Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   DBX26_RS12325 Genome accession   NZ_CP028943
Coordinates   2680818..2682503 (+) Length   561 a.a.
NCBI ID   WP_118119348.1    Uniprot ID   -
Organism   Vibrio sp. dhg     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2675818..2687503
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DBX26_RS12300 (DBX26_12290) pdhR 2677110..2677877 (-) 768 WP_014232947.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  DBX26_RS12305 (DBX26_12295) ampD 2678287..2678832 (-) 546 WP_118119344.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  DBX26_RS12315 (DBX26_12305) nadC 2679205..2680092 (+) 888 WP_020333946.1 carboxylating nicotinate-nucleotide diphosphorylase -
  DBX26_RS12320 (DBX26_12310) - 2680351..2680818 (+) 468 WP_118119346.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  DBX26_RS12325 (DBX26_12315) pilB 2680818..2682503 (+) 1686 WP_118119348.1 type IV-A pilus assembly ATPase PilB Machinery gene
  DBX26_RS12330 (DBX26_12320) pilC 2682534..2683757 (+) 1224 WP_118119350.1 type II secretion system F family protein Machinery gene
  DBX26_RS12335 (DBX26_12325) pilD 2683825..2684694 (+) 870 WP_118119352.1 A24 family peptidase Machinery gene
  DBX26_RS12340 (DBX26_12330) coaE 2684695..2685309 (+) 615 WP_014232954.1 dephospho-CoA kinase -
  DBX26_RS12345 (DBX26_12335) zapD 2685336..2686076 (+) 741 WP_014232955.1 cell division protein ZapD -
  DBX26_RS12350 (DBX26_12340) yacG 2686150..2686344 (+) 195 WP_014232956.1 DNA gyrase inhibitor YacG -
  DBX26_RS12355 (DBX26_12345) rplS 2686686..2687039 (-) 354 WP_005379971.1 50S ribosomal protein L19 -

Sequence

Protein


Download         Length: 561 a.a.        Molecular weight: 61918.68 Da        Isoelectric Point: 5.5078

>NTDB_id=288735 DBX26_RS12325 WP_118119348.1 2680818..2682503(+) (pilB) [Vibrio sp. dhg]
MVSSLSTILRQSGLLSLAQEQSLIEQVNASGISMPEALVNSGIFTTSELAAHLSSIFGLPCESVSHYDYTALCQKLGLRE
LITSHHALPLERTPSTLTLAIADPTNQQAEDDFRFATGLQIELVIADFSELDAAIRRLYGRALGQERSGLKEINQEELAN
LVDVGADEIDNIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYEKMYRVRLRCDGILIETQQPPNHLSRRLSARIKI
LSKLDIAERRMPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSASLDIDKLGYSDQQKQLYLDALRRPQGMI
LMTGPTGSGKTVSLYTGLSILNKPEINISTAEDPVEINLSGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETVIRLTNMGVESFNLASSLSLIIAQRLARKLCPYCKQPQEVTAALQHIGIQATDQ
IYQANPNGCNHCTHGYSGRTGIYEVMRFDENLSEALIKGASVHQLEKLAIRNGMSTLQMSGIEKLKQGVTSFSELQRVLY
F

