Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   LOY49_RS22405 Genome accession   NZ_CP087167
Coordinates   5010829..5011701 (+) Length   290 a.a.
NCBI ID   WP_258603693.1    Uniprot ID   -
Organism   Pseudomonas atacamensis strain B21-050     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 5005829..5016701
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LOY49_RS22380 (LOY49_22350) - 5006075..5006374 (+) 300 WP_024014339.1 DUF2845 domain-containing protein -
  LOY49_RS22385 (LOY49_22355) - 5006610..5006963 (-) 354 WP_016773155.1 BON domain-containing protein -
  LOY49_RS22390 (LOY49_22360) pilA/pilAI 5007258..5007680 (-) 423 WP_258603688.1 pilin Machinery gene
  LOY49_RS22395 (LOY49_22365) pilB 5007907..5009607 (+) 1701 WP_258603690.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LOY49_RS22400 (LOY49_22370) pilC 5009610..5010827 (+) 1218 WP_258603692.1 type II secretion system F family protein Machinery gene
  LOY49_RS22405 (LOY49_22375) pilD 5010829..5011701 (+) 873 WP_258603693.1 A24 family peptidase Machinery gene
  LOY49_RS22410 (LOY49_22380) coaE 5011698..5012321 (+) 624 WP_258603694.1 dephospho-CoA kinase -
  LOY49_RS22415 (LOY49_22385) yacG 5012318..5012518 (+) 201 WP_016773149.1 DNA gyrase inhibitor YacG -
  LOY49_RS22420 (LOY49_22390) - 5012526..5012741 (-) 216 WP_056790451.1 hypothetical protein -
  LOY49_RS22425 (LOY49_22395) - 5012807..5013496 (-) 690 WP_258603695.1 energy-coupling factor ABC transporter permease -
  LOY49_RS22430 (LOY49_22400) - 5013687..5014313 (+) 627 WP_007909887.1 DUF1780 domain-containing protein -
  LOY49_RS22435 (LOY49_22405) - 5014310..5014837 (+) 528 WP_125925984.1 MOSC domain-containing protein -
  LOY49_RS22440 (LOY49_22410) - 5014889..5015062 (+) 174 WP_007909875.1 DUF3094 domain-containing protein -
  LOY49_RS22445 (LOY49_22415) - 5015126..5016424 (+) 1299 WP_016773144.1 NAD(P)/FAD-dependent oxidoreductase -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31878.08 Da        Isoelectric Point: 7.3655

>NTDB_id=627129 LOY49_RS22405 WP_258603693.1 5010829..5011701(+) (pilD) [Pseudomonas atacamensis strain B21-050]
MPIDELFAVYPLAFAVSALLLGLVVGSFLNVVVWRLPKMLERDWRQQAHDVLGLPSETPVPTYNLMLPHSACPHCGHRIR
PWENIPLLSYLLLRGRCSACSAPISKRYPLTELACGLLSAFIAWHLGFGWPAGLLILLTWGLLAMSLIDCEHQLLPDVLV
LPLLWLGLIVNSFGVFVALPDALWGAVAGYLALWSVFWLFKLLTGKDGIGHGDFKLLALLGAWGGWQILPLTILLSSLVG
AILGVVMLRLRAQETSTPIPFGPFLAIAGWIALLWGGQITDFYWQSVGLK

Nucleotide


Download         Length: 873 bp        

>NTDB_id=627129 LOY49_RS22405 WP_258603693.1 5010829..5011701(+) (pilD) [Pseudomonas atacamensis strain B21-050]
ATGCCTATCGATGAACTGTTTGCTGTGTATCCGCTGGCCTTTGCGGTCAGCGCGCTGCTGCTCGGGCTGGTGGTCGGCAG
CTTCCTCAATGTTGTGGTCTGGCGCCTGCCGAAAATGCTCGAGCGCGACTGGCGCCAGCAAGCCCATGATGTGCTCGGCC
TGCCCAGCGAAACGCCCGTGCCGACCTACAACCTGATGCTGCCGCACTCCGCGTGCCCGCATTGCGGACACCGGATCCGC
CCGTGGGAAAACATTCCGCTGCTCAGTTATCTGCTGCTGCGCGGGCGCTGCTCGGCCTGTTCGGCGCCGATCAGTAAACG
CTACCCGCTGACCGAACTGGCCTGCGGCCTGCTGTCGGCATTCATCGCCTGGCATCTGGGCTTCGGCTGGCCGGCGGGCT
TGCTGATCTTGCTGACGTGGGGCTTGCTGGCGATGAGTCTGATCGACTGCGAACATCAGCTGCTGCCCGATGTGCTGGTG
CTGCCGCTGCTGTGGCTGGGGCTGATCGTCAACAGCTTCGGCGTGTTCGTGGCGTTGCCCGATGCGTTGTGGGGCGCGGT
GGCGGGTTATCTGGCGCTGTGGTCGGTGTTCTGGCTGTTCAAACTGCTCACCGGCAAGGACGGCATCGGTCATGGTGATT
TCAAGCTGCTGGCCTTGCTTGGCGCTTGGGGTGGCTGGCAGATTCTGCCGCTGACGATTCTGTTGTCATCCTTGGTGGGG
GCGATTTTGGGCGTCGTCATGCTGCGCCTGCGCGCCCAGGAAACCTCGACGCCGATCCCCTTCGGACCCTTTCTGGCAAT
TGCCGGCTGGATTGCCTTGCTCTGGGGTGGTCAAATAACCGACTTCTATTGGCAGTCTGTCGGTTTGAAATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(137-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-125)


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

54.225

97.931

0.531
  pilD Vibrio campbellii strain DS40M4

52.632

98.276

0.517
  pilD Neisseria gonorrhoeae MS11

45.993

98.966

0.455
  pilD Acinetobacter nosocomialis M2

47.253

94.138

0.445
  pilD Acinetobacter baumannii D1279779

47.08

94.483

0.445