Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   LCF41_RS15140 Genome accession   NZ_CP084032
Coordinates   3328775..3329620 (-) Length   281 a.a.
NCBI ID   WP_225085306.1    Uniprot ID   -
Organism   Pectobacterium colocasium strain LJ1     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 3323775..3334620
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LCF41_RS15095 dbpA 3324043..3325425 (-) 1383 WP_225085303.1 ATP-dependent RNA helicase DbpA -
  LCF41_RS15100 - 3325544..3325798 (-) 255 WP_347881000.1 substrate-binding domain-containing protein -
  LCF41_RS22375 - 3325805..3325918 (-) 114 Protein_2964 ABC transporter ATP-binding protein -
  LCF41_RS15105 - 3325932..3326054 (-) 123 WP_284144920.1 iron chelate uptake ABC transporter family permease subunit -
  LCF41_RS15110 - 3326054..3326305 (-) 252 Protein_2966 iron chelate uptake ABC transporter family permease subunit -
  LCF41_RS15115 - 3326302..3326586 (-) 285 Protein_2967 hypothetical protein -
  LCF41_RS15120 - 3326576..3327601 (+) 1026 WP_225085305.1 LLM class flavin-dependent oxidoreductase -
  LCF41_RS15125 ypdK 3327960..3328034 (+) 75 WP_099606229.1 membrane protein YpdK -
  LCF41_RS15130 - 3328254..3328460 (-) 207 WP_225088193.1 YciI family protein -
  LCF41_RS15135 - 3328564..3328671 (-) 108 Protein_2971 hypothetical protein -
  LCF41_RS15140 pilD 3328775..3329620 (-) 846 WP_225085306.1 A24 family peptidase Machinery gene
  LCF41_RS15145 - 3329728..3330474 (-) 747 WP_225085307.1 type II secretion system protein N -
  LCF41_RS15150 - 3330464..3330958 (-) 495 WP_225085308.1 type II secretion system protein M -
  LCF41_RS15155 gspL 3330955..3332232 (-) 1278 WP_225085309.1 type II secretion system protein GspL -
  LCF41_RS15160 gspK 3332229..3333215 (-) 987 WP_225085310.1 type II secretion system minor pseudopilin GspK -
  LCF41_RS15165 gspJ 3333212..3333862 (-) 651 WP_225085311.1 type II secretion system minor pseudopilin GspJ -
  LCF41_RS15170 gspI 3333862..3334227 (-) 366 WP_180741890.1 type II secretion system minor pseudopilin GspI -

Sequence

Protein


Download         Length: 281 a.a.        Molecular weight: 31278.28 Da        Isoelectric Point: 7.9960

>NTDB_id=609093 LCF41_RS15140 WP_225085306.1 3328775..3329620(-) (pilD) [Pectobacterium colocasium strain LJ1]
MDDLREFAQVFPAWWYGALGVLGLIVGSFLNVVIYRLPIMLERRWRQDIELQTGVTDAGQATRYNLWWPPSSCPHCQQAI
AVKDNIPLFSWLWLRGRSRCCYQPVSVQYPLVEAITMLAFLAAGLLWLPGMALCGALILLSFLVVLTVIDIKTLLLPDVL
TLSLLWIGLLFNLSETFVPLRDAVVGAMAGYLSLWLLYWVFKYATGKDALGYGDFKLLAALGAWLGWQALPNLVLVAALS
GLIVTLIWRGLRKEDAAKPLAFGPWLAIGGVFSVMMNGFNL

Nucleotide


Download         Length: 846 bp        

>NTDB_id=609093 LCF41_RS15140 WP_225085306.1 3328775..3329620(-) (pilD) [Pectobacterium colocasium strain LJ1]
GTGGACGATTTAAGGGAATTCGCACAGGTGTTTCCAGCATGGTGGTATGGTGCGCTGGGCGTATTGGGATTGATTGTTGG
CAGCTTTCTGAACGTAGTGATTTATCGCTTGCCGATTATGTTGGAACGGCGCTGGCGGCAAGACATCGAGCTGCAAACCG
GCGTAACGGATGCCGGGCAGGCTACGCGCTATAACCTGTGGTGGCCGCCTTCGTCCTGCCCGCACTGCCAGCAGGCGATT
GCGGTGAAGGATAACATCCCGTTGTTCAGTTGGCTGTGGCTACGCGGTCGCTCCCGCTGCTGTTATCAACCGGTGTCTGT
ACAGTATCCGCTGGTGGAAGCCATCACCATGCTGGCTTTTCTGGCTGCGGGGTTGCTGTGGCTGCCCGGTATGGCGCTGT
GTGGGGCGCTAATCTTGCTGTCCTTTCTGGTGGTGCTGACCGTTATTGATATAAAAACGCTGCTGCTGCCGGATGTGCTT
ACGCTGTCGCTCTTGTGGATAGGGCTATTGTTTAACCTGTCGGAGACATTTGTTCCATTACGTGATGCCGTGGTCGGTGC
GATGGCGGGCTATTTGTCCCTGTGGCTACTTTACTGGGTATTTAAATATGCCACTGGCAAAGACGCGCTGGGGTACGGTG
ATTTTAAGTTGCTGGCTGCACTGGGAGCCTGGCTGGGCTGGCAGGCATTACCGAATCTGGTTTTGGTGGCGGCGCTGAGT
GGTCTGATCGTGACGCTTATTTGGCGTGGATTGCGTAAAGAAGATGCGGCTAAACCGCTGGCCTTTGGCCCCTGGCTGGC
AATAGGTGGCGTGTTCAGCGTGATGATGAACGGGTTCAATCTGTAG

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(137-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-123)


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

50

96.085

0.48
  pilD Neisseria gonorrhoeae MS11

48.438

91.103

0.441
  pilD Vibrio campbellii strain DS40M4

45.725

95.73

0.438
  pilD Acinetobacter baumannii D1279779

43.629

92.171

0.402
  pilD Acinetobacter nosocomialis M2

43.629

92.171

0.402