Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   KI610_RS16645 Genome accession   NZ_CP075189
Coordinates   3477786..3478640 (+) Length   284 a.a.
NCBI ID   WP_226496065.1    Uniprot ID   -
Organism   Ferribacterium limneticum strain 77     
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 3465110..3477786 3477786..3478640 flank 0


Gene organization within MGE regions


Location: 3465110..3478640
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  KI610_RS16575 (KI610_16490) - 3465110..3465511 (-) 402 WP_226496053.1 polymer-forming cytoskeletal protein -
  KI610_RS16580 (KI610_16495) - 3465523..3466101 (-) 579 WP_226496054.1 DUF6776 family protein -
  KI610_RS16585 (KI610_16500) rpsI 3466435..3466827 (-) 393 WP_226403796.1 30S ribosomal protein S9 -
  KI610_RS16590 (KI610_16505) rplM 3466837..3467265 (-) 429 WP_117607868.1 50S ribosomal protein L13 -
  KI610_RS16595 (KI610_16510) - 3467769..3468197 (+) 429 WP_226496055.1 OsmC family protein -
  KI610_RS16600 (KI610_16515) coq7 3468214..3468837 (-) 624 WP_226496056.1 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone monooxygenase -
  KI610_RS16605 (KI610_16520) - 3468842..3469357 (-) 516 WP_226496057.1 CNP1-like family protein -
  KI610_RS16610 (KI610_16525) - 3469360..3469908 (-) 549 WP_226496058.1 RNA pyrophosphohydrolase -
  KI610_RS16615 (KI610_16530) - 3470019..3471749 (+) 1731 WP_226496059.1 proline--tRNA ligase -
  KI610_RS16620 (KI610_16535) - 3471737..3472348 (+) 612 WP_226496060.1 lytic transglycosylase domain-containing protein -
  KI610_RS16625 (KI610_16540) ffh 3472418..3473773 (-) 1356 WP_226496061.1 signal recognition particle protein -
  KI610_RS16630 (KI610_16545) - 3473803..3474642 (+) 840 WP_226496062.1 inner membrane protein YpjD -
  KI610_RS16635 (KI610_16550) pilB 3474829..3476544 (+) 1716 WP_226496063.1 type IV-A pilus assembly ATPase PilB Machinery gene
  KI610_RS16640 (KI610_16555) pilC 3476560..3477786 (+) 1227 WP_226496064.1 type II secretion system F family protein Machinery gene
  KI610_RS16645 (KI610_16560) pilD 3477786..3478640 (+) 855 WP_226496065.1 A24 family peptidase Machinery gene

Sequence

Protein


Download         Length: 284 a.a.        Molecular weight: 30103.74 Da        Isoelectric Point: 7.6629

>NTDB_id=568534 KI610_RS16645 WP_226496065.1 3477786..3478640(+) (pilD) [Ferribacterium limneticum strain 77]
MLPETLGGLAAAAGLLGLCVGSFLNVVIHRLPKMMEQEWQAQCAELRGEQGATAAEPLSLAKPRSRCPTCGHQITAIENI
PLVSYLLILKGKCSGCHARISPRYPIIEALTGLVSAYVAWHFGPTLQAAGALILVWSLIALAAIDLDTQLLPDSITLPLL
WLGLTLNLWGAYADLPSAVVGAMLGYLALWSVFWLFKLVTGKEGMGYGDFKLLAALGAWLGWQMLPAIILLSSVVGAIVG
ITLIVATRHGRNVPIPFGPYLAAAGGIALFWGNSITHSYLGLIG

Nucleotide


Download         Length: 855 bp        

>NTDB_id=568534 KI610_RS16645 WP_226496065.1 3477786..3478640(+) (pilD) [Ferribacterium limneticum strain 77]
ATGCTTCCGGAAACCCTGGGCGGTCTGGCTGCTGCGGCGGGGCTGCTTGGCCTGTGTGTTGGCAGTTTTCTCAATGTAGT
CATTCACCGACTACCCAAAATGATGGAGCAGGAATGGCAGGCGCAATGTGCCGAATTGCGCGGAGAGCAGGGAGCGACCG
CGGCAGAGCCTCTATCACTGGCAAAACCACGCTCACGCTGCCCTACCTGTGGCCACCAAATTACAGCCATCGAGAATATC
CCGCTTGTCAGCTATCTGTTGATTCTCAAGGGTAAATGCTCGGGATGTCATGCGCGCATTTCGCCCCGCTATCCGATCAT
CGAGGCGCTTACTGGCCTCGTATCGGCCTATGTTGCCTGGCATTTCGGCCCGACACTTCAAGCGGCCGGCGCACTCATAT
TGGTCTGGTCCCTGATTGCACTCGCCGCCATCGACCTCGACACTCAACTGTTGCCGGACTCGATTACGCTACCATTGCTC
TGGCTGGGTCTCACTCTTAACCTGTGGGGAGCATATGCCGACCTGCCCTCCGCGGTCGTCGGCGCGATGCTCGGCTATTT
GGCGCTGTGGAGCGTATTTTGGCTATTCAAGCTGGTCACTGGCAAGGAAGGCATGGGCTATGGCGATTTCAAACTACTTG
CCGCACTGGGCGCATGGCTGGGCTGGCAGATGCTGCCAGCCATTATCCTGCTCTCCTCGGTGGTCGGTGCCATCGTCGGC
ATCACGCTGATCGTTGCCACCCGGCACGGACGCAACGTTCCGATTCCGTTCGGCCCCTACCTCGCGGCAGCTGGAGGCAT
CGCTCTTTTCTGGGGCAATTCGATCACGCACAGCTATCTTGGTCTTATCGGTTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(132-241)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(15-122)


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

57.407

95.07

0.546
  pilD Acinetobacter nosocomialis M2

54.122

98.239

0.532
  pilD Acinetobacter baumannii D1279779

54.122

98.239

0.532
  pilD Vibrio campbellii strain DS40M4

55.185

95.07

0.525
  pilD Neisseria gonorrhoeae MS11

50.379

92.958

0.468