Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   X874_RS04110 Genome accession   NZ_CP006944
Coordinates   857358..858749 (+) Length   463 a.a.
NCBI ID   WP_025247572.1    Uniprot ID   -
Organism   Mannheimia varigena USDA-ARS-USMARC-1312     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 852358..863749
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  X874_RS04085 (X874_8090) - 852762..853457 (+) 696 WP_025247567.1 aspartate/glutamate racemase family protein -
  X874_RS04090 (X874_8100) - 853475..854785 (+) 1311 WP_025247568.1 anaerobic C4-dicarboxylate transporter -
  X874_RS04095 (X874_8110) - 855012..855245 (+) 234 WP_025247569.1 YgjV family protein -
  X874_RS04100 (X874_8120) radA 855299..856678 (-) 1380 WP_025247570.1 DNA repair protein RadA -
  X874_RS04105 (X874_8130) pilA 856858..857337 (+) 480 WP_025247571.1 prepilin peptidase-dependent pilin Machinery gene
  X874_RS04110 (X874_8140) pilB 857358..858749 (+) 1392 WP_025247572.1 GspE/PulE family protein Machinery gene
  X874_RS04115 (X874_8150) pilC 858742..859938 (+) 1197 WP_025247573.1 type II secretion system F family protein Machinery gene
  X874_RS04120 (X874_8160) - 859942..860598 (+) 657 WP_025247574.1 prepilin peptidase -
  X874_RS04125 (X874_8170) coaE 860630..861265 (+) 636 WP_025247575.1 dephospho-CoA kinase -
  X874_RS04130 (X874_8180) yacG 861247..861432 (+) 186 WP_025217069.1 DNA gyrase inhibitor YacG -
  X874_RS04135 (X874_8190) holA 861433..862455 (-) 1023 WP_025247576.1 DNA polymerase III subunit delta -
  X874_RS04140 (X874_8200) lptE 862495..862983 (-) 489 WP_025217071.1 LPS assembly lipoprotein LptE -

Sequence

Protein


Download         Length: 463 a.a.        Molecular weight: 52422.09 Da        Isoelectric Point: 5.4981

>NTDB_id=115072 X874_RS04110 WP_025247572.1 857358..858749(+) (pilB) [Mannheimia varigena USDA-ARS-USMARC-1312]
MEYTVTDLTSQEMIEISGEQWAKNCNEKQILLRYLAVPLQETQSQLWLAVDDMQNISACEIFAFIYHKQIEPVLISSDEL
KFLLNALSPEQSSLQSEIYEDNVAYSLAHSEQIDRNDPIIQILDNLFKFCLKNNASDIHLEPQKEKLLIRLRIDGVLHIY
KTLPQSLSSRLISRIKLLAKLDISEIRLPQDGQFHFKTMLAETLDFRVSTLPTHFGEKVVLRLQKNKPTNLDFLELGFNQ
NQKETLLNALNQPQGLILVTGPTGSGKSITLYSALSHLNTSEKHILTAEDPIEIEIEGIIQTQVNRGINLDFSQLLRTFL
RQDPDIVMLGEIRDEESAEIALRASQTGHLVLSTLHTNDAPSAIERLLQLGIKEYELQNALLLVVAQRLLRRICTKCRGA
GCEHCYQGYKGRIGVYQLFSRSAKNFDKTTACLDFETLAESAKEKLAEGKTNQAEIFRVLGNG

