Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101389
Name   oriT_pKPYL2 in_silico
Organism   Raoultella ornithinolytica strain Nonyl 4-3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAGQDL010000005 (121850..121899 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pKPYL2
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1272 GenBank   WP_211843980
Name   traI_J9871_RS29565_pKPYL2 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190842.96 Da        Isoelectric Point: 6.2717

>WP_211843980.1 conjugative transfer relaxase/helicase TraI [Raoultella ornithinolytica]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGGPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKLKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGSWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQFVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKKAEQTAREMAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)

TrwC relaxase (TrwC)

(10-284)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(577-629)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(635-714)


  Protein structure



No available structure.




T4CP

ID   883 GenBank   WP_040088247
Name   traD_J9871_RS29570_pKPYL2 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 85925.03 Da        Isoelectric Point: 5.1149

>WP_040088247.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRATEPSALRLTTVPLIKPKAAAAAAAAATVSSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDNVEIGGNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 115124..122457

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J9871_RS29595 110701..112728 - 2028 Protein_98 type IV secretion system protein TraC -
J9871_RS29600 112800..113198 - 399 WP_015065631 hypothetical protein -
J9871_RS29605 113223..113627 - 405 WP_023320104 hypothetical protein -
J9871_RS29610 113694..114011 - 318 WP_016530481 hypothetical protein -
J9871_RS29615 114012..114230 - 219 WP_004171484 hypothetical protein -
J9871_RS29620 114254..114541 - 288 WP_052451814 hypothetical protein -
J9871_RS30275 114570..114968 - 399 WP_223177007 hypothetical protein -
J9871_RS29630 115124..115693 - 570 WP_015065628 type IV conjugative transfer system lipoprotein TraV traV
J9871_RS29635 115713..115868 - 156 WP_172694479 hypothetical protein -
J9871_RS29640 115904..116317 - 414 Protein_107 conjugal transfer pilus-stabilizing protein TraP -
J9871_RS29645 116310..117734 - 1425 WP_040088218 F-type conjugal transfer pilus assembly protein TraB traB
J9871_RS29650 117734..118474 - 741 WP_040088216 type-F conjugative transfer system secretin TraK traK
J9871_RS29655 118461..119027 - 567 WP_040088214 type IV conjugative transfer system protein TraE traE
J9871_RS29660 119047..119352 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
J9871_RS29665 119366..119734 - 369 WP_211843981 type IV conjugative transfer system pilin TraA -
J9871_RS29670 119788..120159 - 372 WP_004208838 TraY domain-containing protein -
J9871_RS29675 120243..120938 - 696 WP_074187711 transcriptional regulator TraJ family protein -
J9871_RS29680 121145..121537 - 393 WP_004206766 conjugal transfer relaxosome DNA-binding protein TraM -
J9871_RS29685 121972..122457 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
J9871_RS29690 122490..122819 - 330 WP_011977736 DUF5983 family protein -
J9871_RS29695 122852..123673 - 822 WP_064161333 DUF932 domain-containing protein -
J9871_RS29700 124502..124903 - 402 WP_015065522 helix-turn-helix domain-containing protein -
J9871_RS29705 124904..125182 - 279 WP_020801586 helix-turn-helix transcriptional regulator -
J9871_RS29710 125172..125492 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
J9871_RS29715 125573..125797 - 225 WP_014343499 hypothetical protein -
J9871_RS29720 125808..126020 - 213 WP_019706020 hypothetical protein -
J9871_RS29725 126081..126437 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   1833 GenBank   NZ_JAGQDL010000005
Plasmid name   pKPYL2 Incompatibility group   IncFIA
Plasmid size   161630 bp Coordinate of oriT [Strand]   121850..121899 [+]
Host baterium   Raoultella ornithinolytica strain Nonyl 4-3

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9