Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106232
Name   oriT_pKP57-mcr8 in_silico
Organism   Klebsiella pneumoniae strain 57
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP088130 (62747..62796 [-], 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_pKP57-mcr8
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4175 GenBank   WP_172691966
Name   traI_LRM34_RS28035_pKP57-mcr8 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   4192 GenBank   WP_228303505
Name   traD_LRM34_RS28030_pKP57-mcr8 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: 62189..90304

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LRM34_RS27840 (LRM34_27840) 58239..58619 + 381 WP_020802391 hypothetical protein -
LRM34_RS27845 (LRM34_27845) 58685..59032 + 348 WP_032445771 hypothetical protein -
LRM34_RS27850 (LRM34_27850) 59127..59273 + 147 WP_004152750 hypothetical protein -
LRM34_RS27855 (LRM34_27855) 59324..60157 + 834 WP_032445769 N-6 DNA methylase -
LRM34_RS27860 (LRM34_27860) 60973..61794 + 822 WP_004152492 DUF932 domain-containing protein -
LRM34_RS27865 (LRM34_27865) 61827..62156 + 330 WP_011977736 DUF5983 family protein -
LRM34_RS27870 (LRM34_27870) 62189..62674 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
LRM34_RS27875 (LRM34_27875) 63065..63481 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
LRM34_RS27880 (LRM34_27880) 63681..64400 + 720 WP_172691949 conjugal transfer protein TrbJ -
LRM34_RS27885 (LRM34_27885) 64533..64736 + 204 WP_171486139 TraY domain-containing protein -
LRM34_RS27890 (LRM34_27890) 64801..65169 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LRM34_RS27895 (LRM34_27895) 65183..65488 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LRM34_RS27900 (LRM34_27900) 65508..66074 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
LRM34_RS27905 (LRM34_27905) 66061..66801 + 741 WP_172691947 type-F conjugative transfer system secretin TraK traK
LRM34_RS27910 (LRM34_27910) 66801..68225 + 1425 WP_185775340 F-type conjugal transfer pilus assembly protein TraB traB
LRM34_RS27915 (LRM34_27915) 68298..68882 + 585 WP_040120377 type IV conjugative transfer system lipoprotein TraV traV
LRM34_RS27920 (LRM34_27920) 69205..69423 + 219 WP_004171484 hypothetical protein -
LRM34_RS27925 (LRM34_27925) 69424..69741 + 318 WP_114473059 hypothetical protein -
LRM34_RS27930 (LRM34_27930) 69808..70212 + 405 WP_100748549 hypothetical protein -
LRM34_RS27935 (LRM34_27935) 70237..70635 + 399 WP_167875005 hypothetical protein -
LRM34_RS27940 (LRM34_27940) 70707..73346 + 2640 WP_150388098 type IV secretion system protein TraC virb4
LRM34_RS27945 (LRM34_27945) 73346..73735 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
LRM34_RS27950 (LRM34_27950) 73735..74370 + 636 WP_020325113 type-F conjugative transfer system protein TraW traW
LRM34_RS27955 (LRM34_27955) 74405..74806 + 402 WP_004194979 hypothetical protein -
LRM34_RS27960 (LRM34_27960) 74803..75792 + 990 WP_032441886 conjugal transfer pilus assembly protein TraU traU
LRM34_RS27965 (LRM34_27965) 75805..76443 + 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
LRM34_RS27970 (LRM34_27970) 76502..78457 + 1956 WP_172691973 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LRM34_RS27975 (LRM34_27975) 78489..78725 + 237 WP_114499720 conjugal transfer protein TrbE -
LRM34_RS28165 78722..78907 + 186 WP_042922350 hypothetical protein -
LRM34_RS27980 (LRM34_27980) 78953..79279 + 327 WP_016529362 hypothetical protein -
LRM34_RS27985 (LRM34_27985) 79300..80052 + 753 WP_172691972 type-F conjugative transfer system pilin assembly protein TraF traF
LRM34_RS27990 (LRM34_27990) 80063..80302 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
LRM34_RS27995 (LRM34_27995) 80274..80831 + 558 WP_172691971 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LRM34_RS28000 (LRM34_28000) 80878..81324 + 447 WP_172691970 conjugal transfer protein TrbF -
LRM34_RS28005 (LRM34_28005) 81314..82681 + 1368 WP_185775342 conjugal transfer pilus assembly protein TraH traH
LRM34_RS28010 (LRM34_28010) 82681..85530 + 2850 WP_172691976 conjugal transfer mating-pair stabilization protein TraG traG
LRM34_RS28015 (LRM34_28015) 85536..86063 + 528 WP_040120388 conjugal transfer protein TraS -
LRM34_RS28020 (LRM34_28020) 86252..86983 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
LRM34_RS28025 (LRM34_28025) 87176..87865 + 690 WP_172691968 hypothetical protein -
LRM34_RS28030 (LRM34_28030) 87992..90304 + 2313 WP_228303505 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   6669 GenBank   NZ_CP088130
Plasmid name   pKP57-mcr8 Incompatibility group   IncFIA
Plasmid size   100928 bp Coordinate of oriT [Strand]   62747..62796 [-]
Host baterium   Klebsiella pneumoniae strain 57

Cargo genes

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