Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104621
Name   oriT_YL6-1|p1 in_silico
Organism   Klebsiella michiganensis strain YL6-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084416 (26939..26987 [-], 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    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_YL6-1|p1
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3321 GenBank   WP_075606914
Name   traI_LDP80_RS29470_YL6-1|p1 insolico UniProt ID   A0A6M3HIK1
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190386.65 Da        Isoelectric Point: 5.5084

>WP_075606914.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTNNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADTRAKELASAPAAPVKTDVPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
KPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDTAVVRQSPF
SDAVSVLAQDRPTMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLSADARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKMSLKETLSMLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKSEGVLGEKDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLTVAEGERLAVLGKIPDTRLKGGESVTVLKAEEGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQGTARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIASQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
SQIQAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDNVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQVTPEQVPRKDGAWVPENSVVEFTPAQEEAIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKSTRTLNPKADQAQQHIDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESAYVGLSRMKQHVQVYTDNREGWIKAINNSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1432-1552)

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

(577-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1157)

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

(634-713)


  Protein structure



No available structure.




Auxiliary protein

ID   1484 GenBank   WP_020805752
Name   WP_020805752_YL6-1|p1 insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   3259 GenBank   WP_075606915
Name   traD_LDP80_RS29465_YL6-1|p1 insolico UniProt ID   _
Length   772 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 772 a.a.        Molecular weight: 86712.47 Da        Isoelectric Point: 5.0825

>WP_075606915.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLILMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGKSLEYNSEQILADKYTIWCGEQLWTSFVFAAIVSLTVCIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKHSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDIWRECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFSEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLKNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKSRPKIAEGFILRNLDTRTDARLDTLLEAREAESSHARTLFTPDAPAPELAEKDEKVGNPPEQSQPAE
SSGTPATVKVPSTAKTPEADESGQSPEVSNPAALLTKVVTVPLTRPRPAAATGTAAVASATDVRATPAGG
TEQALETQPAEQGQDMLPPGVNEYGEIDDMHAWDEWQSGEQTQRDMQRREEVNINHSHRRDEQDDIEIGG
NF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29366..55616

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDP80_RS29290 (LDP80_29330) 25807..26349 + 543 WP_053390246 antirestriction protein -
LDP80_RS29295 (LDP80_29335) 26372..26794 - 423 WP_077268549 transglycosylase SLT domain-containing protein -
LDP80_RS29300 (LDP80_29340) 27298..27690 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
LDP80_RS29305 (LDP80_29345) 27928..28629 + 702 WP_223174962 hypothetical protein -
LDP80_RS29310 (LDP80_29350) 28715..28915 + 201 WP_048289787 TraY domain-containing protein -
LDP80_RS29315 (LDP80_29355) 28984..29352 + 369 WP_064343525 type IV conjugative transfer system pilin TraA -
LDP80_RS29320 (LDP80_29360) 29366..29671 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
LDP80_RS29325 (LDP80_29365) 29687..30253 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
LDP80_RS29330 (LDP80_29370) 30240..30974 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
LDP80_RS29335 (LDP80_29375) 30974..32395 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
LDP80_RS29340 (LDP80_29380) 32388..32822 + 435 WP_020322358 conjugal transfer protein TraP -
LDP80_RS29345 (LDP80_29385) 32856..33440 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
LDP80_RS29350 (LDP80_29390) 34053..34241 + 189 WP_053390286 hypothetical protein -
LDP80_RS29355 (LDP80_29395) 34325..34726 + 402 WP_064343532 hypothetical protein -
LDP80_RS29360 (LDP80_29400) 34723..35022 + 300 WP_053390308 hypothetical protein -
LDP80_RS29365 (LDP80_29405) 35110..35493 + 384 WP_042946290 hypothetical protein -
LDP80_RS29370 (LDP80_29410) 35586..38225 + 2640 WP_064343533 type IV secretion system protein TraC virb4
LDP80_RS29375 (LDP80_29415) 38225..38617 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
LDP80_RS29380 (LDP80_29420) 38614..39240 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
LDP80_RS29385 (LDP80_29425) 39284..40243 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
LDP80_RS29390 (LDP80_29430) 40256..40903 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
LDP80_RS29395 (LDP80_29435) 40900..41283 + 384 WP_053390297 hypothetical protein -
LDP80_RS29400 (LDP80_29440) 41280..43235 + 1956 WP_064343537 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LDP80_RS29405 (LDP80_29445) 43267..43527 + 261 WP_225025344 hypothetical protein -
LDP80_RS29410 (LDP80_29450) 43520..44131 + 612 WP_053390217 hypothetical protein -
LDP80_RS29415 (LDP80_29455) 44121..44363 + 243 WP_053390218 conjugal transfer protein TrbE -
LDP80_RS29420 (LDP80_29460) 44409..44735 + 327 WP_053390219 hypothetical protein -
LDP80_RS29425 (LDP80_29465) 44756..45508 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
LDP80_RS29430 (LDP80_29470) 45519..45755 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
LDP80_RS29435 (LDP80_29475) 45730..46290 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LDP80_RS29440 (LDP80_29480) 46277..47647 + 1371 WP_075606918 conjugal transfer pilus assembly protein TraH traH
LDP80_RS29445 (LDP80_29485) 47647..50526 + 2880 WP_064386194 conjugal transfer mating-pair stabilization protein TraG traG
LDP80_RS29450 (LDP80_29490) 50543..51211 + 669 WP_128317877 hypothetical protein -
LDP80_RS29455 (LDP80_29495) 51564..52295 + 732 WP_064386198 conjugal transfer complement resistance protein TraT -
LDP80_RS29460 (LDP80_29500) 52487..53179 + 693 WP_202395549 hypothetical protein -
LDP80_RS29465 (LDP80_29505) 53298..55616 + 2319 WP_075606915 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5060 GenBank   NZ_CP084416
Plasmid name   YL6-1|p1 Incompatibility group   -
Plasmid size   101530 bp Coordinate of oriT [Strand]   26939..26987 [-]
Host baterium   Klebsiella michiganensis strain YL6-1

Cargo genes

Drug resistance gene   blaKPC-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -