Detailed information    

experimental Experimentally validated

Overview

Name   pilB   Type   Machinery gene
Locus tag   A4U84_RS08525 Genome accession   NZ_CP015099
Coordinates   1767762..1769147 (-) Length   461 a.a.
NCBI ID   WP_010787006.1    Uniprot ID   -
Organism   Glaesserella parasuis strain SC1401     
Function   type IV pilus biogenesis and function   
DNA binding and uptake

Function

The expression levels of candidate uptake components were significantly lower than in SC1401, respectively. These results revealed that the highly naturally competent strain SC1401 up-regulated most of the candidate natural competence-related regulons/components.


Genomic Context

Location: 1762762..1774147
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  A4U84_RS08500 (A4U84_08500) clpP 1762779..1763360 (+) 582 WP_010787003.1 ATP-dependent Clp endopeptidase proteolytic subunit ClpP -
  A4U84_RS08505 (A4U84_08505) clpX 1763367..1764617 (+) 1251 WP_035491633.1 ATP-dependent protease ATP-binding subunit ClpX -
  A4U84_RS08510 (A4U84_08510) dapE 1764691..1765824 (-) 1134 WP_005711772.1 succinyl-diaminopimelate desuccinylase -
  A4U84_RS08515 (A4U84_08515) - 1765908..1766576 (-) 669 WP_005711775.1 prepilin peptidase -
  A4U84_RS08520 (A4U84_08520) pilC 1766573..1767769 (-) 1197 WP_005711777.1 type II secretion system F family protein Machinery gene
  A4U84_RS08525 (A4U84_08525) pilB 1767762..1769147 (-) 1386 WP_010787006.1 GspE/PulE family protein Machinery gene
  A4U84_RS08530 (A4U84_08530) pilA 1769195..1769659 (-) 465 WP_005711781.1 pilin Machinery gene
  A4U84_RS08535 (A4U84_08535) radA 1769847..1771223 (+) 1377 WP_021115532.1 DNA repair protein RadA -
  A4U84_RS08540 (A4U84_08540) gmk 1771276..1771902 (-) 627 WP_005711785.1 guanylate kinase -
  A4U84_RS08545 (A4U84_08545) gpt 1772140..1772619 (-) 480 WP_005714020.1 xanthine phosphoribosyltransferase -

Sequence

Protein


Download         Length: 461 a.a.        Molecular weight: 52808.65 Da        Isoelectric Point: 5.3881

>NTDB_id=1384 A4U84_RS08525 WP_010787006.1 1767762..1769147(-) (pilB) [Glaesserella parasuis strain SC1401]
MSQYTICEQQTERIFDISPSRWQKNCEEKQLLLRYLAVPVQETEHKLWLAVDDENNLTACEIFAFMTHKQIEPVVIASDE
LKYLLNALSPEQQPIYEESELAFVEQEQEQLNLNDPIIQLLDNLFKFCLAQNASDIHIEPRKQKLIIRLRIDGVLHLYKS
LSIQLASRLISRIKLLAKLDISELRQPQDGQFSFTTALADTLDFRVSSLPTIYGEKLVLRLQKNKPTSFDFLQLGFNPQQ
QTTLLNALKQPQGLILVTGPTGSGKSITLYSALNYLNQMDKHILTAEDPVEIEIDGLIQTQVNRSIQLDFSQLLRTFLRQ
DPDIIMLGEIRDEESAKMALRASQTGHLVLSTLHTNDALSAVERLLQLGIQEYEIQNSLLLVIAQRLVRKLCKKCRGVGC
DECYQGYRGRIGVYQCLSRTAKKFDKQTAYLDFSSLRESAKQKIEQQLTNETEVDRVLGYE

