Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   AB3467_RS21705 Genome accession   NZ_CP162521
Coordinates   5055817..5056689 (+) Length   290 a.a.
NCBI ID   WP_025261832.1    Uniprot ID   -
Organism   Pseudomonas cichorii strain UPB 461     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 5050817..5061689
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AB3467_RS21690 (AB3467_21580) - 5052283..5052672 (-) 390 WP_038400031.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  AB3467_RS21695 (AB3467_21585) pilB 5052898..5054595 (+) 1698 WP_025261830.1 type IV-A pilus assembly ATPase PilB Machinery gene
  AB3467_RS21700 (AB3467_21590) pilC 5054598..5055815 (+) 1218 WP_025261831.1 type II secretion system F family protein Machinery gene
  AB3467_RS21705 (AB3467_21595) pilD 5055817..5056689 (+) 873 WP_025261832.1 A24 family peptidase Machinery gene
  AB3467_RS21710 (AB3467_21600) coaE 5056686..5057309 (+) 624 WP_025261833.1 dephospho-CoA kinase -
  AB3467_RS21715 (AB3467_21605) yacG 5057306..5057515 (+) 210 WP_025261834.1 DNA gyrase inhibitor YacG -
  AB3467_RS21720 (AB3467_21610) - 5057509..5057976 (-) 468 WP_025261835.1 hypothetical protein -
  AB3467_RS21725 (AB3467_21615) - 5058094..5059977 (-) 1884 WP_025261836.1 methyl-accepting chemotaxis protein -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31865.94 Da        Isoelectric Point: 8.0279

>NTDB_id=1026915 AB3467_RS21705 WP_025261832.1 5055817..5056689(+) (pilD) [Pseudomonas cichorii strain UPB 461]
MPLLDFLASSMLAFVIFTSVLGLLVGSFLNVVVYRLPKMMDRDWKIQAREILGLPAEPKPDTFNLILPHSSCPQCNHRIR
AWENIPVISYLALGGKCSNCKTAISKRYPLVELTCGIVSGYIAWHFGFGWQAAAMLVLSWGLLAMSLIDADHQLLPDSLV
LPLLWLGLIVNAFGLFTSLNDAIWGAVAGYLALWSVFWLFKLLTGKEGMGYGDFKLLGMLGAWGGWQILPLTIFLSSLVG
AVLGVILMRIRQVEAGTPIPFGPYLAIAGWIALLWGGQITDSYLQFAGFK

Nucleotide


Download         Length: 873 bp        

>NTDB_id=1026915 AB3467_RS21705 WP_025261832.1 5055817..5056689(+) (pilD) [Pseudomonas cichorii strain UPB 461]
ATGCCCCTTCTCGATTTCCTGGCCAGCTCCATGCTGGCCTTCGTCATTTTCACCTCTGTTCTAGGCCTGCTGGTTGGCAG
CTTTCTCAATGTGGTGGTTTATCGCCTGCCCAAAATGATGGATCGCGACTGGAAGATTCAGGCACGGGAAATACTGGGAC
TGCCCGCCGAGCCCAAGCCGGATACTTTCAACCTGATCCTTCCGCATTCCAGTTGCCCGCAATGCAACCACCGGATTCGC
GCCTGGGAAAACATTCCGGTCATCAGTTATCTGGCCCTCGGCGGTAAATGCTCGAACTGCAAGACAGCGATCAGCAAACG
CTACCCGCTGGTCGAACTGACCTGCGGGATAGTGTCAGGCTACATTGCCTGGCATTTCGGTTTTGGCTGGCAGGCTGCGG
CGATGCTGGTGCTGAGCTGGGGCTTGTTGGCCATGAGCCTGATCGATGCCGATCACCAACTACTGCCGGACTCCCTGGTC
CTTCCCCTGTTATGGCTGGGGCTTATCGTCAATGCCTTTGGCCTGTTCACATCCCTCAATGATGCCATCTGGGGAGCCGT
GGCCGGCTATCTGGCGCTGTGGTCGGTGTTCTGGCTATTCAAGTTGCTAACCGGCAAGGAAGGCATGGGTTACGGTGACT
TCAAGTTGCTCGGCATGCTCGGGGCCTGGGGCGGCTGGCAGATCCTGCCGTTGACGATCTTTTTATCGTCGCTGGTGGGC
GCTGTGCTGGGCGTGATCCTGATGCGCATTCGCCAGGTCGAGGCGGGAACGCCGATTCCCTTCGGTCCTTATCTGGCCAT
CGCGGGGTGGATCGCTTTGCTCTGGGGTGGTCAAATAACCGACTCCTATTTGCAGTTTGCCGGTTTCAAATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(136-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)


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 campbellii strain DS40M4

53.846

94.138

0.507
  pilD Vibrio cholerae strain A1552

53.676

93.793

0.503
  pilD Acinetobacter baumannii D1279779

50

97.931

0.49
  pilD Acinetobacter nosocomialis M2

49.296

97.931

0.483
  pilD Neisseria gonorrhoeae MS11

52.326

88.966

0.466

Multiple sequence alignment