Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   LDO36_RS16310 Genome accession   NZ_AP025155
Coordinates   3616489..3618177 (+) Length   562 a.a.
NCBI ID   WP_126606908.1    Uniprot ID   -
Organism   Vibrio penaeicida strain TUMSAT-OK2     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 3611489..3623177
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LDO36_RS16290 pdhR 3612496..3613263 (-) 768 WP_101112467.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  LDO36_RS16295 ampD 3613840..3614397 (-) 558 WP_126606913.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  LDO36_RS16300 nadC 3614881..3615768 (+) 888 WP_126606912.1 carboxylating nicotinate-nucleotide diphosphorylase -
  LDO36_RS16305 - 3616063..3616485 (+) 423 WP_126606910.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  LDO36_RS16310 pilB 3616489..3618177 (+) 1689 WP_126606908.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LDO36_RS16315 pilC 3618187..3619419 (+) 1233 WP_126606907.1 type II secretion system F family protein Machinery gene
  LDO36_RS16320 pilD 3619479..3620348 (+) 870 WP_126606905.1 A24 family peptidase Machinery gene
  LDO36_RS16325 coaE 3620400..3620999 (+) 600 WP_126606903.1 dephospho-CoA kinase -
  LDO36_RS16330 zapD 3621037..3621777 (+) 741 WP_126606901.1 cell division protein ZapD -
  LDO36_RS16335 yacG 3621847..3622041 (+) 195 WP_126606900.1 DNA gyrase inhibitor YacG -
  LDO36_RS16340 mutT 3622133..3622546 (-) 414 WP_126606898.1 8-oxo-dGTP diphosphatase MutT -
  LDO36_RS16345 rplS 3622704..3623057 (-) 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=90131 LDO36_RS16310 WP_126606908.1 3616489..3618177(+) (pilB) [Vibrio penaeicida strain TUMSAT-OK2]
MHTNLASILRQADIISEAHELAIIERIGSTGGTVPSAIAALGIIPVFELTQHIAEIFGLSVIETNQYDYLPLCEQLGLRD
LITRYNALPVESTNNTLFIALSDPTIVEAEEEFRFATNQQVEILLCDERELTSCIRRMYGKNRVDSSTGAKEITQEELAD
LVQVGDDEFDSAEDLSLDDAPVSRFIHQVLFDAVRKGASDIHFEPYEETYRIRMRCDGILIQANSPAPQLGRRLAARLKI
LSKLDIAERRLPQDGRIKLKLSDTTAIDLRVSTLPTLWGEKIVLRLLDSSSANLNIDMLGYSEEQKALYIEALRRPQGMI
LMTGPTGSGKTVSLYTGLSILNTVERNISTAEDPVEINLAGINQVQIRPKIGFTFAAALKSFLRQDPDIVMLGEIRDFET
AEIAIKAAQTGHLVLSTLHTNSAAETVIRLGNMGVEPYNLSSSLSLIIAQRLARRLCPHCKIPHQLSPALLDKHRIETST
PIFQASKEGCADCNSGYSGRIGIYEVMPFDAEMQQAISHKANIAEIEMLAVKNGMKTLSQSGIEILKQGITSYQELQRVL
YL

Nucleotide


Download         Length: 1689 bp        

>NTDB_id=90131 LDO36_RS16310 WP_126606908.1 3616489..3618177(+) (pilB) [Vibrio penaeicida strain TUMSAT-OK2]
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