP_156201043.1 hypothetical protein -
  WM2015_RS09535 (WM2015_1880) - 2246707..2247600 (+) 894 WP_082169626.1 glycosyltransferase family 2 protein -
  WM2015_RS09540 - 2247659..2248663 (-) 1005 WP_156201046.1 hypothetical protein -
  WM2015_RS09545 (WM2015_1882) - 2248615..2249241 (-) 627 WP_049725826.1 class I SAM-dependent methyltransferase -
  WM2015_RS09550 (WM2015_1883) - 2249771..2251681 (+) 1911 WP_049725827.1 hypothetical protein -
  WM2015_RS16360 (WM2015_1884) pilA2 2251955..2252404 (+) 450 WP_281173112.1 pilin Machinery gene
  WM2015_RS16365 (WM2015_1885) - 2252660..2253097 (+) 438 WP_049725829.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  WM2015_RS09565 (WM2015_1886) pilB 2253206..2254930 (+) 1725 WP_049725830.1 type IV-A pilus assembly ATPase PilB Machinery gene
  WM2015_RS09570 (WM2015_1887) pilC 2255170..2256390 (+) 1221 WP_049725831.1 type II secretion system F family protein Machinery gene
  WM2015_RS09575 (WM2015_1888) pilD 2256521..2257342 (+) 822 WP_049727044.1 A24 family peptidase Machinery gene
  WM2015_RS09580 (WM2015_1889) - 2257610..2258311 (-) 702 WP_049725832.1 response regulator transcription factor -
  WM2015_RS09585 (WM2015_1890) - 2258494..2260386 (-) 1893 WP_169751138.1 sulfatase-like hydrolase/transferase -
  WM2015_RS09590 (WM2015_1891) rho 2260519..2261775 (-) 1257 WP_049725834.1 transcription termination factor Rho -
  WM2015_RS09595 (WM2015_1892) trxA 2262042..2262368 (-) 327 WP_049725835.1 thioredoxin TrxA -
  WM2015_RS09600 (WM2015_1893) - 2262584..2263879 (+) 1296 WP_049725836.1 DEAD/DEAH box helicase -
  WM2015_RS09605 (WM2015_1894) - 2263948..2264844 (+) 897 WP_049725837.1 type II secretion system protein N -
  WM2015_RS09610 (WM2015_1895) - 2264841..2266757 (+) 1917 WP_049725838.1 secretin N-terminal domain-containing protein -
  WM2015_RS09615 (WM2015_1896) gspE 2266747..2268225 (+) 1479 WP_049725839.1 type II secretion system ATPase GspE -
  WM2015_RS09620 (WM2015_1897) - 2268230..2269426 (+) 1197 WP_049725840.1 type II secretion system F family protein -

Sequence

Protein


Download         Length: 273 a.a.        Molecular weight: 30214.96 Da        Isoelectric Point: 6.8292

>NTDB_id=151959 WM2015_RS09575 WP_049727044.1 2256521..2257342(+) (pilD) [Wenzhouxiangella marina strain KCTC 42284]
MIVFVFGLLVGSFLNVVILRLPARLMHDWRCQCRELLEIEQDQEASQPPSLVFTRSHCPQCGKAIAWYDNVPLLSWLVLK
ARCRNCQKRIPFRYPLVEFSTAVLSVIVVQAFGPSPEALGALVLTWSLVALTGIDFDQQLLPDQITLPLLWLGLLVNLQW
GLFASLEEAVIGAAAGYGVLWAVFHLFKLLTGKEGMGFGDFKLLAALGAWLGWWMLPVIILLASFVGAVVGIVLMIATRH
GKDVPIAFGPYLAAAGFIALLYGDRIVDFWLYS

Nucleotide


Download         Length: 822 bp        

>NTDB_id=151959 WM2015_RS09575 WP_049727044.1 2256521..2257342(+) (pilD) [Wenzhouxiangella marina strain KCTC 42284]
ATGATAGTCTTCGTTTTCGGCCTTCTCGTCGGATCCTTTCTCAATGTCGTGATCCTGCGCCTTCCGGCGCGCCTGATGCA
CGACTGGCGCTGCCAGTGCCGAGAACTGCTCGAAATCGAGCAGGACCAGGAGGCCAGTCAGCCCCCCAGCCTGGTGTTCA
CCCGCTCGCACTGCCCCCAGTGCGGCAAGGCGATCGCCTGGTACGACAATGTTCCGTTGCTCAGCTGGCTGGTCCTGAAG
GCGCGTTGCCGGAATTGCCAGAAGCGCATTCCGTTCCGCTACCCCCTGGTCGAGTTCAGCACTGCGGTGCTTTCGGTGAT
CGTCGTCCAGGCCTTCGGGCCCTCCCCCGAGGCGCTCGGCGCCCTGGTGCTGACCTGGTCATTGGTTGCCCTGACCGGCA
TCGACTTCGATCAGCAGCTGCTGCCGGACCAGATCACCCTGCCCCTGCTCTGGCTGGGACTGCTGGTCAACCTCCAGTGG
GGGCTGTTCGCCAGCCTGGAAGAGGCCGTGATCGGTGCTGCCGCGGGCTACGGCGTCCTCTGGGCGGTGTTCCACCTGTT
CAAGCTGCTGACCGGCAAGGAAGGCATGGGCTTCGGCGACTTCAAGCTGCTGGCGGCCCTTGGTGCCTGGCTGGGCTGGT
GGATGCTGCCGGTCATCATCCTGCTGGCCTCTTTCGTGGGGGCCGTCGTCGGGATCGTGCTCATGATCGCGACCCGCCAT
GGCAAGGACGTTCCGATCGCCTTCGGCCCCTACCTGGCCGCGGCCGGCTTCATCGCTCTGCTGTACGGTGATCGGATCGT
GGATTTCTGGTTGTATAGCTGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(5-111)

Type IV leader peptidase family (Peptidase_A24)

(122-232)


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 nosocomialis M2

49.814

98.535

0.491
  pilD Acinetobacter baumannii D1279779

49.442

98.535

0.487
  pilD Vibrio cholerae strain A1552

49.442

98.535

0.487
  pilD Vibrio campbellii strain DS40M4

48.327

98.535

0.476
  pilD Neisseria gonorrhoeae MS11

47.232

99.267

0.469

Multiple sequence alignment