Nucleotide


Download         Length: 1686 bp        

>NTDB_id=288735 DBX26_RS12325 WP_118119348.1 2680818..2682503(+) (pilB) [Vibrio sp. dhg]
ATGGTTAGTAGCTTATCAACGATTCTTCGCCAATCAGGGTTACTTAGCTTAGCCCAAGAACAGTCGTTAATAGAGCAAGT
CAACGCTTCCGGTATTTCGATGCCGGAAGCGTTAGTCAATTCTGGTATATTCACTACTAGCGAACTCGCGGCTCACCTAA
GTTCAATCTTTGGCTTACCCTGCGAATCCGTATCTCACTATGATTACACCGCGCTGTGCCAAAAATTGGGGCTGCGTGAA
CTGATCACGAGTCACCATGCATTGCCACTGGAGAGAACGCCTTCGACGTTAACTCTCGCCATTGCCGACCCAACGAACCA
ACAAGCTGAAGATGATTTTCGCTTTGCAACCGGATTGCAAATCGAACTCGTCATTGCGGATTTTTCGGAGCTTGATGCTG
CGATTCGCCGTTTGTACGGTCGCGCGTTAGGTCAGGAGAGATCAGGCTTAAAAGAGATCAACCAAGAAGAGTTGGCTAAT
TTGGTTGACGTCGGTGCAGATGAAATCGATAACATCGAAGACTTAAGTCAGGACGAGTCACCGGTTAGCCGCTATATCAA
CCAAATTTTGCTTGATGCTGTGCGTAAAGGGGCATCCGATATCCACTTTGAGCCTTATGAAAAAATGTATCGGGTTCGCC
TGCGTTGCGACGGTATTCTGATTGAGACTCAACAGCCGCCAAACCATTTAAGCCGACGCTTATCAGCCCGAATCAAAATT
CTGTCCAAGCTTGATATTGCTGAAAGGCGTATGCCGCAAGACGGTCGAATAAAGTTAAAGCTTAATCAAGACACTGCGAT
TGATATGCGAGTGTCCACCTTACCCACTCTATTCGGAGAAAAAATCGTATTACGACTGCTCGACAGCAGCTCAGCTTCTC
TGGATATCGATAAACTAGGCTACAGTGACCAGCAAAAGCAGCTGTACTTAGATGCTCTGCGTCGCCCACAAGGCATGATT
TTAATGACTGGCCCAACCGGCAGCGGCAAAACCGTCTCGTTGTACACAGGGCTGAGCATACTCAATAAACCAGAGATCAA
TATTTCTACGGCTGAAGACCCGGTCGAAATCAACCTCTCCGGAATTAATCAGGTTCAGGTTCAGCCTAAGATAGGCTTTG
GTTTCGCCGAGGCACTGCGATCTTTCCTGCGTCAAGACCCTGATGTAGTGATGGTGGGAGAAATCCGCGATCTGGACACA
GCAGAAATCGCGATTAAGGCATCTCAAACCGGACACTTAGTCCTCTCGACACTCCACACAAATTCAGCCGCTGAAACCGT
TATCCGCCTAACGAATATGGGCGTTGAAAGCTTTAACCTCGCCTCGTCGCTCAGCCTTATTATTGCCCAGCGCTTAGCCC
GTAAGCTTTGCCCGTACTGTAAACAGCCTCAAGAGGTTACCGCCGCGTTACAACATATCGGGATTCAAGCGACTGACCAG
ATTTATCAAGCCAACCCAAATGGCTGCAACCACTGTACACACGGCTATTCGGGACGAACTGGCATCTATGAGGTGATGCG
TTTCGATGAAAATCTATCCGAAGCACTGATTAAAGGAGCCTCGGTACATCAACTGGAAAAACTCGCCATCCGTAACGGGA
TGAGCACACTACAAATGTCAGGTATTGAAAAGCTTAAGCAAGGCGTCACAAGCTTTAGCGAACTGCAGCGCGTGCTCTAC
TTTTAA

Domains

Predicted by InterproScan.

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

(38-142)

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 parahaemolyticus RIMD 2210633

89.661

100

0.897
  pilB Vibrio campbellii strain DS40M4

86.275

100

0.863
  pilB Vibrio cholerae strain A1552

72.598

100

0.727
  pilB Acinetobacter baumannii D1279779

51.048

93.583

0.478
  pilB Acinetobacter baylyi ADP1

47.576

99.287

0.472
  pilB Legionella pneumophila strain ERS1305867

48.983

96.435

0.472
  pilF Neisseria gonorrhoeae MS11

44.149

100

0.444
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.522

100

0.378
  pilF Thermus thermophilus HB27

36.17

100

0.364
  pilB/pilB1 Synechocystis sp. PCC 6803

36.511

99.109

0.362

Multiple sequence alignment