Nucleotide


Download         Length: 1392 bp        

>NTDB_id=115072 X874_RS04110 WP_025247572.1 857358..858749(+) (pilB) [Mannheimia varigena USDA-ARS-USMARC-1312]
ATGGAGTATACAGTTACAGATTTAACTAGCCAAGAAATGATTGAAATTTCTGGTGAGCAATGGGCAAAGAATTGTAATGA
AAAGCAGATTTTATTGCGATATTTAGCCGTTCCGTTGCAAGAAACACAATCTCAATTATGGTTGGCGGTGGATGATATGC
AAAATATCAGTGCTTGTGAGATTTTTGCCTTTATCTACCATAAGCAAATTGAACCTGTTTTGATTTCCTCCGATGAGTTG
AAGTTTCTGCTCAATGCGCTTTCACCAGAGCAGAGTAGCTTGCAGAGTGAAATTTATGAGGATAATGTAGCGTATTCATT
AGCACATTCGGAGCAAATAGACAGAAACGATCCGATTATCCAAATTTTAGATAATCTGTTTAAATTCTGTTTAAAAAATA
ACGCATCAGATATTCATCTTGAACCGCAAAAAGAGAAGTTGCTTATTCGGTTAAGAATTGACGGTGTATTACATATTTAT
AAAACACTTCCGCAAAGTTTATCTAGCAGGTTGATTTCTCGCATTAAGCTGTTAGCTAAATTAGATATTAGCGAAATCCG
TTTGCCACAAGATGGGCAATTTCATTTCAAAACGATGTTAGCGGAAACTTTAGATTTCCGAGTTTCTACTTTGCCTACTC
ATTTTGGCGAAAAGGTCGTCCTTCGGCTTCAAAAGAATAAACCGACTAATTTGGATTTTTTGGAGTTAGGTTTTAACCAA
AACCAAAAAGAAACATTACTCAATGCACTCAACCAACCTCAAGGATTAATTCTGGTAACAGGTCCAACAGGTAGCGGAAA
AAGTATCACTTTATATAGTGCATTAAGCCATCTCAATACTAGCGAAAAGCATATATTAACCGCTGAAGATCCGATTGAAA
TTGAGATAGAAGGTATTATTCAAACCCAAGTAAACAGGGGCATTAATCTTGATTTCAGCCAACTGTTGAGAACCTTTCTC
CGCCAAGATCCCGACATCGTTATGCTTGGTGAAATTCGTGATGAAGAGAGTGCTGAAATTGCCCTAAGAGCATCTCAAAC
AGGGCATTTAGTGCTTTCTACTTTGCACACAAACGATGCTCCTTCTGCCATAGAACGATTATTGCAACTCGGAATTAAAG
AATATGAGTTACAAAATGCGTTATTGTTAGTAGTTGCTCAACGCTTGTTAAGAAGGATTTGTACAAAATGCAGAGGGGCT
GGTTGTGAGCATTGCTATCAAGGCTACAAAGGAAGAATTGGGGTATATCAACTATTCAGCCGATCTGCAAAAAATTTTGA
CAAAACGACCGCTTGTTTAGATTTTGAAACCTTAGCTGAAAGTGCGAAAGAAAAATTAGCGGAAGGAAAAACCAATCAGG
CAGAAATTTTTAGGGTGTTAGGAAATGGCTAA

Domains

Predicted by InterproScan.

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

(29-93)

Type II/IV secretion system protein (T2SSE)

(131-392)


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 Glaesserella parasuis strain SC1401

72.451

99.568

0.721
  pilB Haemophilus influenzae 86-028NP

56.733

97.84

0.555
  pilB Haemophilus influenzae Rd KW20

56.416

97.624

0.551
  pilB Vibrio parahaemolyticus RIMD 2210633

40.562

100

0.436
  pilB Vibrio cholerae strain A1552

40.562

100

0.436
  pilB Vibrio campbellii strain DS40M4

40.568

100

0.432
  pilB Legionella pneumophila strain ERS1305867

39.754

100

0.419
  pilB Acinetobacter baylyi ADP1

35.645

100

0.4
  pilB Acinetobacter baumannii D1279779

36.401

100

0.384
  ctsE Campylobacter jejuni subsp. jejuni 81-176

41.007

90.065

0.369
  pilF Neisseria gonorrhoeae MS11

39.294

91.793

0.361

Multiple sequence alignment