Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200091
Name   oriT_ICEclc-2 experimental
Organism   Pseudomonas putida clc
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AJ617740 ( 94918..95237 [+], 320 nt)
oriT length   320 nt
IRs (inverted repeats)      IR1: 188..193, 201..206  (CCCTTT..AAAGGC)
  IR2: 194..199, 211..216  (ACCTTT..AAAGGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   (1) In oriT_ICEclc, there is a dual oriT system. In this system, both oriTs are functional and compared to the ICEclc only harbors one oriT, there is a fourfold increase of transfer rate in ICEclc that habors the dual oriT system [PMID:21255116, PMID:22016851].
 (2) The relaxase orf50240_ICEclc processes both oriTs in a different manner. For nicking-rejoining oriT_ICEclc-2, other factors would be required [PMID:21255116, PMID:22016851].

  oriT sequence  


Download         Length: 320 nt

>oriT_ICEclc-2
CCATGGCCGAGCGGTCGTGCTTGCGCCAGCGAAGGAACGTCGTTCCCGCGCCAGTTGTCTGCTGGGCCAGCTCGATGGGTAGCAGGTGGAAGGGATGCCCGACTGCCTGTTGCAGCACCTGTCGCTGCGCCAAGCCAATCAGTTCGTCGCGCATGGCGAAGCACTGGCTGGCCCAGGCCTCGAAGTCCCCTTTACCTTTAAAAGGCTTTAAAAGGCCTTTTAGAGAGGCCGCGTGTTCCAGCCGCATGAAGGCTTCCTGTTGCAGGCCCCGGAAGTAGCGGATCGGTTGGTTCAGATCGCTCATGCCGGTTCGTCCTCAC

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Ryo Miyazaki et al. (2011) A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13. Molecular microbiology. 79(3):743-58. [PMID:21255116]


Relaxase

ID   1094 GenBank   CAE92900
Name   orf50240_ICEclc experimental UniProt ID   Q706Q0
Length   615 a.a. PDB ID   
Note   

  Relaxase protein sequence


Download         Length: 615 a.a.        Molecular weight: 67419.64 Da        Isoelectric Point: 7.4238

>CAE92900.1 hypothetical protein [Pseudomonas putida]
MLSLFQRKRPVVASAPSPAPSNDLPKGRLRPESAASLLATPRRQKLLEHIWQRTSLSRKQFATLYRAPLE
RYAELVQRFPASEAHHHAYPGGMLDHGLEIVAYALKLRQSHLLPAGSTPEDQAAQSEAWTAAVAYAALLH
DVGKLAVDLHVELADGSTWHPWHGPLRQPYRFRYREDREYRLHSAATGLLYRQLLDAQLLDWLSGYPALW
GPLLYVLAGQYEHAGVLGELVVQADRASVAQELGGDPARAMAAPKHALQRKLLDGLRYLLKEELKLNQPE
ASDGWLTEDALWLVSKTVSDKLRAHLLSQGIDGIPANNTAVFNVLQDHGMLHPTTDGKAVWRATVTSATG
WSHSFTLLRLAPALIWEPGERPVPFAGTVAIDAVPNDKSVAQPAAVAETTQEGQEAPPWESSSVAVPSPA
TQTVPDVLEDMLAMVGMGNSSGTQQDEEATSHAADATPSEAPMPAMAAASPPSPVPPAAPSSATAQPSGE
HFMAWLKQGIVSRRLIINDAKALVHTVSDTAYLVSPGVFQRYAREHPQVGMLAKQESQQDWQWVQKRFEK
LQLHRKHINGLNVWACSVTGSRKSRQLHGYLLRDPLPLFGKVPPNNPYLSILQSI

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(27-340)

Putative conjugal transfer nickase/helicase TraI C-term (TraI_2_C)

(488-610)


  Protein structure


Source ID Structure
AlphaFold DB Q706Q0

  Reference


[1] Ryo Miyazaki et al. (2011) A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13. Molecular microbiology. 79(3):743-58. [PMID:21255116]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 53593..74302

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_48 48928..49731 + 804 CAE92899 putative transcriptional regulator -
Locus_49 50246..52093 - 1848 CAE92900 hypothetical protein -
Locus_50 52330..52716 + 387 CAE92901 hypothetical protein -
Locus_51 52716..53174 + 459 CAE92902 hypothetical protein -
Locus_52 53202..53579 + 378 CAE92903 hypothetical protein -
Locus_53 53593..55110 - 1518 CAE92904 hypothetical protein tfc19
Locus_54 55126..55485 - 360 CAE92905 hypothetical protein tfc18
Locus_55 55482..56879 - 1398 CAE92906 hypothetical protein tfc22
Locus_56 56889..57836 - 948 CAE92907 hypothetical protein tfc23
Locus_57 57833..58279 - 447 CAE92908 hypothetical protein tfc24
Locus_58 58438..58932 - 495 CAE92909 putative DNA repair protein -
Locus_59 59116..59880 - 765 CAE92910 putative protein-disulfide isomerase -
Locus_60 59894..62761 - 2868 CAE92911 conserved hypothetical protein with VirB4 domain virb4
Locus_61 62761..63201 - 441 CAE92912 hypothetical protein tfc15
Locus_62 63182..64600 - 1419 CAE92913 hypothetical protein tfc14
Locus_63 64590..65522 - 933 CAE92914 hypothetical protein tfc13
Locus_64 65519..66211 - 693 CAE92915 hypothetical protein tfc12
Locus_65 66208..66618 - 411 CAE92916 hypothetical protein tfc11
Locus_66 66631..66990 - 360 CAE92917 hypothetical protein tfc10
Locus_67 67007..67240 - 234 CAE92918 hypothetical protein tfc9
Locus_68 67237..67620 - 384 CAE92919 hypothetical protein tfc8
Locus_69 67806..68210 + 405 CAE92920 hypothetical protein -
Locus_70 68247..68996 - 750 CAE92921 hypothetical protein tfc7
Locus_71 68993..71179 - 2187 CAE92922 hypothetical protein -
Locus_72 71184..71732 - 549 CAE92923 hypothetical protein tfc5
Locus_73 71729..72319 - 591 CAE92924 hypothetical protein virB1
Locus_74 72301..73020 - 720 CAE92925 hypothetical protein tfc3
Locus_75 73035..73685 - 651 CAE92926 hypothetical protein -
Locus_76 73682..74302 - 621 CAE92927 hypothetical protein tfc2
Locus_77 74442..75311 - 870 CAE92928 hypothetical protein -
Locus_78 75425..77704 - 2280 CAE92929 putative DNA/RNA helicase -
Locus_79 77804..78913 - 1110 CAE92930 hypothetical protein -

Host bacterium

ID   98 Element type   ICE (Integrative and conjugative element)
Element name   ICEclc GenBank   AJ617740
Element size   105032 bp Coordinate of oriT [Strand]   51849..52332 [+]; 94918..95237 [+]
Host bacterium   Pseudomonas putida clc

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   bphA1
Symbiosis gene   -
Anti-CRISPR   -