Detailed information    

insolico Bioinformatically predicted

Overview

Name   rpoN/rpoN1   Type   Machinery gene
Locus tag   PDMSB3_RS01995 Genome accession   NZ_LR699553
Coordinates   417506..419023 (-) Length   505 a.a.
NCBI ID   WP_007179408.1    Uniprot ID   A0A5Q4ZA90
Organism   Paraburkholderia dioscoreae strain Msb3     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 412506..424023
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PDMSB3_RS01970 (PDMSB3_0417) - 413321..413953 (-) 633 WP_007179414.1 LON peptidase substrate-binding domain-containing protein -
  PDMSB3_RS01975 (PDMSB3_0418) rapZ 413993..414886 (-) 894 WP_035517717.1 RNase adapter RapZ -
  PDMSB3_RS01980 (PDMSB3_0419) hprK 414983..415951 (-) 969 WP_007179412.1 HPr(Ser) kinase/phosphatase -
  PDMSB3_RS01985 (PDMSB3_0420) ptsN 416091..416606 (-) 516 WP_007179411.1 PTS IIA-like nitrogen regulatory protein PtsN -
  PDMSB3_RS01990 (PDMSB3_0421) hpf 416898..417257 (-) 360 WP_007179410.1 ribosome hibernation-promoting factor, HPF/YfiA family -
  PDMSB3_RS01995 (PDMSB3_0422) rpoN/rpoN1 417506..419023 (-) 1518 WP_007179408.1 RNA polymerase factor sigma-54 Machinery gene
  PDMSB3_RS02000 (PDMSB3_0423) lptB 419231..420016 (-) 786 WP_007179407.1 LPS export ABC transporter ATP-binding protein -
  PDMSB3_RS02005 (PDMSB3_0424) lptA 420013..420684 (-) 672 WP_007179406.1 lipopolysaccharide transport periplasmic protein LptA -
  PDMSB3_RS02010 (PDMSB3_0425) lptC 420705..421313 (-) 609 WP_007179405.1 LPS export ABC transporter periplasmic protein LptC -
  PDMSB3_RS02015 (PDMSB3_0426) - 421310..421870 (-) 561 WP_007179404.1 HAD family hydrolase -
  PDMSB3_RS02020 (PDMSB3_0427) kdsD 421870..422853 (-) 984 WP_007179403.1 arabinose 5-phosphate isomerase KdsD -

Sequence

Protein


Download         Length: 505 a.a.        Molecular weight: 55392.50 Da        Isoelectric Point: 5.0733

>NTDB_id=1129336 PDMSB3_RS01995 WP_007179408.1 417506..419023(-) (rpoN/rpoN1) [Paraburkholderia dioscoreae strain Msb3]
MKASLQLRLSQHLALTPQLQQSIRLLQLSTLELQQEVAMAISQNPLLENEDDWIASPLRVAADGSLIAQAPNSSAPPDQM
GGSTSSSSSSSSERAENGEPQGVDEYNGLAGDSNGDASQWNLDDYGRSGNASDDDDLPPLQIHESSTSLRDHLMAQLRVT
QASPRDRALVTFLIESLDDDGYLAATLEEVLADLPEELEVDLDELNAALALLHSFDPAGVGARSASECLKLQLLRLDASP
TRTLALEIVAHHLELLAARDFTRLRKHLKANDDDLRDAHVLIRSLEPFPGAAYGKAEADYVVPDIMVRKTAQGWQAELNP
EVVPKLRINHLYANILRNNRGDPGSGSLRQQLQEARWLIKNIQQRFETILRVAQAIVERQKSFFVHGEIAMRPLVLREIA
DTLGLHESTVSRVTTGKYMLTPFGTLEFKYFFGSHVSTDTGGAASSTAIRALIKQLIGAENPKSPLSDSRIAELLAEQGF
VVARRTVAKYREALKIPAVNLRKSL

