Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   PVK79_RS04015 Genome accession   NZ_CP118496
Coordinates   907697..908596 (-) Length   299 a.a.
NCBI ID   WP_274804052.1    Uniprot ID   -
Organism   Pseudoalteromonas rhizosphaerae strain hCg-42     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 902697..913596
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PVK79_RS03990 raiA 903061..903417 (+) 357 WP_145235189.1 ribosome-associated translation inhibitor RaiA -
  PVK79_RS03995 - 903623..904795 (+) 1173 WP_145235524.1 divalent metal cation transporter -
  PVK79_RS04000 yacG 904946..905176 (-) 231 WP_182735849.1 DNA gyrase inhibitor YacG -
  PVK79_RS04005 pilB 905244..906923 (-) 1680 WP_145235193.1 type IV-A pilus assembly ATPase PilB Machinery gene
  PVK79_RS04010 coaE 907063..907695 (-) 633 WP_257325349.1 dephospho-CoA kinase -
  PVK79_RS04015 pilD 907697..908596 (-) 900 WP_274804052.1 A24 family peptidase Machinery gene
  PVK79_RS04020 pilC 909851..911077 (-) 1227 WP_257325350.1 type II secretion system F family protein Machinery gene
  PVK79_RS04025 - 911080..912396 (-) 1317 WP_257325351.1 hypothetical protein -
  PVK79_RS04030 - 912451..912900 (-) 450 WP_257325352.1 pilin -

Sequence

Protein


Download         Length: 299 a.a.        Molecular weight: 33175.71 Da        Isoelectric Point: 6.8417

>NTDB_id=792830 PVK79_RS04015 WP_274804052.1 907697..908596(-) (pilD) [Pseudoalteromonas rhizosphaerae strain hCg-42]
MQNFFLDIITVMQNQLWFYLLTVGLVSLCIGSFLNVVIYRLPIMMQREWQTECRVLLADDLKPTKADNTEAEFNLVKPNS
TCPKCKTAIKPWQNIPVISWLLLKGRCASCSNPISVRYPIVEMLTAVLSLIVAYTFGATEQALLYILITWVLVALTFIDI
DHMLLPDQLTLPLVWLALIAAVMGITISPTDAIIGAACGYLSLWSVFWLFKLITGKEGMGYGDFKLLAVFGALLGWQSLL
TIVLLSSVVGAIIGIALLSIQGKDKATPIPFGPYLAIAGWVTLLWGTQIQVFYFNLLGY

Nucleotide


Download         Length: 900 bp        

>NTDB_id=792830 PVK79_RS04015 WP_274804052.1 907697..908596(-) (pilD) [Pseudoalteromonas rhizosphaerae strain hCg-42]
ATGCAAAATTTCTTTCTCGATATAATCACTGTTATGCAAAACCAATTATGGTTTTATTTACTCACTGTTGGCTTAGTGAG
CCTGTGTATTGGCAGTTTTTTGAATGTAGTTATTTACCGGTTGCCGATAATGATGCAACGTGAATGGCAAACAGAATGCC
GTGTTTTACTGGCTGACGATTTAAAACCCACAAAAGCTGATAATACAGAAGCTGAGTTTAATCTGGTCAAGCCTAACTCT
ACTTGCCCAAAATGCAAAACTGCCATTAAGCCTTGGCAAAACATTCCTGTTATTAGCTGGTTATTGTTAAAAGGTCGCTG
CGCTAGTTGCAGTAACCCTATTTCAGTACGTTACCCAATTGTTGAAATGCTTACTGCGGTTTTAAGCTTAATAGTGGCCT
ACACCTTTGGCGCGACTGAGCAGGCACTACTGTATATTTTAATTACTTGGGTGCTCGTCGCCCTGACCTTTATTGACATT
GATCATATGCTACTGCCTGACCAACTCACCTTACCTTTAGTCTGGTTAGCATTAATTGCTGCGGTAATGGGCATCACTAT
CTCCCCAACAGATGCCATTATTGGTGCAGCATGTGGTTACTTAAGCCTCTGGAGCGTATTTTGGCTATTTAAACTGATCA
CCGGTAAAGAAGGCATGGGCTATGGTGATTTTAAATTACTGGCGGTATTTGGCGCATTGCTTGGCTGGCAATCATTACTC
ACCATTGTTTTATTATCGAGTGTAGTGGGCGCTATTATTGGTATCGCATTATTGAGTATTCAAGGCAAAGATAAAGCCAC
GCCAATTCCATTTGGGCCTTATTTAGCCATTGCCGGCTGGGTTACTTTGTTATGGGGCACACAAATCCAAGTATTTTATT
TTAATTTGTTAGGTTATTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(147-255)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(26-136)


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 baumannii D1279779

53.633

96.656

0.518
  pilD Acinetobacter nosocomialis M2

53.287

96.656

0.515
  pilD Vibrio cholerae strain A1552

53.901

94.314

0.508
  pilD Vibrio campbellii strain DS40M4

52.778

96.321

0.508
  pilD Neisseria gonorrhoeae MS11

45.525

85.953

0.391