Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101771
Name   oriT_pA8sk2_3 in_silico
Organism   Klebsiella pneumoniae strain CPE7
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JACYGQ010000006 (102341..102390 [+], 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_pA8sk2_3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1488 GenBank   WP_015065542
Name   traI_IYY95_RS27995_pA8sk2_3 insolico UniProt ID   K7R3U7
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190318.03 Da        Isoelectric Point: 6.2890

>WP_015065542.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALAVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   1164 GenBank   WP_015065541
Name   traD_IYY95_RS28000_pA8sk2_3 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: 86025.00 Da        Isoelectric Point: 5.0577

>WP_015065541.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
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: 73983..102948

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IYY95_RS28000 73983..76295 - 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4
IYY95_RS28005 76424..77113 - 690 WP_015065540 hypothetical protein -
IYY95_RS28010 77305..78036 - 732 WP_032329926 conjugal transfer complement resistance protein TraT -
IYY95_RS28015 78345..78869 - 525 WP_015065538 hypothetical protein -
IYY95_RS28020 78880..81723 - 2844 WP_015065537 conjugal transfer mating-pair stabilization protein TraG traG
IYY95_RS28025 81723..83093 - 1371 WP_004159274 conjugal transfer pilus assembly protein TraH traH
IYY95_RS28030 83080..83508 - 429 WP_015065560 hypothetical protein -
IYY95_RS28035 83501..84073 - 573 WP_023292147 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IYY95_RS28040 84045..84284 - 240 WP_004152687 type-F conjugative transfer system pilin chaperone TraQ -
IYY95_RS28045 84295..85047 - 753 WP_020803149 type-F conjugative transfer system pilin assembly protein TraF traF
IYY95_RS28050 85068..85394 - 327 WP_004144402 hypothetical protein -
IYY95_RS28055 85407..85655 - 249 WP_004152675 hypothetical protein -
IYY95_RS28060 85633..85887 - 255 WP_004152674 conjugal transfer protein TrbE -
IYY95_RS28065 85919..87874 - 1956 WP_030003482 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IYY95_RS28070 87933..88571 - 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
IYY95_RS28075 88584..89573 - 990 WP_011977785 conjugal transfer pilus assembly protein TraU traU
IYY95_RS28080 89570..89959 - 390 WP_015065532 hypothetical protein -
IYY95_RS28085 90001..90627 - 627 WP_009309871 type-F conjugative transfer system protein TraW traW
IYY95_RS28090 90627..91016 - 390 WP_004152506 type-F conjugative transfer system protein TrbI -
IYY95_RS28095 91016..93655 - 2640 WP_004152505 type IV secretion system protein TraC virb4
IYY95_RS28100 93727..94125 - 399 WP_011977783 hypothetical protein -
IYY95_RS28105 94133..94522 - 390 WP_004153076 hypothetical protein -
IYY95_RS28110 94565..94969 - 405 WP_004152503 hypothetical protein -
IYY95_RS28115 95036..95347 - 312 WP_004152502 hypothetical protein -
IYY95_RS28120 95348..95566 - 219 WP_004152501 hypothetical protein -
IYY95_RS28125 95672..96082 - 411 WP_004152499 hypothetical protein -
IYY95_RS28130 96214..96798 - 585 WP_004161368 type IV conjugative transfer system lipoprotein TraV traV
IYY95_RS28135 96912..98336 - 1425 WP_004155033 F-type conjugal transfer pilus assembly protein TraB traB
IYY95_RS28140 98336..99076 - 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
IYY95_RS28145 99063..99629 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
IYY95_RS28150 99649..99954 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
IYY95_RS28155 99968..100336 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
IYY95_RS28160 100401..100604 - 204 WP_171486139 TraY domain-containing protein -
IYY95_RS28165 100737..101456 - 720 WP_015065526 hypothetical protein -
IYY95_RS28170 101656..102072 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
IYY95_RS28175 102463..102948 + 486 WP_015065525 transglycosylase SLT domain-containing protein virB1
IYY95_RS28180 102981..103310 - 330 WP_015065524 DUF5983 family protein -
IYY95_RS28185 103343..104165 - 823 Protein_125 DUF932 domain-containing protein -
IYY95_RS28190 104994..105395 - 402 WP_015065522 helix-turn-helix domain-containing protein -
IYY95_RS28195 105396..105674 - 279 WP_020801586 helix-turn-helix transcriptional regulator -
IYY95_RS28200 105664..105984 - 321 WP_015065521 type II toxin-antitoxin system RelE/ParE family toxin -
IYY95_RS28205 106065..106289 - 225 WP_014343499 hypothetical protein -
IYY95_RS28210 106300..106512 - 213 WP_019706020 hypothetical protein -
IYY95_RS28215 106573..106929 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   2215 GenBank   NZ_JACYGQ010000006
Plasmid name   pA8sk2_3 Incompatibility group   IncFII
Plasmid size   125942 bp Coordinate of oriT [Strand]   102341..102390 [+]
Host baterium   Klebsiella pneumoniae strain CPE7

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, aac(6')-Ib-cr, blaOXA-1, aac(3)-IIa, tet(A), qnrB1, dfrA14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9