Detailed information    

insolico Bioinformatically predicted

Overview

Name   rpoN/rpoN1   Type   Machinery gene
Locus tag   SR858_RS23890 Genome accession   NZ_CP140152
Coordinates   5436896..5438380 (-) Length   494 a.a.
NCBI ID   WP_019923405.1    Uniprot ID   -
Organism   Duganella zoogloeoides strain ATCC 25935     
Function   type IV pilus biogenesis and function (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 5433901..5444504 5436896..5438380 within 0


Gene organization within MGE regions


Location: 5433901..5444504
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SR858_RS23870 (SR858_23870) - 5434196..5434417 (+) 222 WP_026637563.1 hypothetical protein -
  SR858_RS23875 (SR858_23875) - 5434347..5435441 (-) 1095 WP_019923402.1 enoyl-CoA hydratase/isomerase family protein -
  SR858_RS23880 (SR858_23880) - 5435438..5436400 (-) 963 WP_019923403.1 alginate lyase family protein -
  SR858_RS23885 (SR858_23885) hpf 5436461..5436820 (-) 360 WP_019923404.1 ribosome hibernation-promoting factor, HPF/YfiA family -
  SR858_RS23890 (SR858_23890) rpoN/rpoN1 5436896..5438380 (-) 1485 WP_019923405.1 RNA polymerase factor sigma-54 Machinery gene
  SR858_RS23895 (SR858_23895) lptB 5438384..5439136 (-) 753 WP_019923406.1 LPS export ABC transporter ATP-binding protein -
  SR858_RS23900 (SR858_23900) lptA 5439138..5439740 (-) 603 WP_019923407.1 lipopolysaccharide transport periplasmic protein LptA -
  SR858_RS23905 (SR858_23905) lptC 5439750..5440352 (-) 603 WP_026637565.1 LPS export ABC transporter periplasmic protein LptC -
  SR858_RS23910 (SR858_23910) - 5440352..5441350 (-) 999 WP_019923409.1 KpsF/GutQ family sugar-phosphate isomerase -
  SR858_RS23915 (SR858_23915) - 5441477..5443459 (+) 1983 WP_019923410.1 monovalent cation:proton antiporter family protein -
  SR858_RS23920 (SR858_23920) bluB 5443497..5444150 (+) 654 WP_019923411.1 5,6-dimethylbenzimidazole synthase -
  SR858_RS23925 (SR858_23925) - 5444241..5444504 (+) 264 WP_019923412.1 hypothetical protein -

Sequence

Protein


Download         Length: 494 a.a.        Molecular weight: 54787.40 Da        Isoelectric Point: 5.0455

>NTDB_id=913088 SR858_RS23890 WP_019923405.1 5436896..5438380(-) (rpoN/rpoN1) [Duganella zoogloeoides strain ATCC 25935]
MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQLLTDNPLLERLDDPLDHSLRLLSDGAISQQAPSGEAPSESG
PQEAAPAGEADAYEGPAADTESTTAEADMDWSDAGRSKAPDDEDARPQIEAHHCTLREHLMEQMRVTVLELRDRALVELI
IDALDENGYLEEALDEIHARLPEELEVELDELQTALSLLQSFDPAGVGARNAAECLALQIKRLPGIALVTRRMAVAIVEK
HLTWFAQRDFNKLKKALLCDDEDLREVQTVIRQCNPHPGAAFASDVSDYVVPDVIVKKSRTGWQVSLNNDVMPRLRVNAM
YANLLKQKKGEGGEGAMGAQLQEAKWLIKNMRQRFDTILRVAQAIVERQKNFFSHGAVAMRPLVLREIADTLGLHESTIS
RVTTQKYMLTPHGMFELKYFFGSHVATEAGGEASSTAIRALIVQLTGAEDPKNPLSDSKIADMLGEQGMVIARRTVAKYR
EALKIPPVSLRKSL

