Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   R2K28_RS02960 Genome accession   NZ_OY734020
Coordinates   648892..649758 (-) Length   288 a.a.
NCBI ID   WP_316369671.1    Uniprot ID   -
Organism   Candidatus Thiodiazotropha sp. CDECU1 isolate 46184     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 643892..654758
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  R2K28_RS02945 purE 644700..645200 (+) 501 WP_316367904.1 5-(carboxyamino)imidazole ribonucleotide mutase -
  R2K28_RS02950 clpB 645467..648061 (+) 2595 WP_316367905.1 ATP-dependent chaperone ClpB -
  R2K28_RS02955 coaE 648296..648892 (-) 597 WP_316367906.1 dephospho-CoA kinase -
  R2K28_RS02960 pilD 648892..649758 (-) 867 WP_316369671.1 A24 family peptidase Machinery gene
  R2K28_RS02965 pilC 649804..651033 (-) 1230 WP_316367907.1 type II secretion system F family protein Machinery gene
  R2K28_RS02970 pilB 651037..652752 (-) 1716 WP_316367908.1 type IV-A pilus assembly ATPase PilB Machinery gene
  R2K28_RS02975 - 653239..653694 (-) 456 WP_316367909.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -

Sequence

Protein


Download         Length: 288 a.a.        Molecular weight: 32183.10 Da        Isoelectric Point: 7.6856

>NTDB_id=1160746 R2K28_RS02960 WP_316369671.1 648892..649758(-) (pilD) [Candidatus Thiodiazotropha sp. CDECU1 isolate 46184]
MVDFLQQNHWAFLLTVILIGLVVGSFLNVVIHRLPKMMEQQWRRDCQELEGALSEEETAPYNLNRPASHCPKCGHKIRPW
ENIPIISWLMLKGRCSQCNTLISPRYPIIEAVTAILSLAVAIHFGFTWATLAALLLTWALIALSVIDFDVQLLPDNITLP
FLWLGLLLSLAGVFTDTSTAIIGAAAGYLSLWSVYQLFKRLTGKEGMGYGDFKLLAMLGAWLGWQYLPQIILLSALVGAV
VGILLIVVRGRDRNIPIPFGPYLAAAGWISLMWGEQINNAYLRWSGMY

Nucleotide


Download         Length: 867 bp        

>NTDB_id=1160746 R2K28_RS02960 WP_316369671.1 648892..649758(-) (pilD) [Candidatus Thiodiazotropha sp. CDECU1 isolate 46184]
ATAGTCGACTTCCTACAGCAAAACCATTGGGCGTTCCTGCTCACTGTCATCCTGATCGGTTTGGTGGTGGGAAGCTTTCT
CAATGTGGTGATCCATCGTCTACCAAAGATGATGGAGCAACAGTGGCGCAGGGATTGCCAGGAGCTGGAAGGTGCCCTCA
GCGAAGAGGAGACCGCCCCCTACAACCTCAACCGACCGGCATCCCACTGCCCGAAATGCGGCCATAAGATACGCCCCTGG
GAGAATATCCCCATTATCAGTTGGCTGATGCTTAAAGGCCGCTGCTCCCAGTGCAATACCTTGATCAGCCCCAGATACCC
GATTATTGAAGCCGTCACCGCAATCCTTTCGTTGGCGGTGGCAATCCATTTCGGTTTCACCTGGGCAACCCTGGCAGCGC
TGTTGCTGACCTGGGCCCTGATCGCCCTCAGCGTGATCGATTTCGATGTCCAGTTGCTCCCCGACAATATCACCCTCCCC
TTTCTTTGGTTGGGACTGCTGTTGAGTCTTGCGGGTGTGTTTACCGATACCAGCACCGCTATCATCGGCGCCGCGGCCGG
TTACCTCTCCCTATGGAGTGTCTACCAGCTCTTCAAACGACTCACCGGCAAGGAGGGCATGGGGTATGGTGATTTCAAAC
TGTTGGCAATGCTCGGAGCCTGGCTTGGTTGGCAATACCTGCCGCAGATCATTCTACTCTCTGCCCTCGTCGGTGCAGTA
GTCGGTATCCTGTTGATCGTCGTGCGCGGACGGGATCGCAATATCCCCATCCCCTTCGGCCCCTATCTGGCGGCAGCCGG
TTGGATCAGTCTGATGTGGGGCGAACAGATCAACAACGCCTATCTGCGCTGGTCCGGTATGTACTGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(18-124)

Type IV leader peptidase family (Peptidase_A24)

(135-243)


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 campbellii strain DS40M4

52.448

99.306

0.521
  pilD Acinetobacter baumannii D1279779

51.93

98.958

0.514
  pilD Vibrio cholerae strain A1552

52.313

97.569

0.51
  pilD Acinetobacter nosocomialis M2

51.228

98.958

0.507
  pilD Neisseria gonorrhoeae MS11

50.593

87.847

0.444

Multiple sequence alignment