Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   X808_RS04060 Genome accession   NZ_CP006943
Coordinates   852843..854234 (+) Length   463 a.a.
NCBI ID   WP_025217065.1    Uniprot ID   -
Organism   Mannheimia varigena USDA-ARS-USMARC-1296     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 847843..859234
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  X808_RS04035 (X808_7980) - 848247..848942 (+) 696 WP_025217060.1 amino acid racemase -
  X808_RS04040 (X808_7990) - 848960..850270 (+) 1311 WP_025217061.1 anaerobic C4-dicarboxylate transporter -
  X808_RS04045 (X808_8000) - 850497..850730 (+) 234 WP_025217062.1 YgjV family protein -
  X808_RS04050 (X808_8010) radA 850784..852163 (-) 1380 WP_025217063.1 DNA repair protein RadA -
  X808_RS04055 (X808_8020) pilA 852343..852822 (+) 480 WP_025217064.1 prepilin peptidase-dependent pilin Machinery gene
  X808_RS04060 (X808_8030) pilB 852843..854234 (+) 1392 WP_025217065.1 GspE/PulE family protein Machinery gene
  X808_RS04065 (X808_8040) pilC 854227..855423 (+) 1197 WP_025217066.1 type II secretion system F family protein Machinery gene
  X808_RS04070 (X808_8050) - 855427..856083 (+) 657 WP_025217067.1 prepilin peptidase -
  X808_RS04075 (X808_8060) coaE 856115..856750 (+) 636 WP_025217068.1 dephospho-CoA kinase -
  X808_RS04080 (X808_8070) yacG 856732..856917 (+) 186 WP_025217069.1 DNA gyrase inhibitor YacG -
  X808_RS04085 (X808_8080) holA 856918..857940 (-) 1023 WP_025217070.1 DNA polymerase III subunit delta -
  X808_RS04090 (X808_8090) lptE 857980..858468 (-) 489 WP_025217071.1 LPS assembly lipoprotein LptE -

Sequence

Protein


Download         Length: 463 a.a.        Molecular weight: 52375.08 Da        Isoelectric Point: 5.4981

>NTDB_id=115049 X808_RS04060 WP_025217065.1 852843..854234(+) (pilB) [Mannheimia varigena USDA-ARS-USMARC-1296]
MEYTVTDLTSQEMIEISGEQWAKNCNEKQILLRYLAVPLQETQSQLWLAVDDMQNISACEIFAFIYHKQIEPVLISSDEL
KFLLNALSPEQSSLQSEIYEDNVAYSLAHSEQIDRNDPIIQILDNLFKFCLKNNASDIHLEPQKEKLLIRLRIDGVLHIY
KTLPQSLSSRLISRIKLLAKLDISEIRLPQDGQFHFKTMLAETLDFRVSTLPTHFGEKVVLRLQKNKPTNLDFLELGFNQ
NQKETLLNALNQPQGLILVTGPTGSGKSITLYSALSHLNTSEKHILTAEDPIEIEIEGIIQTQVNRGINLDFSQLLRTFL
RQDPDIVMLGEIRDEESAEIALRASQTGHLVLSTLHTNDAPSAIERLLQLGIKEYELQNALLLVVAQRLLRRICTKCRGA
GCEHCYQGYKGRIGVYQLFSRTAKNFEKTTACLDFATLSESAKEKLAEGKTDQAEILRVLGNG

Nucleotide


Download         Length: 1392 bp        

>NTDB_id=115049 X808_RS04060 WP_025217065.1 852843..854234(+) (pilB) [Mannheimia varigena USDA-ARS-USMARC-1296]
ATGGAGTATACAGTTACAGATTTAACTAGCCAAGAAATGATTGAAATTTCTGGTGAGCAATGGGCAAAGAATTGTAATGA
AAAGCAGATTTTATTGCGATATTTAGCTGTTCCGTTGCAAGAAACACAATCTCAATTATGGTTGGCGGTGGATGATATGC
AAAATATCAGTGCTTGTGAGATTTTTGCCTTTATCTACCATAAGCAAATTGAACCTGTTTTGATTTCCTCCGATGAGTTG
AAGTTTCTGCTCAATGCGCTTTCACCAGAGCAGAGTAGCTTGCAGAGTGAAATTTATGAGGATAATGTAGCGTATTCATT
AGCACATTCGGAGCAAATAGACAGAAACGATCCGATTATCCAAATTTTAGATAATCTGTTTAAATTCTGTTTAAAAAATA
ACGCATCAGATATTCATCTTGAACCGCAAAAAGAGAAGTTGCTTATTCGGTTAAGAATTGACGGTGTATTACATATTTAT
AAAACACTTCCGCAAAGTTTATCTAGCAGGTTGATTTCTCGCATTAAGCTGTTAGCTAAATTAGATATTAGCGAAATCCG
TTTGCCACAAGATGGGCAATTTCATTTCAAAACGATGTTAGCGGAAACTTTAGATTTCCGAGTTTCTACTTTGCCTACTC
ATTTTGGCGAAAAGGTCGTCCTTCGGCTTCAAAAGAATAAACCGACTAATTTGGATTTTTTGGAGTTAGGTTTTAACCAA
AACCAAAAAGAAACATTACTCAATGCACTCAACCAACCTCAAGGATTAATTCTGGTAACAGGTCCAACAGGTAGCGGAAA
AAGTATCACTTTATATAGTGCATTAAGCCATCTCAATACTAGCGAAAAGCATATATTAACCGCTGAAGATCCGATTGAAA
TTGAGATAGAAGGTATTATTCAAACCCAAGTAAACAGGGGCATTAATCTTGATTTCAGCCAACTGTTGAGAACCTTTCTC
CGCCAAGATCCCGACATCGTTATGCTTGGTGAAATTCGTGATGAAGAGAGTGCTGAAATTGCCCTAAGAGCATCTCAAAC
AGGGCATTTAGTGCTTTCTACTTTGCACACAAACGATGCTCCTTCTGCCATAGAACGATTATTGCAACTCGGAATTAAAG
AATATGAGTTACAAAATGCGTTATTGTTAGTAGTAGCTCAACGCTTGTTAAGAAGGATTTGTACAAAATGCAGAGGGGCT
GGTTGTGAGCATTGCTATCAAGGCTACAAAGGGCGAATTGGGGTGTATCAACTTTTTAGCCGAACTGCAAAAAATTTTGA
AAAAACGACCGCTTGTTTAGATTTTGCAACCTTATCGGAAAGTGCAAAAGAAAAATTAGCGGAAGGAAAAACCGATCAGG
CTGAAATTTTAAGGGTATTAGGTAATGGCTAA

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

72.234

99.568

0.719
  pilB Haemophilus influenzae 86-028NP

56.733

97.84

0.555
  pilB Haemophilus influenzae Rd KW20

56.637

97.624

0.553
  pilB Vibrio cholerae strain A1552

40.562

100

0.436
  pilB Vibrio parahaemolyticus RIMD 2210633

40.562

100

0.436
  pilB Vibrio campbellii strain DS40M4

40.568

100

0.432
  pilB Legionella pneumophila strain ERS1305867

39.344

100

0.415
  pilB Acinetobacter baylyi ADP1

35.838

100

0.402
  pilB Acinetobacter baumannii D1279779

36.605

100

0.387
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

36.653

100

0.374
  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