Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   LDP65_RS16330 Genome accession   NZ_AP025152
Coordinates   3616900..3618588 (+) Length   562 a.a.
NCBI ID   WP_126606908.1    Uniprot ID   -
Organism   Vibrio penaeicida strain TUMSAT-OK1     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 3611900..3623588
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LDP65_RS16310 pdhR 3612907..3613674 (-) 768 WP_101112467.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  LDP65_RS16315 ampD 3614251..3614808 (-) 558 WP_126606913.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  LDP65_RS16320 nadC 3615292..3616179 (+) 888 WP_126606912.1 carboxylating nicotinate-nucleotide diphosphorylase -
  LDP65_RS16325 - 3616474..3616896 (+) 423 WP_126606910.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  LDP65_RS16330 pilB 3616900..3618588 (+) 1689 WP_126606908.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LDP65_RS16335 pilC 3618598..3619830 (+) 1233 WP_126606907.1 type II secretion system F family protein Machinery gene
  LDP65_RS16340 pilD 3619890..3620759 (+) 870 WP_126606905.1 A24 family peptidase Machinery gene
  LDP65_RS16345 coaE 3620811..3621410 (+) 600 WP_126606903.1 dephospho-CoA kinase -
  LDP65_RS16350 zapD 3621448..3622188 (+) 741 WP_126606901.1 cell division protein ZapD -
  LDP65_RS16355 yacG 3622258..3622452 (+) 195 WP_126606900.1 DNA gyrase inhibitor YacG -
  LDP65_RS16360 mutT 3622544..3622957 (-) 414 WP_126606898.1 8-oxo-dGTP diphosphatase MutT -
  LDP65_RS16365 rplS 3623115..3623468 (-) 354 WP_101112478.1 50S ribosomal protein L19 -

Sequence

Protein


Download         Length: 562 a.a.        Molecular weight: 62204.30 Da        Isoelectric Point: 4.9839

>NTDB_id=90087 LDP65_RS16330 WP_126606908.1 3616900..3618588(+) (pilB) [Vibrio penaeicida strain TUMSAT-OK1]
MHTNLASILRQADIISEAHELAIIERIGSTGGTVPSAIAALGIIPVFELTQHIAEIFGLSVIETNQYDYLPLCEQLGLRD
LITRYNALPVESTNNTLFIALSDPTIVEAEEEFRFATNQQVEILLCDERELTSCIRRMYGKNRVDSSTGAKEITQEELAD
LVQVGDDEFDSAEDLSLDDAPVSRFIHQVLFDAVRKGASDIHFEPYEETYRIRMRCDGILIQANSPAPQLGRRLAARLKI
LSKLDIAERRLPQDGRIKLKLSDTTAIDLRVSTLPTLWGEKIVLRLLDSSSANLNIDMLGYSEEQKALYIEALRRPQGMI
LMTGPTGSGKTVSLYTGLSILNTVERNISTAEDPVEINLAGINQVQIRPKIGFTFAAALKSFLRQDPDIVMLGEIRDFET
AEIAIKAAQTGHLVLSTLHTNSAAETVIRLGNMGVEPYNLSSSLSLIIAQRLARRLCPHCKIPHQLSPALLDKHRIETST
PIFQASKEGCADCNSGYSGRIGIYEVMPFDAEMQQAISHKANIAEIEMLAVKNGMKTLSQSGIEILKQGITSYQELQRVL
YL

