Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   A8O29_RS02460 Genome accession   NZ_CP054058
Coordinates   374377..375147 (-) Length   256 a.a.
NCBI ID   WP_174081213.1    Uniprot ID   -
Organism   Scandinavium goeteborgense strain CCUG 66741     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
Genomic island 373302..387419 374377..375147 within 0


Gene organization within MGE regions


Location: 373302..387419
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  A8O29_RS02450 (A8O29_002450) bfd 373567..373761 (+) 195 WP_125355016.1 bacterioferritin-associated ferredoxin -
  A8O29_RS02455 (A8O29_002455) bfr 373837..374313 (+) 477 WP_125355013.1 bacterioferritin -
  A8O29_RS02460 (A8O29_002460) pilD 374377..375147 (-) 771 WP_174081213.1 prepilin peptidase Machinery gene
  A8O29_RS02465 (A8O29_002465) gspM 375140..375610 (-) 471 WP_125355012.1 type II secretion system protein GspM -
  A8O29_RS02470 (A8O29_002470) gspL 375607..376755 (-) 1149 WP_125355011.1 type II secretion system protein GspL -
  A8O29_RS02475 (A8O29_002475) gspK 376752..377756 (-) 1005 WP_125355010.1 type II secretion system minor pseudopilin GspK -
  A8O29_RS02480 (A8O29_002480) gspJ 377753..378370 (-) 618 WP_125355009.1 type II secretion system minor pseudopilin GspJ -
  A8O29_RS02485 (A8O29_002485) gspI 378354..378728 (-) 375 WP_125355008.1 type II secretion system minor pseudopilin GspI -
  A8O29_RS02490 (A8O29_002490) gspH 378725..379222 (-) 498 WP_125355007.1 type II secretion system minor pseudopilin GspH -
  A8O29_RS02495 (A8O29_002495) gspG 379225..379668 (-) 444 WP_125355006.1 type II secretion system major pseudopilin GspG -
  A8O29_RS02500 (A8O29_002500) gspF 379679..380890 (-) 1212 WP_125355005.1 type II secretion system inner membrane protein GspF -
  A8O29_RS02505 (A8O29_002505) gspE 380887..382401 (-) 1515 WP_275942413.1 type II secretion system ATPase GspE -
  A8O29_RS02510 (A8O29_002510) gspD 382407..384419 (-) 2013 WP_125355004.1 type II secretion system secretin GspD -
  A8O29_RS02515 (A8O29_002515) - 384438..385238 (-) 801 WP_125355003.1 type II secretion system protein N -
  A8O29_RS02520 (A8O29_002520) - 385420..386961 (+) 1542 WP_125355002.1 peptidoglycan-binding domain-containing protein -
  A8O29_RS02525 (A8O29_002525) - 386958..387419 (+) 462 WP_125355001.1 hypothetical protein -

Sequence

Protein


Download         Length: 256 a.a.        Molecular weight: 28654.21 Da        Isoelectric Point: 7.9975

>NTDB_id=450463 A8O29_RS02460 WP_174081213.1 374377..375147(-) (pilD) [Scandinavium goeteborgense strain CCUG 66741]
MDKAIEIILMGILGLLTGSFMNVVVYRVPRGLKDENAPLSNIAWPGSCCPQCQHPIRYHDNVPLLSWLWLKGRCRDCHAR
ISPRYPLTEGICGLVFALMTSLFPLLPETVAICLLFWFLLALTQIDAQHCLLPDKLTLPLLWLGLLYHCFFMRIDLHDAV
LGAIAGYLTLWLVYQAFRLLAGKEGMGFGDFKLLAALGAWCGWQALPGILLLSSMLALIYTLGRLTLNGNKQAHIAFGPW
LSVAGWLSFLWQTWNG

Nucleotide


Download         Length: 771 bp        

>NTDB_id=450463 A8O29_RS02460 WP_174081213.1 374377..375147(-) (pilD) [Scandinavium goeteborgense strain CCUG 66741]
ATGGATAAAGCCATTGAAATCATCCTGATGGGTATTTTAGGTTTGCTTACCGGCAGCTTTATGAATGTCGTGGTCTACCG
GGTACCACGAGGTCTCAAAGACGAGAACGCGCCGCTCAGCAATATCGCCTGGCCCGGATCTTGTTGTCCCCAGTGCCAAC
ACCCGATTCGTTACCATGATAACGTTCCGCTTCTCAGTTGGCTGTGGTTGAAAGGTCGCTGCCGTGATTGCCATGCCCGG
ATCTCCCCGCGCTATCCTTTGACGGAAGGGATTTGTGGCCTGGTGTTTGCGCTAATGACCAGCCTCTTCCCCCTGCTCCC
TGAAACCGTGGCCATCTGCCTGCTGTTTTGGTTTCTGCTGGCATTAACACAGATCGACGCACAGCATTGTTTATTGCCCG
ACAAACTGACATTGCCACTGTTGTGGCTGGGTTTGCTCTATCACTGTTTTTTTATGCGCATCGATCTGCATGATGCCGTA
CTGGGGGCAATCGCTGGCTATCTGACGCTGTGGCTGGTTTATCAGGCGTTTCGGCTGTTGGCCGGCAAAGAAGGGATGGG
CTTTGGCGATTTCAAATTGCTCGCCGCATTGGGGGCATGGTGTGGGTGGCAGGCGTTACCGGGCATCCTGTTACTGTCAT
CGATGCTGGCGCTAATTTATACTTTGGGTCGCCTTACCTTAAACGGCAACAAACAAGCGCACATCGCTTTCGGCCCGTGG
TTGAGCGTAGCGGGCTGGCTGAGTTTTCTGTGGCAAACCTGGAATGGCTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(114-222)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(12-100)


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

46.97

100

0.484
  pilD Vibrio campbellii strain DS40M4

44.106

100

0.453
  pilD Neisseria gonorrhoeae MS11

44.747

100

0.449
  pilD Acinetobacter nosocomialis M2

41.923

100

0.426
  pilD Acinetobacter baumannii D1279779

41.538

100

0.422