Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121986
Name   oriT_pKPYL2 in_silico
Organism   Raoultella ornithinolytica strain Yangling I2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013340 (64187..64268 [+], 82 nt)
oriT length   82 nt
IRs (inverted repeats)      27..32, 35..40  (GCCACC..GGTGGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 82 nt

>oriT_pKPYL2
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13861 GenBank   WP_064357930
Name   traI_ATN83_RS26635_pKPYL2 insolico UniProt ID   _
Length   642 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 642 a.a.        Molecular weight: 74304.29 Da        Isoelectric Point: 8.8672

>WP_064357930.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MNAIIPPKRRDKKSSFVQLVAYVSVRDDVPLKDELKEDQRFQRPSRSRQAIFDRLVDYMNRSEGTITEQI
TDMSPEGDVRCSVDGVICQHNLMSVETAAMEMNSIAMQNLHVKDAVYHYILSWQEDENPSDDQVFDSVKY
SLKRLGMEENQYVAGIHRDTDNLHVHVAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNIVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNAMFREKNASWEKLHQVMNDAGLML
ETSGKGLIVRDVCGDEKLAVKSSRVHPSMTLSRLEPALGTFVPSPRSAEMVKQSVQTPYSDKLHVRDRGA
RAKRRQARADARIDLRERYGKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIALKAERQKLYDEGMMRPLTYRAWTEQQALHGDQAALSQLRGWSYRQNRKNRTPQASENI
IYCAPADDTSLLKADGYEARLHRDGAVVYSRQGQDAIIDRGDRVEVINPYDDGDLNTRIAVDMVAWKSGE
RVEFSRDGCFAYAAGDAVAAHNLHHRDSIIVPSDREQYDYTREKFNQLKGRYTDSEREALRQQYDERYYD
DVRNNDDSSYKP

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(52-310)


  Protein structure



No available structure.




T4CP

ID   16229 GenBank   WP_064357960
Name   trbC_ATN83_RS26775_pKPYL2 insolico UniProt ID   _
Length   730 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 730 a.a.        Molecular weight: 82695.78 Da        Isoelectric Point: 6.0387

>WP_064357960.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacterales]
MQQKQKPVDAARLQRQVHQSMVEEMAYRTGPLLLAIIAIFGAAIVWPVLLWAAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLNRHMEKAAGVFYTGYERTLDGGREIWLRMDDLTRHLI
LMATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFLWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTIIDPTETAEFAAKSAGMEYQAIQDSMEYRAGAIGGSYADTGRVTVQEKPKLPFDELQALN
QGEQATVFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLSHLLPAKVRRDRPRPASINRIMA
IVKNDNIRHAPDSMIIQDGVLYAIADEAMYFDEVSPVPPDTVRRATQLLSLAASVLTETRGRYSVEYPEP
EKLSVKKDELEKYQHIHQSAVTQQVDGFVY

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(439-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 74383..96108

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ATN83_RS26650 (ATN83_p20111) 69530..70024 - 495 WP_064357935 molybdopterin-dependent oxidoreductase -
ATN83_RS26655 (ATN83_p20112) 70017..70946 - 930 WP_064357981 glycosyltransferase family 9 protein -
ATN83_RS26660 (ATN83_p20113) 71006..71848 - 843 WP_032440572 helix-turn-helix domain-containing protein -
ATN83_RS26665 (ATN83_p20115) 72458..72685 + 228 WP_032440573 hypothetical protein -
ATN83_RS28660 73036..73404 + 369 WP_136129316 hypothetical protein -
ATN83_RS26670 (ATN83_p20117) 73417..73896 + 480 WP_064357937 lytic transglycosylase domain-containing protein -
ATN83_RS26675 (ATN83_p20118) 73922..74386 + 465 WP_225546581 DotD/TraH family lipoprotein -
ATN83_RS26680 (ATN83_p20119) 74383..75201 + 819 WP_064357938 type IV secretory system conjugative DNA transfer family protein traI
ATN83_RS26685 (ATN83_p20120) 75179..76366 + 1188 WP_081042498 plasmid transfer ATPase TraJ virB11
ATN83_RS26690 (ATN83_p20121) 76363..76629 + 267 WP_032440577 IcmT/TraK family protein traK
ATN83_RS26695 (ATN83_p20122) 76647..79862 + 3216 WP_064357941 LPD7 domain-containing protein -
ATN83_RS26700 (ATN83_p20123) 79896..80249 + 354 WP_064357942 hypothetical protein traL
ATN83_RS26705 (ATN83_p20124) 80323..80991 + 669 WP_196548568 DotI/IcmL/TraM family protein traM
ATN83_RS26710 (ATN83_p20125) 81002..82105 + 1104 WP_081042499 DotH/IcmK family type IV secretion protein traN
ATN83_RS26715 (ATN83_p20126) 82109..83437 + 1329 WP_064357943 conjugal transfer protein TraO traO
ATN83_RS26720 (ATN83_p20127) 83444..84163 + 720 WP_064357945 conjugal transfer protein TraP traP
ATN83_RS26725 (ATN83_p20128) 84173..84706 + 534 WP_064357947 conjugal transfer protein TraQ traQ
ATN83_RS26730 (ATN83_p20129) 84762..85163 + 402 WP_032440588 DUF6750 family protein traR
ATN83_RS26735 (ATN83_p20130) 85207..85770 + 564 WP_064357949 hypothetical protein traT
ATN83_RS26740 (ATN83_p20131) 85780..88827 + 3048 WP_064357951 hypothetical protein traU
ATN83_RS26745 (ATN83_p20132) 88837..90033 + 1197 WP_064357952 conjugal transfer protein TraW traW
ATN83_RS26750 (ATN83_p20133) 90030..90611 + 582 WP_064357954 conjugal transfer protein TraX -
ATN83_RS26755 (ATN83_p20134) 90653..92797 + 2145 WP_064357955 DotA/TraY family protein traY
ATN83_RS26760 (ATN83_p20135) 92863..93486 + 624 WP_064357957 plasmid IncI1-type surface exclusion protein ExcA -
ATN83_RS26765 (ATN83_p20136) 93588..95006 + 1419 WP_071887238 hypothetical protein trbA
ATN83_RS26770 (ATN83_p20137) 95017..96108 + 1092 WP_064357959 thioredoxin fold domain-containing protein trbB
ATN83_RS26775 (ATN83_p20138) 96110..98302 + 2193 WP_064357960 F-type conjugative transfer protein TrbC -
ATN83_RS26780 (ATN83_p20139) 98348..98881 + 534 WP_096807525 phospholipase D family protein -
ATN83_RS28665 (ATN83_p20140) 98893..99144 + 252 WP_064357964 hypothetical protein -
ATN83_RS26790 (ATN83_p20142) 99469..100473 - 1005 WP_000427623 IS110-like element IS4321 family transposase -

Host bacterium

ID   22413 GenBank   NZ_CP013340
Plasmid name   pKPYL2 Incompatibility group   -
Plasmid size   140936 bp Coordinate of oriT [Strand]   64187..64268 [+]
Host baterium   Raoultella ornithinolytica strain Yangling I2

Cargo genes

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