Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilF   Type   Machinery gene
Locus tag   EJD96_RS01965 Genome accession   NZ_CP034395
Coordinates   371280..372413 (-) Length   377 a.a.
NCBI ID   WP_139969539.1    Uniprot ID   -
Organism   Herbaspirillum seropedicae strain AU13965     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 366280..377413
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  EJD96_RS01935 (EJD96_01935) - 366907..367338 (+) 432 WP_139969531.1 NUDIX domain-containing protein -
  EJD96_RS01940 (EJD96_01940) yacG 367376..367561 (-) 186 WP_013232399.1 DNA gyrase inhibitor YacG -
  EJD96_RS01945 (EJD96_01945) zapD 367591..368346 (-) 756 WP_013232400.1 cell division protein ZapD -
  EJD96_RS01950 (EJD96_01950) coaE 368499..369119 (-) 621 WP_139969533.1 dephospho-CoA kinase -
  EJD96_RS01955 (EJD96_01955) pilD 369131..369994 (-) 864 WP_139969535.1 prepilin peptidase Machinery gene
  EJD96_RS01960 (EJD96_01960) - 370046..371293 (-) 1248 WP_139969537.1 type II secretion system F family protein -
  EJD96_RS01965 (EJD96_01965) pilF 371280..372413 (-) 1134 WP_139969539.1 GspE/PulE family protein Machinery gene
  EJD96_RS01970 (EJD96_01970) - 372577..373881 (-) 1305 WP_139969541.1 HlyC/CorC family transporter -
  EJD96_RS01980 (EJD96_01980) infA 374310..374573 (+) 264 WP_013232407.1 translation initiation factor IF-1 -
  EJD96_RS01985 (EJD96_01985) - 374685..374936 (+) 252 WP_244940135.1 hypothetical protein -
  EJD96_RS01995 (EJD96_01995) ispB 375175..376104 (-) 930 WP_013232409.1 octaprenyl diphosphate synthase -
  EJD96_RS02000 (EJD96_02000) rplU 376472..376783 (+) 312 WP_006713215.1 50S ribosomal protein L21 -
  EJD96_RS02005 (EJD96_02005) rpmA 376832..377089 (+) 258 WP_013232410.1 50S ribosomal protein L27 -

Sequence

Protein


Download         Length: 377 a.a.        Molecular weight: 40984.47 Da        Isoelectric Point: 8.7185

>NTDB_id=331069 EJD96_RS01965 WP_139969539.1 371280..372413(-) (pilF) [Herbaspirillum seropedicae strain AU13965]
MQASETPLADDVPVVRLLYKLLADAVSMGASDLHFEPFEHYCRVRLRIDGILHELAQPPLSLKDKLATRLKILARLDIAE
KRLPQDGKMRLALETRTVDFRVSTLPTQFGEKIVLRILDTEQATLALEQLGYEPAQLQALQQAITRPHGMVLMTGPTGSG
KTVSLYACLQRLNRPGINIATAEDPVEINLPGINQVSINERAGLNFAVALRAFLRQDPDVLMVGEIRDLDTADIAIKAAQ
TGHLVLSTLHTNDAPATLTRLLNMGVPAYNIAASVSLIVAQRLVRRLCSCRRPARDASGSFVPHGCPACSHTGYRGRTGI
YQVMPVSATMQSLIQAQAGTQDIARQARAEGVIDLRRAGLLKALRGDTSLGEVLAST

Nucleotide


Download         Length: 1134 bp        

>NTDB_id=331069 EJD96_RS01965 WP_139969539.1 371280..372413(-) (pilF) [Herbaspirillum seropedicae strain AU13965]
ATGCAAGCTTCCGAGACTCCCCTGGCCGACGACGTCCCTGTCGTGCGGCTCTTGTACAAGCTCTTGGCTGACGCCGTCAG
CATGGGCGCATCGGACCTGCATTTCGAGCCCTTCGAACATTATTGCCGGGTGCGCCTGCGCATCGACGGGATACTGCATG
AACTGGCACAGCCGCCGCTGAGCCTGAAGGACAAGCTGGCGACCCGGCTCAAGATCCTGGCGCGACTGGATATCGCCGAA
AAGCGCCTGCCCCAGGATGGCAAGATGCGCCTGGCCCTGGAAACCCGCACAGTGGACTTTCGCGTCTCGACCCTGCCCAC
GCAGTTCGGCGAGAAGATCGTGCTGCGCATCCTCGACACCGAGCAGGCCACCCTCGCGCTGGAACAGCTGGGCTACGAGC
CGGCCCAGCTGCAGGCGCTGCAACAGGCCATTACGCGGCCGCATGGGATGGTGCTCATGACCGGCCCCACCGGCTCGGGC
AAGACGGTCTCGCTGTATGCCTGCCTGCAGCGGCTGAACCGTCCAGGCATCAACATCGCCACTGCCGAGGACCCGGTCGA
GATCAACCTGCCCGGCATCAACCAGGTCAGCATCAACGAACGCGCCGGCCTGAACTTTGCGGTGGCGCTGCGGGCCTTCC
TGCGCCAGGACCCGGACGTGCTGATGGTGGGCGAGATCCGCGACCTCGACACCGCCGACATCGCCATCAAGGCCGCGCAG
ACCGGCCATCTGGTGCTCTCCACCCTGCATACCAATGACGCCCCGGCCACGCTCACGCGCCTGCTCAACATGGGCGTGCC
GGCCTACAACATCGCCGCCTCGGTCAGCCTGATCGTGGCCCAGCGGCTGGTGCGCAGGCTGTGCAGTTGCCGCCGCCCGG
CGCGCGACGCGTCGGGCAGCTTCGTGCCGCATGGCTGCCCGGCATGCAGCCATACCGGCTATCGCGGCCGCACCGGCATC
TACCAGGTCATGCCGGTGAGTGCCACGATGCAGTCGCTCATCCAGGCCCAGGCCGGCACCCAGGATATCGCCCGGCAGGC
CCGCGCCGAGGGTGTCATCGACCTGCGCCGCGCCGGCCTGCTCAAGGCCTTGCGCGGCGACACCAGCCTGGGAGAAGTCC
TTGCCAGCACCTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(20-286)


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
  pilF Neisseria gonorrhoeae MS11

57.436

100

0.594
  pilB Vibrio cholerae strain A1552

55.013

100

0.568
  pilB Acinetobacter baumannii D1279779

55.013

100

0.568
  pilB Vibrio campbellii strain DS40M4

55.673

100

0.56
  pilB Vibrio parahaemolyticus RIMD 2210633

55.409

100

0.557
  pilB Acinetobacter baylyi ADP1

55.118

100

0.557
  pilB Legionella pneumophila strain ERS1305867

51.163

100

0.525
  pilB/pilB1 Synechocystis sp. PCC 6803

44.221

100

0.467
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

44.162

100

0.462
  pilF Thermus thermophilus HB27

43.325

100

0.456
  pilB Haemophilus influenzae 86-028NP

44.947

99.735

0.448
  pilB Haemophilus influenzae Rd KW20

48.773

86.472

0.422
  ctsE Campylobacter jejuni subsp. jejuni 81-176

40.682

100

0.411
  pilB Glaesserella parasuis strain SC1401

46.541

84.35

0.393

Multiple sequence alignment