Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104057
Name   oriT_pKP4 in_silico
Organism   Klebsiella pneumoniae strain KP4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OL804388 (73183..73232 [-], 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_pKP4
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3002 GenBank   WP_172691966
Name   traI_MCP63_RS00610_pKP4 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: 190320.99 Da        Isoelectric Point: 6.1403

>WP_172691966.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDHPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWEPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWMKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(11-283)

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

AAA domain (AAA_30)

(970-1156)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   2877 GenBank   WP_228303505
Name   traD_MCP63_RS00605_pKP4 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: 85885.99 Da        Isoelectric Point: 5.0596

>WP_228303505.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVIAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNI

  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: 72625..100740

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MCP63_RS00415 68674..69054 + 381 WP_020802391 hypothetical protein -
MCP63_RS00420 69121..69468 + 348 WP_032445771 hypothetical protein -
MCP63_RS00425 69563..69709 + 147 WP_004152750 hypothetical protein -
MCP63_RS00430 69760..70593 + 834 WP_032445769 N-6 DNA methylase -
MCP63_RS00435 71409..72230 + 822 WP_004152492 DUF932 domain-containing protein -
MCP63_RS00440 72263..72592 + 330 WP_011977736 DUF5983 family protein -
MCP63_RS00445 72625..73110 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
MCP63_RS00450 73501..73917 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
MCP63_RS00455 74117..74836 + 720 WP_172691949 conjugal transfer protein TrbJ -
MCP63_RS00460 74969..75172 + 204 WP_171486139 TraY domain-containing protein -
MCP63_RS00465 75237..75605 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
MCP63_RS00470 75619..75924 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
MCP63_RS00475 75944..76510 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
MCP63_RS00480 76497..77237 + 741 WP_172691947 type-F conjugative transfer system secretin TraK traK
MCP63_RS00485 77237..78661 + 1425 WP_185775340 F-type conjugal transfer pilus assembly protein TraB traB
MCP63_RS00490 78734..79318 + 585 WP_040120377 type IV conjugative transfer system lipoprotein TraV traV
MCP63_RS00495 79641..79859 + 219 WP_004171484 hypothetical protein -
MCP63_RS00500 79860..80177 + 318 WP_114473059 hypothetical protein -
MCP63_RS00505 80244..80648 + 405 WP_100748549 hypothetical protein -
MCP63_RS00510 80673..81071 + 399 WP_167875005 hypothetical protein -
MCP63_RS00515 81143..83782 + 2640 WP_150388098 type IV secretion system protein TraC virb4
MCP63_RS00520 83782..84171 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
MCP63_RS00525 84171..84806 + 636 WP_020325113 type-F conjugative transfer system protein TraW traW
MCP63_RS00530 84841..85242 + 402 WP_004194979 hypothetical protein -
MCP63_RS00535 85239..86228 + 990 WP_032441886 conjugal transfer pilus assembly protein TraU traU
MCP63_RS00540 86241..86879 + 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
MCP63_RS00545 86938..88893 + 1956 WP_172691973 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MCP63_RS00550 88925..89161 + 237 WP_114499720 conjugal transfer protein TrbE -
MCP63_RS00665 89158..89343 + 186 WP_042922350 hypothetical protein -
MCP63_RS00555 89389..89715 + 327 WP_016529362 hypothetical protein -
MCP63_RS00560 89736..90488 + 753 WP_172691972 type-F conjugative transfer system pilin assembly protein TraF traF
MCP63_RS00565 90499..90738 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
MCP63_RS00570 90710..91267 + 558 WP_172691971 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MCP63_RS00575 91314..91760 + 447 WP_172691970 conjugal transfer protein TrbF -
MCP63_RS00580 91750..93117 + 1368 WP_185775342 conjugal transfer pilus assembly protein TraH traH
MCP63_RS00585 93117..95966 + 2850 WP_172691976 conjugal transfer mating-pair stabilization protein TraG traG
MCP63_RS00590 95972..96499 + 528 WP_040120388 conjugal transfer protein TraS -
MCP63_RS00595 96688..97419 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
MCP63_RS00600 97612..98301 + 690 WP_172691968 hypothetical protein -
MCP63_RS00605 98428..100740 + 2313 WP_228303505 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4496 GenBank   NZ_OL804388
Plasmid name   pKP4 Incompatibility group   IncFIA
Plasmid size   111364 bp Coordinate of oriT [Strand]   73183..73232 [-]
Host baterium   Klebsiella pneumoniae strain KP4

Cargo genes

Drug resistance gene   mcr-8
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9