Nucleotide


Download         Length: 1689 bp        

>NTDB_id=90087 LDP65_RS16330 WP_126606908.1 3616900..3618588(+) (pilB) [Vibrio penaeicida strain TUMSAT-OK1]
ATGCACACCAACTTAGCTAGCATTCTTCGCCAAGCCGATATTATTAGTGAAGCACATGAACTGGCTATTATTGAGCGCAT
AGGCAGCACTGGGGGCACCGTCCCCAGTGCTATTGCAGCGCTTGGTATTATTCCTGTTTTTGAATTGACTCAGCATATTG
CTGAGATTTTTGGTTTGTCGGTCATAGAAACCAATCAATACGACTACCTTCCGTTATGTGAGCAGCTTGGTCTACGAGAC
CTGATCACTCGCTACAATGCGCTGCCTGTTGAATCCACCAACAATACTCTATTTATTGCGCTATCTGACCCAACGATCGT
TGAAGCAGAAGAAGAGTTTCGCTTTGCTACCAATCAGCAAGTCGAAATCCTGCTTTGTGATGAAAGAGAATTAACCAGCT
GCATTCGTAGAATGTACGGCAAAAATAGAGTCGATAGCAGCACTGGTGCTAAAGAAATCACGCAAGAAGAGCTCGCGGAT
TTGGTTCAAGTGGGTGATGATGAATTTGATTCAGCAGAAGATCTCAGCTTAGACGACGCCCCAGTCAGTCGCTTTATTCA
TCAAGTATTGTTCGATGCAGTACGTAAAGGGGCTTCCGACATTCATTTTGAACCTTATGAAGAAACGTACCGTATCCGGA
TGCGATGCGACGGTATTCTTATTCAAGCCAATAGCCCAGCTCCTCAATTAGGGCGAAGGCTAGCCGCACGATTAAAAATA
CTTTCAAAACTGGATATTGCCGAACGGCGTTTACCTCAAGATGGGCGCATCAAGCTAAAACTCAGCGACACAACTGCGAT
CGATCTTCGGGTATCCACTCTGCCCACGCTTTGGGGAGAGAAAATTGTTCTACGTTTATTGGACAGCAGCAGTGCGAATT
TGAACATCGATATGCTCGGCTATAGTGAAGAACAAAAAGCCTTATATATCGAAGCCCTACGTCGCCCTCAGGGCATGATC
TTAATGACAGGTCCTACAGGGAGCGGTAAAACCGTTTCACTGTACACAGGACTTAGTATTCTCAATACGGTTGAACGCAA
TATTTCAACCGCTGAAGATCCGGTCGAGATCAACCTAGCGGGCATCAACCAAGTCCAAATTCGCCCTAAAATCGGCTTTA
CCTTTGCCGCTGCACTTAAATCCTTTTTGCGCCAAGATCCTGACATCGTGATGCTAGGTGAGATACGAGATTTTGAAACA
GCGGAAATCGCCATCAAGGCGGCTCAAACAGGGCACTTGGTTCTATCGACCTTACATACCAACTCCGCAGCAGAAACGGT
TATTCGGCTAGGCAATATGGGGGTTGAACCTTATAACCTCTCGTCTTCACTGAGTTTGATCATCGCTCAACGTTTAGCAA
GGCGTTTGTGCCCACACTGTAAAATACCGCACCAGCTCTCTCCAGCACTGTTAGACAAACACAGAATTGAGACTAGCACA
CCCATTTTTCAAGCGTCTAAAGAGGGCTGCGCCGATTGCAACTCAGGGTACAGTGGTCGAATTGGTATCTATGAGGTCAT
GCCTTTTGATGCGGAAATGCAGCAAGCTATTTCTCATAAAGCCAATATCGCAGAAATTGAAATGCTAGCGGTTAAAAACG
GTATGAAAACTCTGAGTCAGTCTGGTATTGAAATATTAAAACAAGGCATCACGAGCTACCAAGAACTACAACGCGTTTTG
TATTTGTAA

Domains

Predicted by InterproScan.

Type II secretion system (T2SS), protein E, N-terminal domain (MshEN)

(48-142)

Type II/IV secretion system protein (T2SSE)

(188-455)


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
  pilB Vibrio cholerae strain A1552

66.726

100

0.667
  pilB Vibrio parahaemolyticus RIMD 2210633

66.252

100

0.664
  pilB Vibrio campbellii strain DS40M4

65.364

100

0.655
  pilB Acinetobacter baylyi ADP1

50

95.018

0.475
  pilB Acinetobacter baumannii D1279779

50.965

92.171

0.47
  pilB Legionella pneumophila strain ERS1305867

47.559

98.399

0.468
  pilF Neisseria gonorrhoeae MS11

45.889

93.06

0.427
  pilB/pilB1 Synechocystis sp. PCC 6803

37.205

98.043

0.365
  pilF Thermus thermophilus HB27

38.06

95.374

0.363

Multiple sequence alignment