Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   AMJAP_RS04800 Genome accession   NZ_AP014545
Coordinates   1046316..1047212 (-) Length   298 a.a.
NCBI ID   WP_019621936.1    Uniprot ID   -
Organism   Amphritea japonica ATCC BAA-1530     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1041316..1052212
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AMJAP_RS04780 (AMJAP_0920) argJ 1043218..1044435 (+) 1218 WP_019621932.1 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ -
  AMJAP_RS04785 (AMJAP_0921) - 1044451..1045398 (+) 948 WP_019621933.1 Nudix family hydrolase -
  AMJAP_RS04790 (AMJAP_0922) yacG 1045430..1045669 (-) 240 WP_019621934.1 DNA gyrase inhibitor YacG -
  AMJAP_RS04795 (AMJAP_0923) coaE 1045671..1046279 (-) 609 WP_019621935.1 dephospho-CoA kinase -
  AMJAP_RS04800 (AMJAP_0924) pilD 1046316..1047212 (-) 897 WP_019621936.1 prepilin peptidase Machinery gene
  AMJAP_RS04805 (AMJAP_0925) pilC 1047284..1048510 (-) 1227 WP_019621937.1 type II secretion system F family protein Machinery gene
  AMJAP_RS04810 (AMJAP_0926) pilB 1048588..1050306 (-) 1719 WP_019621938.1 type IV-A pilus assembly ATPase PilB Machinery gene
  AMJAP_RS17820 (AMJAP_0927) - 1050559..1051059 (+) 501 WP_019621939.1 pilin -
  AMJAP_RS04820 (AMJAP_0928) - 1051149..1051508 (+) 360 WP_019621940.1 hypothetical protein -

Sequence

Protein


Download         Length: 298 a.a.        Molecular weight: 32807.58 Da        Isoelectric Point: 5.1433

>NTDB_id=65856 AMJAP_RS04800 WP_019621936.1 1046316..1047212(-) (pilD) [Amphritea japonica ATCC BAA-1530]
MLFELIAANTWLSVSVAFGFALLIGSFLNVVIHRLPLMMEHEWQLMAAEAANNNTTDTGTTEHPKEPATVYNLAQPASTC
PTCGHLIHWYENIPLISYFLILGGKCSSCKTPISLRYPLIELITAAISAAIIYLYGFNLVAFSIVFFSWCLIALTAIDID
HQLLPDKITLPLLWIGLILNSFDYFTSLPSALWGAVLGYLSLWSVYWLFKLITGKEGMGYGDFKLLAALGAWAGADMLPL
IILASSLIGAVVGGLMIAFSRHESQTPIPFGPYLAGAGWIALLWGHDLTDWYLQLLNF

Nucleotide


Download         Length: 897 bp        

>NTDB_id=65856 AMJAP_RS04800 WP_019621936.1 1046316..1047212(-) (pilD) [Amphritea japonica ATCC BAA-1530]
ATGCTGTTTGAACTTATTGCAGCCAATACATGGCTGTCAGTATCAGTGGCTTTTGGATTTGCTCTTCTGATTGGTAGCTT
TCTCAATGTCGTTATCCACCGACTGCCGTTGATGATGGAGCATGAATGGCAGTTAATGGCAGCCGAAGCAGCCAATAACA
ATACAACTGATACGGGCACAACTGAGCACCCTAAAGAGCCTGCGACCGTATATAATTTAGCTCAGCCTGCCTCTACCTGC
CCAACCTGTGGTCACCTGATACACTGGTATGAAAACATTCCTCTTATCAGCTACTTTCTGATACTGGGAGGAAAATGCAG
TAGCTGCAAAACCCCAATATCACTGCGATATCCGCTGATTGAGCTGATAACAGCAGCGATATCTGCCGCTATCATCTACC
TTTATGGCTTTAATCTCGTTGCCTTTAGCATTGTATTTTTTAGCTGGTGCCTGATCGCATTAACCGCTATTGATATAGAT
CATCAACTGCTACCCGACAAAATAACACTGCCACTGCTCTGGATTGGACTGATACTAAATAGTTTCGACTACTTCACCAG
CCTGCCTTCGGCGCTCTGGGGTGCCGTATTGGGTTACCTTTCTCTTTGGTCTGTGTACTGGCTATTTAAGCTGATTACCG
GAAAAGAAGGCATGGGCTATGGTGACTTCAAGCTATTAGCTGCATTAGGCGCATGGGCTGGCGCGGACATGCTGCCATTG
ATTATTCTTGCCTCTTCACTCATTGGCGCCGTAGTTGGCGGCTTGATGATAGCCTTCAGCCGTCATGAGTCTCAAACACC
CATTCCTTTTGGGCCTTATCTGGCTGGAGCTGGCTGGATAGCGCTACTCTGGGGCCATGACCTGACTGATTGGTATCTTC
AGCTATTAAATTTTTAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-133)

Type IV leader peptidase family (Peptidase_A24)

(146-253)


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

52.069

97.315

0.507
  pilD Vibrio campbellii strain DS40M4

50.172

97.651

0.49
  pilD Acinetobacter nosocomialis M2

51.408

95.302

0.49
  pilD Acinetobacter baumannii D1279779

51.056

95.302

0.487
  pilD Neisseria gonorrhoeae MS11

47.584

90.268

0.43

Multiple sequence alignment