Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   NHL60_RS08385 Genome accession   NZ_CP099975
Coordinates   1759748..1760599 (-) Length   283 a.a.
NCBI ID   WP_253451379.1    Uniprot ID   -
Organism   Halomonas sp. Y3     
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 1747867..1759632 1759748..1760599 flank 116


Gene organization within MGE regions


Location: 1747867..1760599
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  NHL60_RS08305 - 1747867..1748574 (+) 708 WP_253451353.1 lipopolysaccharide kinase InaA family protein -
  NHL60_RS08310 - 1748764..1749528 (+) 765 WP_253452093.1 glycosyltransferase family 32 protein -
  NHL60_RS08315 - 1749525..1750577 (-) 1053 WP_253451355.1 polysaccharide pyruvyl transferase family protein -
  NHL60_RS08320 - 1750717..1751796 (+) 1080 WP_253451357.1 glycosyltransferase family 9 protein -
  NHL60_RS08325 - 1751721..1752038 (-) 318 WP_301271110.1 PD-(D/E)XK nuclease domain-containing protein -
  NHL60_RS08330 - 1752046..1753911 (-) 1866 WP_253451361.1 SEC-C metal-binding domain-containing protein -
  NHL60_RS08335 rimO 1753967..1755292 (-) 1326 WP_253451363.1 30S ribosomal protein S12 methylthiotransferase RimO -
  NHL60_RS08340 - 1755513..1755752 (+) 240 WP_253451365.1 DUF2281 domain-containing protein -
  NHL60_RS08345 - 1755749..1756102 (+) 354 WP_253451367.1 type II toxin-antitoxin system PemK/MazF family toxin -
  NHL60_RS08350 - 1756127..1756537 (+) 411 WP_253451369.1 SRPBCC family protein -
  NHL60_RS08355 - 1756660..1756800 (+) 141 WP_253451371.1 hypothetical protein -
  NHL60_RS08360 - 1756979..1757857 (-) 879 WP_253451373.1 DNA replication terminus site-binding protein -
  NHL60_RS08365 yacG 1757865..1758095 (-) 231 WP_253451375.1 DNA gyrase inhibitor YacG -
  NHL60_RS08370 coaE 1758092..1758733 (-) 642 WP_253451377.1 dephospho-CoA kinase -
  NHL60_RS08375 - 1758790..1759632 (-) 843 WP_301271100.1 leucine-rich repeat protein -
  NHL60_RS08385 pilD 1759748..1760599 (-) 852 WP_253451379.1 A24 family peptidase Machinery gene

Sequence

Protein


Download         Length: 283 a.a.        Molecular weight: 30405.70 Da        Isoelectric Point: 7.8611

>NTDB_id=703084 NHL60_RS08385 WP_253451379.1 1759748..1760599(-) (pilD) [Halomonas sp. Y3]
MLDLAPPLLWPLAACLGLCLGSFLNVVIVRLPVMLMLGWRAEAREALELPGESQPTFNLATPRSLCPSCETPIAWHDNLP
VVGWLKRRGRCASCNARISPQYPLVELAGAALTLAVVALFGPSWQGLFVLGACLALLALAVIDLRTQLLPDIVTLPLLWA
GLLYQLLFQPLLLPSAVMGAMAGYLVLWSFYWAFKLITGKEGMGYGDFKLMAALGAWLGWQALPLVLILSAGIGAIVGLL
IQLAVPRLRGAPLPFGPWLALAGWVALLGGEPLMAAYGQFFLL

Nucleotide


Download         Length: 852 bp        

>NTDB_id=703084 NHL60_RS08385 WP_253451379.1 1759748..1760599(-) (pilD) [Halomonas sp. Y3]
TTGCTTGACCTAGCCCCTCCCCTGCTCTGGCCGCTGGCCGCCTGCCTGGGCCTCTGCCTGGGCAGCTTTCTCAACGTGGT
GATCGTGCGCCTGCCGGTAATGCTGATGCTCGGCTGGCGGGCCGAGGCCCGGGAGGCGCTGGAGCTTCCGGGTGAGTCGC
AACCGACATTCAACCTGGCCACGCCCCGCTCCCTGTGCCCGAGCTGCGAGACCCCCATCGCCTGGCACGATAACCTCCCG
GTTGTGGGCTGGCTCAAGCGCCGCGGACGCTGCGCCAGCTGCAACGCCCGCATCAGCCCCCAGTACCCCTTGGTAGAGCT
GGCCGGCGCGGCGCTGACCCTTGCCGTGGTGGCGCTCTTCGGGCCGAGCTGGCAGGGTCTCTTCGTGCTGGGCGCCTGCC
TTGCGCTGCTGGCCCTGGCGGTGATCGACCTGCGCACCCAGCTGCTGCCGGATATCGTCACCCTGCCGCTGCTCTGGGCG
GGGCTTCTCTACCAGCTGCTGTTCCAGCCTCTGCTGCTGCCCAGTGCCGTGATGGGCGCCATGGCGGGCTACCTGGTGCT
ATGGAGCTTCTACTGGGCCTTCAAGCTGATCACCGGCAAGGAGGGCATGGGCTACGGCGACTTCAAGCTGATGGCGGCGC
TGGGTGCCTGGCTGGGCTGGCAGGCCCTCCCCCTGGTGCTGATTCTCTCGGCGGGGATCGGCGCCATCGTCGGCCTTCTG
ATCCAGCTGGCCGTGCCGCGGCTGCGCGGCGCCCCCCTGCCCTTCGGCCCCTGGCTGGCCCTTGCCGGCTGGGTCGCGCT
GCTAGGCGGCGAACCGCTGATGGCCGCCTACGGGCAGTTTTTCCTGCTCTAG

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(16-118)

Type IV leader peptidase family (Peptidase_A24)

(133-239)


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
  pilD Vibrio cholerae strain A1552

50.182

97.173

0.488
  pilD Vibrio campbellii strain DS40M4

47.719

100

0.481
  pilD Acinetobacter baumannii D1279779

46.715

96.82

0.452
  pilD Acinetobacter nosocomialis M2

46.35

96.82

0.449
  pilD Neisseria gonorrhoeae MS11

45.848

97.88

0.449