Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115232
Name   oriT_p7532_tmexCD in_silico
Organism   Klebsiella oxytoca strain C7532
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MZ532981 (79524..79572 [-], 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_p7532_tmexCD
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9733 GenBank   WP_075606914
Name   traI_NX083_RS00595_p7532_tmexCD 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   5719 GenBank   WP_020805752
Name   WP_020805752_p7532_tmexCD 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   11352 GenBank   WP_075606915
Name   traD_NX083_RS00590_p7532_tmexCD 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: 78966..107150

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NX083_RS00405 (EENBGKKG_00080) 76535..76934 + 400 Protein_80 hypothetical protein -
NX083_RS00410 (EENBGKKG_00082) 77750..78571 + 822 WP_032454971 DUF932 domain-containing protein -
NX083_RS00415 (EENBGKKG_00083) 78604..78933 + 330 WP_011977736 DUF5983 family protein -
NX083_RS00420 (EENBGKKG_00084) 78966..79451 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
NX083_RS00425 (EENBGKKG_00085) 79883..80275 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
NX083_RS00430 (EENBGKKG_00086) 80522..81214 + 693 WP_228723673 hypothetical protein -
NX083_RS00435 (EENBGKKG_00087) 81300..81500 + 201 WP_048289787 TraY domain-containing protein -
NX083_RS00440 (EENBGKKG_00088) 81569..81937 + 369 WP_064343525 type IV conjugative transfer system pilin TraA -
NX083_RS00445 (EENBGKKG_00089) 81951..82256 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
NX083_RS00450 (EENBGKKG_00090) 82272..82838 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
NX083_RS00455 (EENBGKKG_00091) 82825..83559 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
NX083_RS00460 (EENBGKKG_00092) 83559..84980 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
NX083_RS00465 (EENBGKKG_00093) 84973..85407 + 435 WP_020322358 conjugal transfer protein TraP -
NX083_RS00470 (EENBGKKG_00094) 85441..86025 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
NX083_RS00475 86102..86326 + 225 WP_053390288 hypothetical protein -
NX083_RS00480 (EENBGKKG_00096) 86638..86826 + 189 WP_053390286 hypothetical protein -
NX083_RS00485 (EENBGKKG_00097) 86910..87311 + 402 WP_064343532 hypothetical protein -
NX083_RS00490 (EENBGKKG_00098) 87308..87607 + 300 WP_053390308 hypothetical protein -
NX083_RS00495 (EENBGKKG_00099) 87695..88078 + 384 WP_042946290 hypothetical protein -
NX083_RS00500 (EENBGKKG_00100) 88171..90810 + 2640 WP_064343533 type IV secretion system protein TraC virb4
NX083_RS00505 (EENBGKKG_00101) 90810..91202 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
NX083_RS00510 (EENBGKKG_00102) 91199..91825 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
NX083_RS00515 (EENBGKKG_00103) 91869..92828 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
NX083_RS00520 (EENBGKKG_00104) 92841..93488 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
NX083_RS00525 (EENBGKKG_00105) 93485..93868 + 384 WP_053390297 hypothetical protein -
NX083_RS00530 (EENBGKKG_00106) 93865..95820 + 1956 WP_064359956 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NX083_RS00535 (EENBGKKG_00107) 95852..96112 + 261 WP_053390216 hypothetical protein -
NX083_RS00540 (EENBGKKG_00108) 96153..96716 + 564 WP_258237681 hypothetical protein -
NX083_RS00545 (EENBGKKG_00109) 96706..96948 + 243 WP_053390218 conjugal transfer protein TrbE -
NX083_RS00550 (EENBGKKG_00110) 96994..97320 + 327 WP_053390219 hypothetical protein -
NX083_RS00555 (EENBGKKG_00111) 97341..98093 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
NX083_RS00560 (EENBGKKG_00112) 98104..98340 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
NX083_RS00565 (EENBGKKG_00113) 98315..98875 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NX083_RS00570 (EENBGKKG_00114) 98862..100232 + 1371 WP_075606918 conjugal transfer pilus assembly protein TraH traH
NX083_RS00575 (EENBGKKG_00115) 100232..103087 + 2856 WP_075606917 conjugal transfer mating-pair stabilization protein TraG traG
NX083_RS00580 (EENBGKKG_00116) 103152..103775 + 624 WP_258237686 hypothetical protein -
NX083_RS00585 (EENBGKKG_00117) 104021..104713 + 693 WP_202395549 hypothetical protein -
NX083_RS00590 (EENBGKKG_00118) 104832..107150 + 2319 WP_075606915 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   15667 GenBank   NZ_MZ532981
Plasmid name   p7532_tmexCD Incompatibility group   IncU
Plasmid size   118281 bp Coordinate of oriT [Strand]   79524..79572 [-]
Host baterium   Klebsiella oxytoca strain C7532

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, ARR-3, blaTEM-1B, aph(3'')-Ib, aph(6)-Id, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -