Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilU   Type   Machinery gene
Locus tag   LRK55_RS04020 Genome accession   NZ_CP088925
Coordinates   854852..856018 (-) Length   388 a.a.
NCBI ID   WP_007507060.1    Uniprot ID   -
Organism   Rhodanobacter denitrificans strain FW104-MT042     
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)
Genomic island 851007..860268 854852..856018 within 0


Gene organization within MGE regions


Location: 851007..860268
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LRK55_RS04005 (LRK55_04005) - 851007..851699 (-) 693 WP_015446997.1 response regulator transcription factor -
  LRK55_RS04010 (LRK55_04010) - 851845..854055 (+) 2211 WP_235644820.1 TonB-dependent siderophore receptor -
  LRK55_RS04015 (LRK55_04015) - 854408..854785 (+) 378 WP_235644821.1 BON domain-containing protein -
  LRK55_RS04020 (LRK55_04020) pilU 854852..856018 (-) 1167 WP_007507060.1 PilT/PilU family type 4a pilus ATPase Machinery gene
  LRK55_RS04025 (LRK55_04025) pilT 856172..857209 (-) 1038 WP_007507061.1 type IV pilus twitching motility protein PilT Machinery gene
  LRK55_RS04030 (LRK55_04030) proC 857578..858402 (+) 825 WP_015446993.1 pyrroline-5-carboxylate reductase -
  LRK55_RS04035 (LRK55_04035) - 858399..858974 (+) 576 WP_007507063.1 YggT family protein -
  LRK55_RS04040 (LRK55_04040) - 859096..860268 (-) 1173 WP_027490870.1 IS4 family transposase -

Sequence

Protein


Download         Length: 388 a.a.        Molecular weight: 43422.86 Da        Isoelectric Point: 6.7735

>NTDB_id=634032 LRK55_RS04020 WP_007507060.1 854852..856018(-) (pilU) [Rhodanobacter denitrificans strain FW104-MT042]
MSDFDFTSFLKLMVHKKASDLFITAGVAPSMKVQGRIVPITQSPLSVQQARDMVLNVMTPGQREEFEKTHECQFAISAQG
VGRFRVSCFYQRNCVGMVLRRIESKIPTIEELTLPPVIKQLAMTKRGIIIFVGATGSGKSTSLASMIGYRNQNSTGHIIT
IEDPIEYVHKHEGCIITQREVGIDTDSWDNALKNTLRQAPDVIMIGEIRTREGMDHAIAFAETGHLVLCTLHANNANQAM
DRILHFFPEDRRQQLLMDLSLNLKGIVAQQLIPTPDGKARRVAVEILLGTPLVQDYIRQGEIHKLKEVMKESTLLGMKTF
DQSLVELYHAGEISYEDALRYADSSNEVRLRIKLAQGGDAHTLSQGLEGVELEESRDAQNFSSNFLNR

Nucleotide


Download         Length: 1167 bp        

>NTDB_id=634032 LRK55_RS04020 WP_007507060.1 854852..856018(-) (pilU) [Rhodanobacter denitrificans strain FW104-MT042]
ATGAGCGACTTCGATTTCACCTCATTCCTGAAGCTGATGGTGCACAAGAAGGCCTCCGACTTGTTCATCACGGCGGGCGT
CGCCCCTTCGATGAAAGTGCAAGGCCGGATCGTGCCGATCACGCAGAGCCCGCTCAGCGTGCAGCAGGCGCGCGACATGG
TGCTCAACGTGATGACGCCGGGCCAGCGCGAGGAGTTCGAGAAGACCCATGAGTGCCAGTTCGCGATCTCCGCGCAAGGC
GTGGGCCGTTTCCGCGTGTCGTGCTTCTACCAGCGCAACTGCGTGGGCATGGTGCTGCGCCGGATCGAGTCGAAGATCCC
CACGATCGAGGAACTGACGCTGCCGCCGGTGATCAAGCAACTGGCGATGACCAAGCGCGGCATCATCATCTTCGTCGGCG
CCACCGGCTCGGGCAAATCGACCTCGCTGGCGTCGATGATCGGCTACCGCAACCAGAACTCGACCGGTCACATCATCACG
ATCGAGGACCCGATCGAGTACGTGCACAAGCACGAAGGCTGCATCATCACCCAGCGCGAGGTCGGCATCGACACCGACAG
CTGGGACAACGCGCTGAAGAACACCCTGCGCCAGGCCCCGGACGTGATCATGATCGGTGAAATCCGCACCCGCGAGGGTA
TGGACCACGCGATCGCCTTTGCCGAAACCGGCCACCTGGTGCTGTGCACGCTGCACGCGAACAACGCCAACCAGGCGATG
GACCGCATCCTGCACTTCTTCCCCGAGGACCGCCGCCAGCAACTGCTGATGGACCTGTCGCTCAACCTGAAGGGCATCGT
GGCGCAGCAGCTGATCCCCACGCCCGACGGCAAGGCGCGCCGGGTCGCGGTGGAGATCCTGCTGGGCACGCCGCTGGTGC
AGGACTACATCCGCCAAGGCGAGATCCACAAGCTGAAGGAGGTGATGAAGGAGTCCACCCTGCTCGGCATGAAGACCTTC
GACCAGAGCCTGGTCGAGCTGTACCACGCCGGCGAGATCAGCTACGAGGACGCGCTGCGCTACGCCGACAGCTCCAACGA
GGTGCGCCTGCGCATCAAGCTGGCCCAGGGCGGCGACGCGCATACCCTGTCGCAAGGCCTGGAAGGCGTCGAGCTGGAGG
AAAGCCGCGACGCGCAGAACTTCAGCAGCAATTTCCTCAACCGCTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(116-272)


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
  pilU Pseudomonas stutzeri DSM 10701

66.578

96.392

0.642
  pilU Acinetobacter baylyi ADP1

63.764

91.753

0.585
  pilU Vibrio cholerae strain A1552

52.809

91.753

0.485
  pilT Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

41.129

95.876

0.394