Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101452
Name   oriT_pCRE17_1 in_silico
Organism   Klebsiella michiganensis strain S17_CRE17
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAHBNO010000003 (138678..138726 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pCRE17_1
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1308 GenBank   WP_268013957
Name   traI_KIN65_RS29595_pCRE17_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: 190675.76 Da        Isoelectric Point: 6.2590

>WP_268013957.1 conjugative transfer relaxase/helicase TraI [Klebsiella michiganensis]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHKTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGI
KVAHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQIPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKALPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)

TrwC relaxase (TrwC)

(10-284)

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

(577-629)

AAA domain (AAA_30)

(970-1157)


  Protein structure



No available structure.




T4CP

ID   924 GenBank   WP_055316029
Name   traD_KIN65_RS29590_pCRE17_1 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: 85961.04 Da        Isoelectric Point: 5.1165

>WP_055316029.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMRKDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPEPGPADTDSHASEQPEPVSPPA
PAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 138120..166929

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KIN65_RS29390 (KIN65_29285) 133259..134155 + 897 WP_004574643 cation transporter -
KIN65_RS29395 (KIN65_29290) 134159..134671 + 513 WP_004863699 signal peptidase II -
KIN65_RS29400 (KIN65_29295) 134693..135982 + 1290 WP_004574636 ISL3-like element ISPpu12 family transposase -
KIN65_RS29405 (KIN65_29300) 136904..137725 + 822 WP_023316395 DUF932 domain-containing protein -
KIN65_RS29410 (KIN65_29305) 137758..138087 + 330 WP_011977736 DUF5983 family protein -
KIN65_RS29415 (KIN65_29310) 138120..138605 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
KIN65_RS29420 (KIN65_29315) 139037..139429 + 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
KIN65_RS29425 (KIN65_29320) 139659..140360 + 702 WP_025712700 hypothetical protein -
KIN65_RS29430 (KIN65_29325) 140446..140646 + 201 WP_046664192 TraY domain-containing protein -
KIN65_RS29435 (KIN65_29330) 140714..141082 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
KIN65_RS29440 (KIN65_29335) 141096..141401 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
KIN65_RS29445 (KIN65_29340) 141421..141987 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
KIN65_RS29450 (KIN65_29345) 141974..142714 + 741 WP_268013948 type-F conjugative transfer system secretin TraK traK
KIN65_RS29455 (KIN65_29350) 142714..144138 + 1425 WP_039698510 F-type conjugal transfer pilus assembly protein TraB traB
KIN65_RS29460 (KIN65_29355) 144212..144796 + 585 WP_020277945 type IV conjugative transfer system lipoprotein TraV traV
KIN65_RS29465 144951..145349 + 399 WP_020277946 hypothetical protein -
KIN65_RS29470 145420..145668 + 249 WP_223175793 hypothetical protein -
KIN65_RS29475 (KIN65_29365) 145692..145910 + 219 WP_004195468 hypothetical protein -
KIN65_RS29480 (KIN65_29370) 145911..146222 + 312 WP_025712701 hypothetical protein -
KIN65_RS29485 (KIN65_29375) 146289..146693 + 405 WP_004197817 hypothetical protein -
KIN65_RS29490 (KIN65_29380) 146736..147035 + 300 WP_020805013 hypothetical protein -
KIN65_RS29495 (KIN65_29385) 147043..147441 + 399 WP_161283539 hypothetical protein -
KIN65_RS29500 (KIN65_29390) 147513..150152 + 2640 WP_268013951 type IV secretion system protein TraC virb4
KIN65_RS29505 (KIN65_29395) 150152..150541 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
KIN65_RS29510 (KIN65_29400) 150541..151167 + 627 WP_025712705 type-F conjugative transfer system protein TraW traW
KIN65_RS29515 (KIN65_29405) 151211..152170 + 960 WP_202560610 conjugal transfer pilus assembly protein TraU traU
KIN65_RS29520 (KIN65_29410) 152183..152821 + 639 WP_022644933 type-F conjugative transfer system pilin assembly protein TrbC trbC
KIN65_RS29525 (KIN65_29415) 152880..154835 + 1956 WP_268013953 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KIN65_RS29530 (KIN65_29420) 154867..155121 + 255 WP_020804203 conjugal transfer protein TrbE -
KIN65_RS29535 (KIN65_29425) 155099..155347 + 249 WP_004152675 hypothetical protein -
KIN65_RS29540 (KIN65_29430) 155360..155686 + 327 WP_004144402 hypothetical protein -
KIN65_RS29545 (KIN65_29435) 155707..156459 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
KIN65_RS29550 (KIN65_29440) 156470..156709 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
KIN65_RS29555 (KIN65_29445) 156681..157238 + 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KIN65_RS29560 (KIN65_29450) 157284..157727 + 444 WP_004194305 F-type conjugal transfer protein TrbF -
KIN65_RS29565 (KIN65_29455) 157705..159084 + 1380 WP_074187349 conjugal transfer pilus assembly protein TraH traH
KIN65_RS29570 (KIN65_29460) 159084..161927 + 2844 WP_268013954 conjugal transfer mating-pair stabilization protein TraG traG
KIN65_RS29575 (KIN65_29465) 161938..162471 + 534 WP_004197891 hypothetical protein -
KIN65_RS29580 (KIN65_29475) 162879..163608 + 730 Protein_192 conjugal transfer complement resistance protein TraT -
KIN65_RS29585 (KIN65_29480) 163801..164490 + 690 WP_013023831 hypothetical protein -
KIN65_RS29590 (KIN65_29485) 164617..166929 + 2313 WP_055316029 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1896 GenBank   NZ_JAHBNO010000003
Plasmid name   pCRE17_1 Incompatibility group   IncFIA
Plasmid size   190288 bp Coordinate of oriT [Strand]   138678..138726 [-]
Host baterium   Klebsiella michiganensis strain S17_CRE17

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, arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9