Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117509
Name   oriT_pCYNDM01 in_silico
Organism   Raoultella ornithinolytica strain B1645-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK510953 (71810..71859 [-], 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    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pCYNDM01
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11154 GenBank   WP_196495579
Name   traI_I6U43_RS00640_pCYNDM01 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190409.68 Da        Isoelectric Point: 5.5496

>WP_196495579.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTNNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADTRAKELASAPAAPVKTDVPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
KPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDTAVVRQSPF
SDAVSVLAQDRPTMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLSADARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKMSLKETLSMLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKSEGVLGEKDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLTVAEGERLAVLGKIPDTRLKGGESVTVLKAEEGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQGTARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIASQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
SQIQAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDNVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQVTPEQVPRKDGAWVPENSVVEFTPAQEEAIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKSTRTLNPKADQAQQHIDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESAYVGLSRMKQHVQVYTDNREGWIKAINHSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(970-1157)

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

(577-628)

TrwC relaxase (TrwC)

(11-283)

DNA helicase TraI (TraI_C)

(1432-1552)

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

(634-713)


  Protein structure



No available structure.




Auxiliary protein

ID   6467 GenBank   WP_053390193
Name   WP_053390193_pCYNDM01 insolico UniProt ID   A0A8G2A327
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14883.89 Da        Isoelectric Point: 4.3779

>WP_053390193.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEVADKINAIVEKRRVEGAKDKDISFSSISTMLLELGLRVYEAQMERKESGFNQMAFNKAL
LESVIKTQFTVNKVLGIECLSPHVSGNPRWEWPGLIENIRDDVQEVMLRFFPDEESEDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   13034 GenBank   WP_075606915
Name   traD_I6U43_RS00635_pCYNDM01 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: 71243..100521

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I6U43_RS00425 66433..67308 + 876 WP_060415463 DUF4942 domain-containing protein -
I6U43_RS00430 68088..68426 + 339 WP_020804855 hypothetical protein -
I6U43_RS00435 68483..68830 + 348 WP_064182675 hypothetical protein -
I6U43_RS00440 68919..69149 + 231 WP_060415465 hypothetical protein -
I6U43_RS00445 69196..70029 + 834 WP_060415466 N-6 DNA methylase -
I6U43_RS00450 70315..70683 - 369 WP_080848162 hypothetical protein -
I6U43_RS00455 70678..71220 + 543 WP_196495582 antirestriction protein -
I6U43_RS00460 71243..71665 - 423 WP_073972322 transglycosylase SLT domain-containing protein virB1
I6U43_RS00465 72171..72563 + 393 WP_053390193 conjugal transfer relaxosome DNA-binding protein TraM -
I6U43_RS00470 73194..73502 + 309 WP_181726265 hypothetical protein -
I6U43_RS00475 73663..73824 + 162 WP_172686697 TraY domain-containing protein -
I6U43_RS00480 73889..74257 + 369 WP_064386081 type IV conjugative transfer system pilin TraA -
I6U43_RS00485 74271..74576 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
I6U43_RS00490 74592..75158 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
I6U43_RS00495 75145..75879 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
I6U43_RS00500 75879..77300 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
I6U43_RS00505 77293..77727 + 435 WP_020322358 conjugal transfer protein TraP -
I6U43_RS00510 77761..78345 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
I6U43_RS00515 78422..78646 + 225 WP_053390288 hypothetical protein -
I6U43_RS00520 78958..79146 + 189 WP_053390286 hypothetical protein -
I6U43_RS00965 79230..79631 + 402 WP_064343532 hypothetical protein -
I6U43_RS00530 79628..79927 + 300 WP_053390308 hypothetical protein -
I6U43_RS00535 80015..80398 + 384 WP_042946290 hypothetical protein -
I6U43_RS00540 80491..83130 + 2640 WP_064343533 type IV secretion system protein TraC virb4
I6U43_RS00545 83130..83522 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
I6U43_RS00550 83519..84145 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
I6U43_RS00555 84189..85148 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
I6U43_RS00560 85161..85808 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
I6U43_RS00565 85805..86188 + 384 WP_053390297 hypothetical protein -
I6U43_RS00570 86185..88140 + 1956 WP_064343537 type-F conjugative transfer system mating-pair stabilization protein TraN traN
I6U43_RS00575 88172..88432 + 261 WP_053390216 hypothetical protein -
I6U43_RS00580 88425..89036 + 612 WP_053390217 hypothetical protein -
I6U43_RS00585 89026..89268 + 243 WP_053390218 conjugal transfer protein TrbE -
I6U43_RS00590 89314..89640 + 327 WP_053390219 hypothetical protein -
I6U43_RS00595 89661..90413 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
I6U43_RS00600 90424..90660 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
I6U43_RS00605 90635..91195 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
I6U43_RS00610 91182..92552 + 1371 WP_075606918 conjugal transfer pilus assembly protein TraH traH
I6U43_RS00615 92552..95431 + 2880 WP_064386194 conjugal transfer mating-pair stabilization protein TraG traG
I6U43_RS00620 95448..96116 + 669 WP_128317877 hypothetical protein -
I6U43_RS00625 96469..97200 + 732 WP_064386198 conjugal transfer complement resistance protein TraT -
I6U43_RS00970 97392..98084 + 693 WP_202395549 hypothetical protein -
I6U43_RS00635 98203..100521 + 2319 WP_075606915 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   17942 GenBank   NZ_MK510953
Plasmid name   pCYNDM01 Incompatibility group   IncFIA
Plasmid size   149440 bp Coordinate of oriT [Strand]   71810..71859 [-]
Host baterium   Raoultella ornithinolytica strain B1645-1

Cargo genes

Drug resistance gene   sul1, qacE, catB8, dfrA14, sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, aac(3)-IId, blaCTX-M-9, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -