Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101439
Name   oriT_pCRE11_1 in_silico
Organism   Klebsiella variicola strain S11_CRE11
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAHBNM010000003 (189209..189258 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pCRE11_1
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1303 GenBank   WP_195352401
Name   traI_KIN49_RS29045_pCRE11_1 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: 190504.71 Da        Isoelectric Point: 6.4600

>WP_195352401.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRAMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAVELACAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRHNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QTQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALITIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIE
KALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRTLNGMIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSDGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASERYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRIWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(971-1154)

TrwC relaxase (TrwC)

(10-284)

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

(635-714)

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

(577-629)

DNA helicase TraI (TraI_C)

(1433-1555)


  Protein structure



No available structure.




T4CP

ID   918 GenBank   WP_015065643
Name   traD_KIN49_RS29050_pCRE11_1 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85851.84 Da        Isoelectric Point: 5.0577

>WP_015065643.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSIVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEAREAEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 161568..189816

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KIN49_RS29050 (KIN49_28905) 161568..163877 - 2310 WP_015065643 type IV conjugative transfer system coupling protein TraD virb4
KIN49_RS29055 (KIN49_28910) 164239..164970 - 732 Protein_170 conjugal transfer complement resistance protein TraT -
KIN49_RS29060 (KIN49_28920) 165160..165687 - 528 WP_016528837 conjugal transfer entry exclusion protein TraS -
KIN49_RS29065 (KIN49_28925) 165693..168542 - 2850 WP_268163271 conjugal transfer mating-pair stabilization protein TraG traG
KIN49_RS29070 (KIN49_28930) 168542..169921 - 1380 WP_011977731 conjugal transfer pilus assembly protein TraH traH
KIN49_RS29075 (KIN49_28935) 169899..170342 - 444 WP_015065638 F-type conjugal transfer protein TrbF -
KIN49_RS29080 (KIN49_28940) 170387..170944 - 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KIN49_RS29085 (KIN49_28945) 170916..171155 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
KIN49_RS29090 (KIN49_28950) 171166..171918 - 753 WP_015065637 type-F conjugative transfer system pilin assembly protein TraF traF
KIN49_RS29095 (KIN49_28955) 171939..172265 - 327 WP_004152685 hypothetical protein -
KIN49_RS31195 172311..172496 - 186 WP_023307535 hypothetical protein -
KIN49_RS29100 (KIN49_28960) 172493..172729 - 237 WP_023307536 conjugal transfer protein TrbE -
KIN49_RS29105 (KIN49_28965) 172761..174716 - 1956 WP_268163272 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KIN49_RS29110 (KIN49_28970) 174775..175413 - 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
KIN49_RS29115 (KIN49_28975) 175426..176385 - 960 WP_015065634 conjugal transfer pilus assembly protein TraU traU
KIN49_RS29120 (KIN49_28980) 176429..177055 - 627 WP_015065633 type-F conjugative transfer system protein TraW traW
KIN49_RS29125 (KIN49_28985) 177055..177444 - 390 WP_004152506 type-F conjugative transfer system protein TrbI -
KIN49_RS29130 (KIN49_28990) 177444..180083 - 2640 WP_016528865 type IV secretion system protein TraC virb4
KIN49_RS29135 (KIN49_28995) 180155..180553 - 399 WP_015065631 hypothetical protein -
KIN49_RS29140 (KIN49_29000) 180578..180982 - 405 WP_023320104 hypothetical protein -
KIN49_RS29145 (KIN49_29005) 181049..181366 - 318 WP_015065629 hypothetical protein -
KIN49_RS29150 (KIN49_29010) 181367..181585 - 219 WP_004171484 hypothetical protein -
KIN49_RS29155 (KIN49_29015) 181609..181899 - 291 WP_032426790 hypothetical protein -
KIN49_RS29160 181928..182326 - 399 WP_223177007 hypothetical protein -
KIN49_RS29165 (KIN49_29025) 182482..183051 - 570 WP_015065628 type IV conjugative transfer system lipoprotein TraV traV
KIN49_RS29170 (KIN49_29030) 183071..183226 - 156 WP_153587559 hypothetical protein -
KIN49_RS29175 (KIN49_29035) 183257..183676 - 420 Protein_195 conjugal transfer pilus-stabilizing protein TraP -
KIN49_RS29180 (KIN49_29040) 183669..185093 - 1425 WP_040228261 F-type conjugal transfer pilus assembly protein TraB traB
KIN49_RS29185 (KIN49_29045) 185093..185833 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
KIN49_RS29190 (KIN49_29050) 185820..186386 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
KIN49_RS29195 (KIN49_29055) 186406..186711 - 306 WP_268163273 type IV conjugative transfer system protein TraL traL
KIN49_RS29200 (KIN49_29060) 186725..187093 - 369 WP_004178060 type IV conjugative transfer system pilin TraA -
KIN49_RS29205 (KIN49_29065) 187147..187518 - 372 WP_004208838 TraY domain-containing protein -
KIN49_RS29210 (KIN49_29070) 187602..188297 - 696 WP_015065624 transcriptional regulator TraJ family protein -
KIN49_RS29215 (KIN49_29075) 188504..188896 - 393 WP_004206766 conjugal transfer relaxosome DNA-binding protein TraM -
KIN49_RS29220 (KIN49_29080) 189331..189816 + 486 WP_268163274 transglycosylase SLT domain-containing protein virB1
KIN49_RS29225 (KIN49_29085) 189849..190178 - 330 WP_011977736 DUF5983 family protein -
KIN49_RS29230 (KIN49_29090) 190211..191032 - 822 WP_110242313 DUF932 domain-containing protein -
KIN49_RS29235 (KIN49_29095) 191853..192419 - 567 WP_001568053 methyltransferase -
KIN49_RS29240 (KIN49_29100) 192467..193822 - 1356 WP_095849300 DUF3560 domain-containing protein -
KIN49_RS29245 (KIN49_29105) 193874..194104 - 231 WP_009310031 hypothetical protein -
KIN49_RS29250 (KIN49_29110) 194196..194423 - 228 WP_001568050 hypothetical protein -

Host bacterium

ID   1883 GenBank   NZ_JAHBNM010000003
Plasmid name   pCRE11_1 Incompatibility group   IncFIB
Plasmid size   211805 bp Coordinate of oriT [Strand]   189209..189258 [+]
Host baterium   Klebsiella variicola strain S11_CRE11

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, fecD, fecE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -