Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   GYK50_RS12405 Genome accession   NZ_CP048752
Coordinates   2927293..2928195 (+) Length   300 a.a.
NCBI ID   WP_093069694.1    Uniprot ID   -
Organism   Psychrobacter pacificensis strain WSY-P01     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2922293..2933195
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GYK50_RS12390 (GYK50_12390) tpiA 2922366..2923178 (-) 813 WP_093069701.1 triose-phosphate isomerase -
  GYK50_RS12395 (GYK50_12395) pilB 2923846..2925561 (+) 1716 WP_093069698.1 type IV-A pilus assembly ATPase PilB Machinery gene
  GYK50_RS12400 (GYK50_12400) pilC 2926062..2927285 (+) 1224 WP_093069696.1 type II secretion system F family protein Machinery gene
  GYK50_RS12405 (GYK50_12405) pilD 2927293..2928195 (+) 903 WP_093069694.1 A24 family peptidase Machinery gene
  GYK50_RS12410 (GYK50_12410) coaE 2928299..2928985 (+) 687 WP_212564039.1 dephospho-CoA kinase -
  GYK50_RS12415 (GYK50_12415) rlmB 2928948..2929718 (-) 771 WP_093069689.1 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB -
  GYK50_RS12420 (GYK50_12420) - 2929965..2930300 (-) 336 WP_058023616.1 pyrimidine/purine nucleoside phosphorylase -
  GYK50_RS12425 (GYK50_12425) recN 2931020..2932699 (+) 1680 WP_212564040.1 DNA repair protein RecN -

Sequence

Protein


Download         Length: 300 a.a.        Molecular weight: 33127.72 Da        Isoelectric Point: 8.9103

>NTDB_id=422634 GYK50_RS12405 WP_093069694.1 2927293..2928195(+) (pilD) [Psychrobacter pacificensis strain WSY-P01]
MQFIQLLQENIALALVVFGLLGLCVGSFLNVVIHRIPLMMIYGWRQECSQFMIEQADMPREHTLPIANVVATDQPITLSR
PASRCPHCAHKIRWYENIPLISWLALKGRCSNCKAAIGLRYPVVELVTALLSVLVIYKFGVNATGLSALVLVWTLVALTG
IDFDTQLLPDRLTFPLAGLGLAVNSQGWFVSPTQSIWGLLFGFLSLWIVVKVFYLITKKHGMGQGDFKLLAVLGAWLGPM
MLPLIILLSSLLGSIVGIILMKKQGESRPFAFGPYIAVAGIVALLYGSDIVSWYLGMYTY

Nucleotide


Download         Length: 903 bp        

>NTDB_id=422634 GYK50_RS12405 WP_093069694.1 2927293..2928195(+) (pilD) [Psychrobacter pacificensis strain WSY-P01]
ATGCAATTCATACAGTTACTACAAGAAAATATAGCTCTAGCCTTGGTCGTATTTGGTTTGTTAGGTCTTTGTGTTGGTAG
TTTTTTAAATGTTGTGATTCATCGTATCCCACTTATGATGATTTACGGTTGGCGACAAGAATGTAGCCAATTTATGATCG
AACAGGCAGATATGCCACGCGAGCATACGTTACCTATAGCGAATGTCGTGGCTACTGACCAACCCATTACTTTGAGTCGA
CCTGCCTCACGCTGCCCCCATTGCGCTCATAAGATCAGATGGTATGAAAACATACCCTTAATCAGCTGGCTGGCACTAAA
AGGGCGCTGCTCAAACTGCAAAGCTGCGATTGGTTTGCGGTATCCTGTAGTTGAGTTAGTAACCGCTTTACTATCGGTGC
TCGTGATCTACAAATTCGGTGTCAATGCAACTGGATTGTCAGCGCTCGTTTTAGTGTGGACACTAGTGGCTCTAACCGGT
ATTGATTTTGATACGCAGCTACTACCCGATCGCCTGACTTTTCCACTAGCAGGTCTAGGATTGGCCGTCAACTCACAAGG
CTGGTTTGTCTCACCAACGCAGTCGATATGGGGTTTACTCTTCGGATTTTTATCACTCTGGATCGTCGTTAAAGTATTCT
ACTTAATCACTAAGAAACATGGGATGGGACAAGGTGATTTTAAATTACTAGCAGTATTAGGTGCTTGGCTCGGGCCCATG
ATGTTGCCATTAATTATTTTATTATCATCCTTGCTTGGGTCGATCGTCGGAATAATCTTGATGAAAAAACAAGGTGAGAG
CAGGCCTTTTGCCTTTGGTCCTTACATTGCTGTCGCAGGCATTGTTGCTTTATTATACGGCTCAGATATCGTCAGCTGGT
ATCTTGGTATGTATACTTACTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(149-258)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-139)


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 Acinetobacter nosocomialis M2

54.514

96

0.523
  pilD Acinetobacter baumannii D1279779

53.819

96

0.517
  pilD Vibrio cholerae strain A1552

48.387

93

0.45
  pilD Vibrio campbellii strain DS40M4

47.038

95.667

0.45
  pilD Neisseria gonorrhoeae MS11

41.786

93.333

0.39

Multiple sequence alignment