Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilU   Type   Machinery gene
Locus tag   DSM104440_RS00680 Genome accession   NZ_CP053073
Coordinates   138807..139946 (-) Length   379 a.a.
NCBI ID   WP_171159803.1    Uniprot ID   A0A6M4H623
Organism   Usitatibacter palustris strain Swamp67     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
ICE 99282..138704 138807..139946 flank 103


Gene organization within MGE regions


Location: 99282..139946
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DSM104440_RS00475 (DSM104440_00096) recG 99282..101297 (+) 2016 WP_212758151.1 ATP-dependent DNA helicase RecG -
  DSM104440_RS00480 (DSM104440_00097) - 101294..101821 (+) 528 WP_171159737.1 chorismate lyase -
  DSM104440_RS00485 (DSM104440_00098) ubiA 101818..102693 (+) 876 WP_171159739.1 4-hydroxybenzoate octaprenyltransferase -
  DSM104440_RS00490 (DSM104440_00099) - 102672..103193 (+) 522 WP_171159741.1 NAD(P)H-dependent oxidoreductase -
  DSM104440_RS00495 (DSM104440_00100) kefC 103199..104977 (+) 1779 WP_171159743.1 glutathione-regulated potassium-efflux system protein KefC -
  DSM104440_RS00500 (DSM104440_00101) - 105259..106527 (+) 1269 WP_171159745.1 acetyl-CoA C-acyltransferase -
  DSM104440_RS00505 (DSM104440_00102) - 106529..107191 (+) 663 WP_171159747.1 ureidoglycolate lyase -
  DSM104440_RS00510 (DSM104440_00103) - 107224..107571 (+) 348 WP_171159749.1 hypothetical protein -
  DSM104440_RS00515 (DSM104440_00104) - 107573..108838 (-) 1266 WP_171159751.1 amidohydrolase family protein -
  DSM104440_RS00520 (DSM104440_00105) - 108847..110544 (-) 1698 WP_171159753.1 SulP family inorganic anion transporter -
  DSM104440_RS00525 (DSM104440_00106) - 110541..111260 (-) 720 WP_171159755.1 response regulator -
  DSM104440_RS00530 (DSM104440_00107) - 111340..113829 (+) 2490 WP_171159757.1 ATP-binding protein -
  DSM104440_RS00535 (DSM104440_00108) - 113926..114822 (+) 897 WP_171159759.1 EAL domain-containing protein -
  DSM104440_RS00540 (DSM104440_00109) - 114949..116043 (+) 1095 WP_171159761.1 GSU2403 family nucleotidyltransferase fold protein -
  DSM104440_RS00545 (DSM104440_00110) - 116173..116475 (+) 303 WP_171159763.1 hypothetical protein -
  DSM104440_RS00550 (DSM104440_00111) - 116666..117289 (+) 624 WP_171159765.1 N-methyl-D-aspartate receptor NMDAR2C subunit -
  DSM104440_RS00555 (DSM104440_00112) - 117380..117868 (+) 489 WP_171159767.1 hypothetical protein -
  DSM104440_RS00560 (DSM104440_00113) - 117868..118455 (+) 588 WP_171159769.1 GNAT family N-acetyltransferase -
  DSM104440_RS00565 (DSM104440_00114) - 118530..118874 (+) 345 WP_171159771.1 toxin -
  DSM104440_RS00570 (DSM104440_00115) - 118871..119218 (+) 348 WP_171159773.1 transcriptional regulator -
  DSM104440_RS00575 (DSM104440_00116) - 119373..119933 (-) 561 WP_171159775.1 hypothetical protein -
  DSM104440_RS19200 (DSM104440_00117) - 119921..120427 (-) 507 WP_212758153.1 RHS repeat-associated core domain-containing protein -
  DSM104440_RS00585 (DSM104440_00118) - 120480..121382 (-) 903 WP_212758154.1 hypothetical protein -
  DSM104440_RS00590 - 121370..121888 (-) 519 WP_171159779.1 RHS repeat-associated core domain-containing protein -
  DSM104440_RS00595 (DSM104440_00121) - 122361..125039 (+) 2679 WP_171159781.1 pre-peptidase C-terminal domain-containing protein -
  DSM104440_RS00600 (DSM104440_00122) - 125048..126349 (+) 1302 WP_246212131.1 DUF6531 domain-containing protein -
  DSM104440_RS00605 (DSM104440_00123) - 126307..129279 (+) 2973 WP_171159785.1 RHS repeat domain-containing protein -
  DSM104440_RS00610 - 129290..129784 (+) 495 WP_171159787.1 hypothetical protein -
  DSM104440_RS00620 (DSM104440_00124) - 131021..131245 (-) 225 WP_171159789.1 hypothetical protein -
  DSM104440_RS19515 - 133459..133986 (-) 528 WP_171159791.1 RHS repeat-associated core domain-containing protein -
  DSM104440_RS19205 - 134308..134865 (-) 558 Protein_124 RHS repeat-associated core domain-containing protein -
  DSM104440_RS19345 (DSM104440_00126) - 135287..135661 (-) 375 WP_171159793.1 hypothetical protein -
  DSM104440_RS00655 - 135843..136247 (-) 405 WP_171159795.1 hypothetical protein -
  DSM104440_RS00665 - 136791..137096 (-) 306 WP_171159797.1 hypothetical protein -
  DSM104440_RS00675 xerC 137691..138704 (+) 1014 WP_171159801.1 site-specific tyrosine recombinase XerC -
  DSM104440_RS00680 (DSM104440_00130) pilU 138807..139946 (-) 1140 WP_171159803.1 PilT/PilU family type 4a pilus ATPase Machinery gene