Nucleotide


Download         Length: 1386 bp        

>NTDB_id=1384 A4U84_RS08525 WP_010787006.1 1767762..1769147(-) (pilB) [Glaesserella parasuis strain SC1401]
ATGTCCCAATACACTATCTGCGAACAACAAACCGAACGCATTTTTGATATATCGCCTAGCCGTTGGCAAAAAAATTGCGA
GGAGAAACAGCTTTTATTGCGTTACCTTGCCGTTCCTGTGCAAGAAACTGAGCATAAATTATGGCTTGCCGTTGATGATG
AAAACAATCTCACCGCTTGCGAAATCTTTGCTTTTATGACCCATAAGCAGATTGAGCCGGTGGTGATTGCTTCTGATGAA
CTGAAATACTTGCTTAACGCTCTCTCGCCTGAACAACAGCCCATTTATGAAGAGAGCGAGCTGGCTTTTGTTGAACAGGA
GCAAGAACAGCTCAACCTAAACGATCCGATTATTCAACTGCTCGATAATCTTTTTAAATTCTGTTTAGCCCAAAATGCGT
CCGACATTCATATTGAACCACGCAAGCAAAAATTGATTATTCGCCTACGCATTGACGGTGTTTTGCACCTGTATAAAAGC
CTGTCTATTCAACTGGCAAGCCGACTTATTTCACGGATAAAACTGCTGGCGAAGCTAGATATTAGTGAATTACGCCAGCC
ACAAGATGGGCAATTTAGCTTTACCACCGCCTTGGCGGACACCCTTGATTTTCGGGTATCTAGCCTGCCGACGATCTACG
GCGAAAAACTGGTATTGCGCCTACAAAAAAACAAACCAACCAGTTTTGATTTTCTGCAACTTGGCTTTAATCCACAACAG
CAGACCACACTACTCAACGCCTTGAAACAACCGCAAGGGCTGATTTTAGTGACAGGACCAACGGGCAGTGGCAAAAGTAT
CACCCTTTACAGCGCCTTAAACTATCTCAACCAAATGGATAAACATATTCTCACCGCCGAAGATCCGGTGGAAATCGAGA
TTGACGGCTTAATTCAAACCCAAGTTAATCGCAGTATTCAACTGGATTTTAGCCAGCTGTTACGCACCTTTCTACGTCAA
GATCCCGACATCATTATGTTAGGCGAAATTCGAGATGAAGAGAGTGCCAAAATGGCGTTACGAGCAAGCCAGACGGGGCA
TTTAGTCCTTTCGACCCTGCATACCAACGACGCACTCTCTGCGGTCGAACGCTTGTTGCAACTGGGTATTCAAGAGTATG
AAATCCAAAATTCACTACTGTTAGTGATTGCACAACGCCTTGTGCGTAAGCTCTGTAAAAAGTGTCGTGGAGTAGGCTGT
GACGAGTGCTATCAAGGCTATAGAGGGCGGATCGGGGTTTACCAATGTTTAAGCAGAACGGCAAAAAAATTCGATAAACA
GACCGCTTACTTGGATTTTTCCAGCCTACGAGAGAGTGCTAAACAGAAAATTGAACAACAACTCACCAATGAAACCGAAG
TGGATAGGGTATTAGGTTATGAATAA

Domains

Predicted by InterproScan.

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

(30-92)

Type II/IV secretion system protein (T2SSE)

(129-390)


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 Haemophilus influenzae Rd KW20

58.093

97.831

0.568
  pilB Haemophilus influenzae 86-028NP

57.456

98.915

0.568
  pilB Vibrio cholerae strain A1552

38.2

100

0.414
  pilB Vibrio parahaemolyticus RIMD 2210633

39.13

100

0.41
  pilB Legionella pneumophila strain ERS1305867

38.211

100

0.408
  pilB Vibrio campbellii strain DS40M4

38.923

100

0.408
  pilB Acinetobacter baumannii D1279779

36.187

100

0.403
  pilB Acinetobacter baylyi ADP1

36.634

100

0.401
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.248

100

0.388
  pilF Neisseria gonorrhoeae MS11

36.421

100

0.375
  pilF Thermus thermophilus HB27

35.01

100

0.362

Multiple sequence alignment    



References

[1] Ke Dai et al. (2018) Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401. Frontiers in Cellular And Infection Microbiology 8:32. [PMID: 29473023]