Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103116
Name   oriT_pG12-KPC-2 in_silico
Organism   Klebsiella pneumoniae strain K47-25
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU665642 (72942..72991 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pG12-KPC-2
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2336 GenBank   WP_004153015
Name   traI_HTH42_RS00610_pG12-KPC-2 insolico UniProt ID   A0A8A5TN24
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190492.51 Da        Isoelectric Point: 6.3661

>WP_004153015.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGMFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRHNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGASGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQKSVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTSFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QTQIRSGQLLNAPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTQAQEKAIQ
KALSEGETLPAGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(635-714)

DNA helicase TraI (TraI_C)

(1433-1555)

TrwC relaxase (TrwC)

(10-284)

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

(577-629)

AAA domain (AAA_30)

(971-1157)


  Protein structure



No available structure.




T4CP

ID   2064 GenBank   WP_004152620
Name   traD_HTH42_RS00605_pG12-KPC-2 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: 85871.84 Da        Isoelectric Point: 5.0101

>WP_004152620.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPEPGPADTDSHASEQPEPVSPPA
PAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 72384..101381

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH42_RS00395 (pG12-KPC-2_40) 67486..67836 + 351 WP_004153414 hypothetical protein -
HTH42_RS00400 (pG12-KPC-2_42) 68466..68819 + 354 WP_004152748 hypothetical protein -
HTH42_RS00405 (pG12-KPC-2_43) 68876..69223 + 348 WP_004152749 hypothetical protein -
HTH42_RS00410 69318..69464 + 147 WP_004152750 hypothetical protein -
HTH42_RS00415 (pG12-KPC-2_44) 69515..70348 + 834 WP_004152751 N-6 DNA methylase -
HTH42_RS00420 (pG12-KPC-2_46) 71168..71989 + 822 WP_004152492 DUF932 domain-containing protein -
HTH42_RS00425 (pG12-KPC-2_47) 72022..72351 + 330 WP_011977736 DUF5983 family protein -
HTH42_RS00430 (pG12-KPC-2_48) 72384..72869 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
HTH42_RS00435 73291..73689 + 399 WP_004152493 conjugal transfer relaxosome DNA-binding protein TraM -
HTH42_RS00440 73863..74549 + 687 WP_004152494 transcriptional regulator TraJ family protein -
HTH42_RS00445 74628..75014 + 387 WP_004152495 TraY domain-containing protein -
HTH42_RS00450 75068..75436 + 369 WP_004152496 type IV conjugative transfer system pilin TraA -
HTH42_RS00455 75450..75755 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HTH42_RS00460 75775..76341 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
HTH42_RS00465 76328..77068 + 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
HTH42_RS00470 77068..78492 + 1425 WP_004155033 F-type conjugal transfer pilus assembly protein TraB traB
HTH42_RS00475 78606..79190 + 585 WP_004161368 type IV conjugative transfer system lipoprotein TraV traV
HTH42_RS00480 (pG12-KPC-2_49) 79322..79732 + 411 WP_004152499 hypothetical protein -
HTH42_RS00485 79838..80056 + 219 WP_004152501 hypothetical protein -
HTH42_RS00490 (pG12-KPC-2_50) 80057..80368 + 312 WP_004152502 hypothetical protein -
HTH42_RS00495 (pG12-KPC-2_51) 80435..80839 + 405 WP_004152503 hypothetical protein -
HTH42_RS00500 (pG12-KPC-2_52) 80882..81271 + 390 WP_004153076 hypothetical protein -
HTH42_RS00505 (pG12-KPC-2_53) 81279..81677 + 399 WP_011977783 hypothetical protein -
HTH42_RS00510 81749..84388 + 2640 WP_004152505 type IV secretion system protein TraC virb4
HTH42_RS00515 84388..84777 + 390 WP_004152506 type-F conjugative transfer system protein TrbI -
HTH42_RS00520 84777..85403 + 627 WP_004152507 type-F conjugative transfer system protein TraW traW
HTH42_RS00525 (pG12-KPC-2_54) 85445..85834 + 390 WP_004152508 hypothetical protein -
HTH42_RS00530 85831..86820 + 990 WP_011977785 conjugal transfer pilus assembly protein TraU traU
HTH42_RS00535 86833..87471 + 639 WP_004152672 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTH42_RS00540 87530..89485 + 1956 WP_004152673 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTH42_RS00545 89517..89771 + 255 WP_004152674 conjugal transfer protein TrbE -
HTH42_RS00550 (pG12-KPC-2_55) 89749..89997 + 249 WP_004152675 hypothetical protein -
HTH42_RS00555 (pG12-KPC-2_56) 90010..90336 + 327 WP_004152676 hypothetical protein -
HTH42_RS00560 90357..91109 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
HTH42_RS00565 91120..91359 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HTH42_RS00570 91331..91888 + 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTH42_RS00575 91934..92377 + 444 WP_004152679 F-type conjugal transfer protein TrbF -
HTH42_RS00580 92355..93734 + 1380 WP_004165169 conjugal transfer pilus assembly protein TraH traH
HTH42_RS00585 93734..96583 + 2850 WP_072241631 conjugal transfer mating-pair stabilization protein TraG traG
HTH42_RS00590 96596..97144 + 549 WP_004152623 conjugal transfer entry exclusion protein TraS -
HTH42_RS00595 97328..98059 + 732 WP_004152622 conjugal transfer complement resistance protein TraT -
HTH42_RS00600 (pG12-KPC-2_57) 98251..98940 + 690 WP_004198206 hypothetical protein -
HTH42_RS00605 99069..101381 + 2313 WP_004152620 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3559 GenBank   NZ_KU665642
Plasmid name   pG12-KPC-2 Incompatibility group   IncFIB
Plasmid size   111926 bp Coordinate of oriT [Strand]   72942..72991 [-]
Host baterium   Klebsiella pneumoniae strain K47-25

Cargo genes

Drug resistance gene   blaKPC-2, blaOXA-9
Virulence gene   -
Metal resistance gene   merD, merA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9