Sequence

Protein


Download         Length: 379 a.a.        Molecular weight: 42369.86 Da        Isoelectric Point: 6.8861

>NTDB_id=442729 DSM104440_RS00680 WP_171159803.1 138807..139946(-) (pilU) [Usitatibacter palustris strain Swamp67]
MEREQSMKFMHDLLRALIARRGSDLFITAGFPPAMKVDGKVTKAMEQSLTPVHTQELARSIMTDKQAAEFEATNECNFAI
SPSGIGRFRVNAFVQQGRVALVLRTITTTIPKFDDLGLPHVLKDVAMTKRGLVIFVGGTGSGKSTSLAAMIGHRNENSYG
HIITIEDPVEYVHEHNNCIVSQREVGVDTDNWFAALKNTLRQAPDVILIGEIRERETMEYGIAFAETGHLCMSTLHANST
NQALDRIINFFPEERRGQLLMDLSLNLKAIISQRLIPKKGVKGRVAAIEIMLNSPLMSDLIFKGEVHEMKALMTRSRELG
MQTFDQALFDLFEADMITYEDALRNADSVNDIRLKIKLESKNAKNRDLGSGLEHLEIVK

Nucleotide


Download         Length: 1140 bp        

>NTDB_id=442729 DSM104440_RS00680 WP_171159803.1 138807..139946(-) (pilU) [Usitatibacter palustris strain Swamp67]
ATGGAACGCGAACAGTCAATGAAGTTCATGCACGACCTCTTGCGCGCACTGATCGCGCGCAGGGGCTCGGACCTCTTCAT
CACCGCGGGCTTCCCGCCGGCGATGAAGGTCGACGGCAAGGTGACCAAGGCGATGGAGCAGAGCCTGACGCCCGTGCACA
CGCAGGAGCTCGCCCGGTCGATCATGACGGACAAGCAGGCGGCGGAATTCGAAGCCACCAACGAGTGCAACTTCGCGATC
AGCCCGTCGGGCATCGGCCGCTTCCGTGTGAACGCGTTCGTGCAGCAGGGCCGCGTGGCCCTCGTGCTGCGGACCATCAC
CACCACGATCCCGAAGTTCGACGATCTCGGCCTTCCGCACGTGCTCAAAGACGTCGCGATGACCAAGCGCGGCCTCGTGA
TCTTCGTGGGCGGCACGGGCTCGGGGAAATCGACCTCGCTCGCCGCGATGATCGGCCACCGCAACGAGAACTCCTACGGC
CACATCATCACGATCGAGGACCCGGTCGAGTACGTGCACGAGCACAACAACTGCATCGTGAGCCAGCGCGAAGTCGGCGT
GGATACGGACAACTGGTTCGCGGCGCTGAAGAACACGCTGCGCCAGGCGCCCGACGTAATCCTCATCGGTGAGATCCGCG
AGCGCGAGACGATGGAGTACGGCATCGCCTTCGCGGAAACCGGCCACTTGTGCATGTCCACGCTGCACGCGAACTCCACC
AACCAGGCGCTCGACCGGATCATCAACTTCTTCCCGGAAGAACGCCGCGGCCAGCTGCTGATGGACTTGTCGCTGAACCT
GAAGGCCATCATCTCGCAGCGCCTCATCCCGAAGAAGGGCGTGAAGGGCCGCGTGGCCGCGATCGAGATCATGCTCAACT
CGCCGCTCATGTCTGACCTCATCTTCAAGGGCGAGGTGCACGAGATGAAGGCGCTGATGACGCGTTCGCGCGAGCTCGGC
ATGCAGACCTTCGACCAGGCGCTCTTCGATCTCTTCGAAGCCGACATGATCACCTACGAAGACGCGCTGCGGAATGCCGA
CTCGGTGAACGACATCCGTCTCAAGATCAAGCTGGAGTCCAAGAACGCGAAGAACCGCGATCTCGGATCGGGACTGGAGC
ACTTGGAAATCGTGAAGTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(112-277)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A6M4H623

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
  pilU Pseudomonas stutzeri DSM 10701

63.61

92.084

0.586
  pilU Acinetobacter baylyi ADP1

56.831

96.57

0.549
  pilU Vibrio cholerae strain A1552

53.591

95.515

0.512
  pilT Pseudomonas aeruginosa PAK

43.114

88.127

0.38
  pilT Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

42.687

88.391

0.377
  pilT Legionella pneumophila strain ERS1305867

41.916

88.127

0.369
  pilT Legionella pneumophila strain Lp02

41.916

88.127

0.369
  pilT Pseudomonas stutzeri DSM 10701

41.916

88.127

0.369
  pilT Acinetobacter nosocomialis M2

41.39

87.335

0.361
  pilT Acinetobacter baumannii D1279779

41.39

87.335

0.361
  pilT Acinetobacter baumannii strain A118

41.39

87.335

0.361