Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   AB1S65_RS16990 Genome accession   NZ_CP160474
Coordinates   4182164..4183063 (+) Length   299 a.a.
NCBI ID   WP_280945980.1    Uniprot ID   -
Organism   Saccharophagus degradans strain HMH0004     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 4177164..4188063
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AB1S65_RS16975 (AB1S65_16975) - 4178424..4178855 (-) 432 WP_280945977.1 pilin -
  AB1S65_RS16980 (AB1S65_16980) pilB 4179213..4180943 (+) 1731 WP_280945978.1 type IV-A pilus assembly ATPase PilB Machinery gene
  AB1S65_RS16985 (AB1S65_16985) pilC 4180947..4182164 (+) 1218 WP_280945979.1 type II secretion system F family protein Machinery gene
  AB1S65_RS16990 (AB1S65_16990) pilD 4182164..4183063 (+) 900 WP_280945980.1 prepilin peptidase Machinery gene
  AB1S65_RS16995 (AB1S65_16995) coaE 4183063..4183674 (+) 612 WP_280945981.1 dephospho-CoA kinase -
  AB1S65_RS17000 (AB1S65_17000) - 4183679..4183891 (+) 213 WP_011467342.1 DNA gyrase inhibitor YacG -
  AB1S65_RS17005 (AB1S65_17005) - 4183888..4184877 (-) 990 WP_280945982.1 Nudix family hydrolase -
  AB1S65_RS17010 (AB1S65_17010) argJ 4184858..4186078 (-) 1221 WP_280945983.1 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ -

Sequence

Protein


Download         Length: 299 a.a.        Molecular weight: 32588.54 Da        Isoelectric Point: 5.2542

>NTDB_id=1021469 AB1S65_RS16990 WP_280945980.1 4182164..4183063(+) (pilD) [Saccharophagus degradans strain HMH0004]
MLELPQFTPEQLIYIYAVVAIIGATIGSFLNVVIYRLPLSLMKGWEQECKEFLASKGEPETPAQNEQESEPFNIAFPASH
CPNCKAPVKAWQNIPIISYLLLKGKCAACNVKISLRYPIVEFVTSVLSVWVVYSLGLTVEAGLVLLLTWSLLVLTLIDVD
HQLLPDNITLPLLWLGLLANTQGHFTDLQSAVIGAVAGYLVLWSVFWLFKLVTGKEGMGFGDFKLLAALGAWMGWQALPV
IIILSSAVGAIIGIGGILIFGKDKNKPIPFGPYLAIAGWIAFFWGDAITGAYLSYATGQ

Nucleotide


Download         Length: 900 bp        

>NTDB_id=1021469 AB1S65_RS16990 WP_280945980.1 4182164..4183063(+) (pilD) [Saccharophagus degradans strain HMH0004]
ATGCTGGAATTACCGCAATTCACTCCTGAGCAACTCATATATATTTATGCTGTTGTCGCCATCATCGGCGCCACCATTGG
CAGTTTTTTAAACGTTGTTATTTACCGGCTCCCACTCTCGCTAATGAAAGGCTGGGAGCAGGAGTGCAAAGAGTTTCTGG
CTTCTAAAGGCGAACCGGAGACTCCAGCACAAAACGAGCAAGAGTCAGAACCCTTCAATATTGCCTTTCCTGCGTCACAC
TGCCCTAACTGCAAGGCTCCTGTTAAGGCCTGGCAAAACATTCCCATTATTAGTTACTTACTGCTAAAAGGTAAGTGCGC
TGCGTGTAATGTAAAAATATCGCTGCGCTACCCTATAGTTGAATTCGTTACTTCGGTACTAAGTGTTTGGGTTGTTTACA
GCCTGGGGCTAACGGTAGAAGCAGGCTTGGTATTGCTATTAACATGGAGCCTACTGGTTTTAACGTTAATTGATGTAGAC
CACCAACTACTGCCAGACAACATCACCCTACCGCTTTTATGGCTGGGGCTACTTGCGAATACTCAAGGGCATTTTACCGA
CCTGCAAAGTGCAGTCATTGGTGCTGTTGCAGGCTACCTAGTACTTTGGAGCGTGTTCTGGTTGTTTAAGCTTGTAACCG
GCAAAGAGGGTATGGGCTTTGGGGATTTCAAGTTACTGGCGGCACTTGGCGCCTGGATGGGCTGGCAAGCCCTGCCGGTA
ATCATTATTTTGTCGTCTGCGGTGGGAGCCATTATAGGTATTGGCGGCATACTTATTTTCGGCAAAGATAAAAACAAGCC
TATTCCTTTCGGCCCATATTTAGCCATAGCGGGTTGGATAGCCTTCTTCTGGGGCGATGCCATTACCGGCGCTTACCTTT
CCTACGCCACCGGCCAATAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-134)

Type IV leader peptidase family (Peptidase_A24)

(146-254)


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

50.171

97.993

0.492
  pilD Acinetobacter baumannii D1279779

50.171

97.993

0.492
  pilD Vibrio cholerae strain A1552

46

100

0.462
  pilD Vibrio campbellii strain DS40M4

45.667

100

0.458
  pilD Neisseria gonorrhoeae MS11

50.186

89.967

0.452

Multiple sequence alignment