Nucleotide


Download         Length: 1518 bp        

>NTDB_id=1129336 PDMSB3_RS01995 WP_007179408.1 417506..419023(-) (rpoN/rpoN1) [Paraburkholderia dioscoreae strain Msb3]
ATGAAAGCCAGCCTCCAACTCCGCCTATCGCAGCATCTTGCGCTGACGCCGCAACTGCAGCAGTCCATCCGGCTGCTTCA
GTTGTCTACGCTCGAATTGCAGCAGGAAGTCGCAATGGCGATCTCGCAGAATCCGCTCCTCGAGAACGAGGACGATTGGA
TCGCGAGCCCGCTGCGCGTGGCGGCCGACGGCTCGCTGATCGCCCAGGCGCCCAATTCTTCCGCTCCGCCCGACCAGATG
GGCGGCAGCACGTCGTCATCGTCCAGCAGCAGCAGCGAGCGCGCCGAGAACGGCGAGCCGCAGGGCGTGGACGAATACAA
CGGCCTCGCGGGCGACAGTAACGGCGACGCGTCGCAATGGAATCTCGACGACTACGGCCGCTCGGGCAACGCCTCGGACG
ACGACGACCTGCCGCCGCTGCAAATCCACGAATCGAGCACCTCGCTGCGCGATCACCTGATGGCGCAATTGCGCGTCACC
CAGGCGAGTCCGCGCGACCGCGCGCTGGTCACCTTCCTGATCGAATCGCTCGACGACGACGGCTACCTTGCCGCCACACT
CGAAGAAGTGCTGGCCGACCTGCCCGAAGAGCTCGAAGTGGATCTCGACGAACTGAATGCCGCGCTTGCGCTGCTGCATA
GCTTCGACCCGGCCGGGGTCGGCGCGCGCTCCGCGTCGGAATGTCTCAAGCTGCAATTGCTGCGGCTCGATGCCTCACCT
ACCCGCACGCTCGCGCTCGAAATCGTTGCGCACCACCTGGAATTGCTCGCGGCGCGCGACTTCACGCGTCTGCGCAAGCA
TCTGAAGGCCAACGACGACGATCTGCGCGACGCACACGTGCTGATCCGCTCGCTCGAACCGTTCCCCGGCGCCGCCTACG
GCAAGGCCGAAGCGGACTATGTCGTGCCGGACATCATGGTGCGTAAAACGGCACAGGGCTGGCAGGCCGAGCTGAACCCC
GAAGTCGTGCCGAAGCTGCGTATCAACCATCTTTACGCGAATATTCTGCGCAATAACCGGGGCGACCCGGGCAGCGGTTC
GTTGCGCCAGCAACTGCAGGAAGCGCGCTGGCTGATCAAAAATATCCAGCAGCGTTTCGAGACGATCCTCAGAGTGGCGC
AAGCTATTGTGGAGCGTCAAAAGAGCTTTTTTGTGCACGGCGAAATTGCCATGCGCCCCTTGGTTTTGCGGGAAATTGCT
GATACGCTGGGCCTACACGAGTCAACTGTCTCGCGTGTGACAACCGGTAAATACATGCTGACCCCATTCGGGACGCTTGA
ATTTAAGTACTTCTTCGGATCACACGTTTCGACTGACACGGGCGGCGCGGCGTCTTCAACGGCGATCCGTGCGCTCATCA
AGCAACTGATAGGAGCGGAAAACCCGAAATCTCCTCTTTCAGACAGCCGCATAGCCGAACTGCTGGCGGAACAGGGCTTC
GTGGTCGCACGGCGTACCGTCGCGAAATATCGTGAAGCGCTCAAGATTCCGGCAGTCAACCTGCGCAAGTCTTTATAG

Domains

Predicted by InterproScan.

Sigma-54, DNA binding domain (Sigma54_DBD)

(348-503)

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

(4-48)

Sigma-54 factor, core binding domain (Sigma54_CBD)

(141-332)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A5Q4ZA90

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

67.525

100

0.675

Multiple sequence alignment