Nucleotide


Download         Length: 1485 bp        

>NTDB_id=913088 SR858_RS23890 WP_019923405.1 5436896..5438380(-) (rpoN/rpoN1) [Duganella zoogloeoides strain ATCC 25935]
ATGAAACAGTCGTTGCAACTGCGGACCTCGCAGCATCTCGCGCTGACGCCCCAACTGCAGCAATCGATCCGCTTGCTGCA
GCTCTCCACGCTGGAGCTGCACCAGGAACTCGAACAACTCCTGACCGACAATCCCTTGCTCGAGCGGTTAGACGACCCGC
TCGACCATTCGCTGCGGCTGTTGTCCGACGGCGCCATCAGCCAGCAGGCGCCGTCCGGCGAAGCGCCGTCCGAATCGGGC
CCGCAGGAAGCGGCGCCCGCCGGCGAGGCCGACGCCTACGAAGGCCCCGCCGCCGATACCGAAAGTACCACCGCCGAAGC
GGACATGGACTGGAGCGACGCCGGCCGCAGCAAGGCGCCCGACGACGAAGACGCGCGTCCGCAAATCGAAGCGCACCACT
GCACCCTGCGCGAACACCTGATGGAGCAGATGCGGGTGACCGTGCTCGAGCTGCGCGACCGCGCGCTGGTCGAGCTGATC
ATCGACGCGCTCGACGAAAACGGCTACCTCGAAGAAGCGCTCGACGAGATCCACGCGCGCCTGCCGGAGGAACTGGAAGT
CGAACTCGACGAGCTGCAAACGGCATTGTCGCTGCTGCAAAGTTTCGACCCGGCCGGCGTGGGGGCGCGCAATGCGGCCG
AGTGCCTGGCGCTGCAAATCAAGCGCTTGCCCGGCATCGCGCTGGTGACGCGACGGATGGCCGTGGCCATCGTCGAAAAG
CACCTGACGTGGTTTGCCCAGCGCGATTTCAACAAGCTGAAAAAAGCGCTGCTGTGCGACGACGAAGACTTGCGCGAAGT
ACAGACCGTGATCCGCCAGTGCAATCCGCACCCCGGTGCGGCGTTCGCGTCCGACGTGTCGGACTACGTGGTGCCGGACG
TGATCGTGAAAAAATCGCGCACCGGCTGGCAGGTCAGCCTGAACAACGACGTCATGCCGCGCCTGCGCGTAAACGCCATG
TACGCCAACCTGCTCAAGCAGAAGAAGGGCGAGGGAGGCGAGGGCGCCATGGGCGCGCAGCTGCAGGAAGCGAAGTGGCT
GATCAAGAATATGCGCCAGCGGTTCGACACCATCCTGCGCGTGGCGCAAGCGATAGTAGAACGACAAAAGAACTTTTTCT
CGCACGGCGCCGTTGCCATGCGCCCCCTTGTGCTTCGCGAAATTGCTGATACACTGGGTTTACACGAGAGCACCATTTCT
CGGGTAACAACTCAGAAATACATGCTGACGCCGCACGGCATGTTTGAGCTGAAATATTTTTTTGGTAGCCACGTCGCCAC
CGAAGCGGGAGGTGAAGCCAGTTCGACGGCGATACGGGCACTGATCGTGCAACTGACAGGAGCTGAAGACCCTAAAAATC
CTTTATCCGACAGTAAGATTGCGGACATGCTGGGAGAACAGGGCATGGTGATTGCGCGACGCACTGTTGCCAAATATCGC
GAAGCCCTCAAAATCCCTCCAGTCAGTCTCCGCAAGTCTTTGTAG

Domains

Predicted by InterproScan.

Sigma-54 factor, Activator interacting domain (AID) (Sigma54_AID)

(4-48)

Sigma-54 factor, core binding domain (Sigma54_CBD)

(129-321)

Sigma-54, DNA binding domain (Sigma54_DBD)

(339-492)


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
  rpoN/rpoN1 Ralstonia pseudosolanacearum GMI1000

61.355

100

0.623