Detailed information    

experimental Experimentally validated

Overview

Name   pilB   Type   Machinery gene
Locus tag   DSB67_RS12665 Genome accession   NZ_CP030788
Coordinates   2641040..2642725 (+) Length   561 a.a.
NCBI ID   WP_010643259.1    Uniprot ID   -
Organism   Vibrio campbellii strain DS40M4     
Function   type IV pilus biogenesis and function   
DNA binding and uptake

Function

Induction of TfoX expression resulted in upregulation of the genes required for DNA uptake and integration (comEC, comEA, comM, comF, and dprA) and pilus structure (pilABCD, pilMNOPQ, and minor pilins VC0857 to -0861) in DS40M4


Genomic Context

Location: 2636040..2647725
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DSB67_RS12640 (DSB67_12645) pdhR 2637608..2638375 (-) 768 WP_005428674.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  DSB67_RS12645 (DSB67_12650) ampD 2638780..2639331 (-) 552 WP_010643266.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  DSB67_RS12650 (DSB67_12655) nadC 2639424..2640311 (+) 888 WP_010643264.1 carboxylating nicotinate-nucleotide diphosphorylase -
  DSB67_RS12660 (DSB67_12665) pilA 2640576..2641040 (+) 465 WP_010643261.1 pilin Machinery gene
  DSB67_RS12665 (DSB67_12670) pilB 2641040..2642725 (+) 1686 WP_010643259.1 type IV-A pilus assembly ATPase PilB Machinery gene
  DSB67_RS12670 (DSB67_12675) pilC 2642760..2643983 (+) 1224 WP_010643257.1 type II secretion system F family protein Machinery gene
  DSB67_RS12675 (DSB67_12680) pilD 2644056..2644925 (+) 870 WP_010643256.1 prepilin peptidase Machinery gene
  DSB67_RS12680 (DSB67_12685) coaE 2644926..2645540 (+) 615 WP_010643253.1 dephospho-CoA kinase -
  DSB67_RS12685 (DSB67_12690) zapD 2645568..2646308 (+) 741 WP_010643252.1 cell division protein ZapD -
  DSB67_RS12690 (DSB67_12695) yacG 2646371..2646565 (+) 195 WP_010643249.1 DNA gyrase inhibitor YacG -
  DSB67_RS12695 (DSB67_12700) rplS 2646902..2647255 (-) 354 WP_005379971.1 50S ribosomal protein L19 -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  tfoX pilB positive effect
  tfoX dprA positive effect
  tfoX pilC positive effect
  tfoX pilD positive effect
  tfoX pilM positive effect
  tfoX pilO positive effect
  tfoX comM positive effect
  tfoX pilA positive effect
  tfoX pilQ positive effect
  tfoX comEC positive effect
  tfoX comEA positive effect
  tfoX pilP positive effect
  tfoX comF positive effect
  tfoX pilN positive effect

Sequence

Protein


Download         Length: 561 a.a.        Molecular weight: 62196.03 Da        Isoelectric Point: 5.1898

>NTDB_id=1401 DSB67_RS12665 WP_010643259.1 2641040..2642725(+) (pilB) [Vibrio campbellii strain DS40M4]
MLTNLSTVLRQAGILTFSQEESLLEQVKASGISMPEALLSSGFFQSHELTEHLSSVFGLSCTSLNQYEYASLCQTLGLRD
LITRHNALPLNRTSSTLILAVADPTNLQAEDDFRFATGLQVELVLADFRELTAAIRRLYGRSLGQEKSGLKEINQDELAG
LVDIGEDEIENIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYENMYRVRLRCDGILIEIQQPPSHLSRRLSARIKI
LSKLDIAERRLPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSAALDINKLGYSDSQKQLYLDALRRPQGMI
LMTGPTGSGKTVSLYTGLSILNKPEINISTAEDPVEIYLPGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETVIRLSNMGVESFNLASSLSLIIAQRLARKLCPYCRQPQEPNSQLQHIGIANTEQ
IFQANPDGCNECTHGYSGRTGIYEVMKFDESLSEALIKGASVHELEKLAIANGMQTLQMSGIEKLKQGITSFRELQRVLY
F

