Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   SDE_RS04540 Genome accession   NC_007912
Coordinates   1116889..1117785 (-) Length   298 a.a.
NCBI ID   WP_011467344.1    Uniprot ID   Q21MF6
Organism   Saccharophagus degradans 2-40     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1111889..1122785
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SDE_RS04520 (Sde_0857) argJ 1113874..1115094 (+) 1221 WP_011467340.1 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ -
  SDE_RS04525 (Sde_0858) - 1115075..1116064 (+) 990 WP_041324216.1 Nudix family hydrolase -
  SDE_RS04530 (Sde_0859) - 1116061..1116273 (-) 213 WP_011467342.1 DNA gyrase inhibitor YacG -
  SDE_RS04535 (Sde_0860) coaE 1116278..1116889 (-) 612 WP_011467343.1 dephospho-CoA kinase -
  SDE_RS04540 (Sde_0861) pilD 1116889..1117785 (-) 897 WP_011467344.1 prepilin peptidase Machinery gene
  SDE_RS04545 (Sde_0862) pilC 1117788..1119005 (-) 1218 WP_011467345.1 type II secretion system F family protein Machinery gene
  SDE_RS04550 (Sde_0863) pilB 1119009..1120730 (-) 1722 WP_011467346.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SDE_RS04555 (Sde_0864) pilA2 1121089..1121508 (+) 420 WP_011467347.1 pilin Machinery gene

Sequence

Protein


Download         Length: 298 a.a.        Molecular weight: 32517.38 Da        Isoelectric Point: 6.0847

>NTDB_id=25562 SDE_RS04540 WP_011467344.1 1116889..1117785(-) (pilD) [Saccharophagus degradans 2-40]
MDFTHFSNLQIAYIYFVVAIIGATIGSFLNVVIYRLPLSLMKGWEQECKEFLASKGEAETPAQNEQESEPFNIAFPASHC
PNCKAPVKAWQNIPIISYLLLKGKCAACNVKISLRYPIVEFVTSVLSIWVVYSLGLTVEAGLVLLLTWSLLVLTLIDVDH
QLLPDNITLPLLWLGLLANTQGHFTDLQSAVIGAVAGYLVLWSVFWLFKLVTGKEGMGFGDFKLLAALGAWMGWQALPVI
IILSSAVGAIIGIGGILIFGKDKNKPIPFGPYLAIAGWIAFFWGDAITGAYLSYATGQ

Nucleotide


Download         Length: 897 bp        

>NTDB_id=25562 SDE_RS04540 WP_011467344.1 1116889..1117785(-) (pilD) [Saccharophagus degradans 2-40]
GTGGATTTCACTCATTTTTCAAACTTACAAATTGCCTACATCTATTTCGTCGTCGCCATTATCGGCGCCACAATTGGTAG
CTTTTTAAACGTTGTTATCTACCGGCTCCCGCTCTCGTTAATGAAAGGCTGGGAGCAGGAGTGCAAAGAGTTTCTGGCTT
CTAAAGGCGAAGCCGAGACTCCAGCACAAAACGAGCAAGAGTCAGAACCCTTCAATATTGCCTTTCCTGCGTCACACTGC
CCTAACTGCAAGGCTCCTGTTAAGGCCTGGCAAAACATTCCCATTATTAGTTACTTACTGCTAAAAGGTAAGTGCGCTGC
GTGTAATGTAAAAATATCGCTGCGCTACCCTATAGTTGAATTCGTTACTTCGGTATTAAGTATTTGGGTTGTTTACAGCT
TGGGGCTAACGGTAGAAGCAGGCTTGGTACTGCTATTAACATGGAGCCTGCTGGTTTTAACGTTAATTGATGTAGACCAC
CAACTACTGCCAGACAACATTACCCTACCGCTTTTGTGGCTGGGGCTACTTGCGAATACTCAAGGGCATTTTACCGACCT
GCAAAGTGCAGTCATTGGTGCTGTTGCAGGCTACCTAGTGCTTTGGAGCGTGTTCTGGTTGTTTAAGCTTGTAACCGGCA
AAGAGGGCATGGGCTTTGGGGATTTCAAGTTACTGGCGGCACTTGGCGCTTGGATGGGCTGGCAAGCTCTGCCGGTAATC
ATTATTTTGTCGTCTGCGGTGGGCGCTATTATTGGTATTGGCGGCATACTTATTTTCGGCAAAGATAAAAACAAGCCTAT
TCCTTTCGGCCCATATTTAGCCATAGCGGGTTGGATAGCCTTCTTCTGGGGCGACGCCATTACCGGCGCTTACCTTTCCT
ACGCCACCGGCCAATAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-132)

Type IV leader peptidase family (Peptidase_A24)

(145-253)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q21MF6

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

51.613

93.624

0.483
  pilD Acinetobacter baumannii D1279779

51.613

93.624

0.483
  pilD Neisseria gonorrhoeae MS11

49.814

90.268

0.45
  pilD Vibrio cholerae strain A1552

46.996

94.966

0.446
  pilD Vibrio campbellii strain DS40M4

46.316

95.638

0.443

Multiple sequence alignment