Nucleotide


Download         Length: 1686 bp        

>NTDB_id=1401 DSB67_RS12665 WP_010643259.1 2641040..2642725(+) (pilB) [Vibrio campbellii strain DS40M4]
ATGCTAACCAACCTCTCAACGGTTCTTCGCCAAGCGGGAATACTGACCTTTTCCCAAGAAGAATCGTTACTTGAACAAGT
AAAAGCTTCTGGCATTTCGATGCCGGAGGCTTTACTCAGTTCTGGCTTTTTCCAATCTCATGAATTAACAGAACACTTAA
GCTCAGTATTCGGGCTTTCTTGCACTTCTCTTAACCAATACGAATACGCTTCGCTATGCCAAACGCTCGGCTTACGCGAT
CTCATCACTCGCCATAACGCTTTGCCGCTTAACCGCACCTCTTCAACTTTGATTCTCGCGGTTGCCGACCCAACAAACCT
TCAAGCCGAAGATGACTTTCGTTTTGCGACAGGCTTGCAAGTCGAGCTTGTCCTCGCTGACTTTCGTGAGCTAACAGCAG
CCATTCGACGTTTATATGGCCGATCACTCGGGCAAGAAAAATCCGGTCTTAAAGAAATCAACCAAGATGAACTGGCGGGT
TTGGTTGATATTGGTGAGGATGAAATTGAGAACATCGAAGATCTCAGCCAAGATGAATCGCCGGTCAGTCGCTATATCAA
CCAAATTTTACTCGATGCTGTCCGTAAAGGGGCTTCCGATATTCACTTCGAGCCTTACGAAAATATGTACCGCGTGCGCT
TGCGTTGCGATGGCATCTTAATTGAAATTCAGCAGCCTCCGAGTCATTTAAGCCGTCGTCTCTCCGCTCGGATAAAAATC
TTATCTAAGCTTGATATCGCCGAGCGTCGTTTACCACAGGATGGGCGAATCAAGCTCAAATTAAACCAAGACACTGCAAT
TGATATGCGTGTCTCCACACTACCAACTCTTTTTGGAGAAAAGATTGTTCTGCGTTTGCTCGACAGCAGTTCTGCAGCAT
TAGATATCAATAAGCTCGGTTATAGCGACTCACAAAAACAACTTTATTTAGATGCCCTGCGCCGTCCGCAAGGTATGATC
CTGATGACAGGCCCAACAGGTAGCGGTAAAACGGTCTCGCTCTATACTGGATTGAGTATTCTTAATAAGCCAGAGATTAA
TATCTCAACCGCTGAAGATCCCGTCGAGATTTACCTGCCCGGCATTAACCAAGTTCAAGTTCAGCCAAAGATCGGCTTTG
GTTTTGCAGAAGCGCTCCGCTCTTTCTTACGTCAAGACCCTGATGTGGTTATGGTGGGCGAGATCCGAGATCTCGACACA
GCAGAAATCGCGATCAAAGCATCACAGACTGGCCACTTAGTTCTCTCCACCTTACACACAAACTCAGCTGCCGAGACTGT
TATTCGCTTGTCTAATATGGGCGTAGAAAGCTTTAACCTCGCCTCTTCTCTCAGTTTGATCATCGCCCAGCGTTTGGCTA
GAAAACTTTGTCCATATTGTAGACAACCTCAAGAGCCAAACAGCCAACTTCAACATATTGGAATCGCCAACACCGAACAG
ATCTTTCAAGCTAATCCCGACGGTTGTAACGAGTGTACCCATGGTTATTCAGGGCGAACCGGCATTTACGAAGTGATGAA
GTTTGATGAATCCCTTTCAGAAGCACTCATCAAAGGCGCCTCGGTACACGAATTAGAAAAACTCGCCATTGCCAATGGTA
TGCAAACCTTACAAATGTCTGGCATCGAAAAACTCAAACAAGGCATTACCAGCTTCCGCGAATTGCAGCGCGTTCTCTAC
TTTTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(188-455)

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

(38-142)


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 parahaemolyticus RIMD 2210633

90.374

100

0.904
  pilB Vibrio cholerae strain A1552

73.488

100

0.736
  pilB Legionella pneumophila strain ERS1305867

47.756

99.287

0.474
  pilB Acinetobacter baumannii D1279779

50.867

92.513

0.471
  pilB Acinetobacter baylyi ADP1

49.903

92.157

0.46
  pilF Neisseria gonorrhoeae MS11

43.838

100

0.446
  pilB Haemophilus influenzae 86-028NP

40.082

100

0.422
  pilB Haemophilus influenzae Rd KW20

40.412

100

0.422
  pilB Glaesserella parasuis strain SC1401

38.923

100

0.408
  pilB/pilB1 Synechocystis sp. PCC 6803

37.374

100

0.396
  pilF Thermus thermophilus HB27

36.833

100

0.369
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

36.38

99.465

0.362

Multiple sequence alignment    



References

[1] Chelsea A Simpson et al. (2019) Diversity in Natural Transformation Frequencies and Regulation across Vibrio Species. MBio 10(6):e02788-19. [PMID: 31848285]