Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120461
Name   oriT_AR_0116|unnamed3 in_silico
Organism   Citrobacter freundii strain AR_0116
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032181 (69973..70021 [+], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_AR_0116|unnamed3
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12885 GenBank   WP_119173777
Name   traI_AM363_RS02515_AR_0116|unnamed3 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190683.66 Da        Isoelectric Point: 6.2410

>WP_119173777.1 conjugative transfer relaxase/helicase TraI [Citrobacter freundii]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGTNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYANQIAFGKLYREALKPLVE
KLGYETDVVGKHGMWEMKDVPVEPFSTRTREVREAAGPDASLKSRDVAALDTRKSKETLDPAEKVVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVKADGPDIGDVVTRAIAGLSDRKVQFTYADVLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLILKDREGDRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQLRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLTQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVAGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPLAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)

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.




Auxiliary protein

ID   7259 GenBank   WP_022644939
Name   WP_022644939_AR_0116|unnamed3 insolico UniProt ID   W8QGP1
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15048.16 Da        Isoelectric Point: 4.5248

>WP_022644939.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEVAEKINAIVEKRRVEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNKAL
LEYVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMLRFFPDEDNEVEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB W8QGP1


T4CP

ID   15134 GenBank   WP_119173778
Name   traD_AM363_RS02520_AR_0116|unnamed3 insolico UniProt ID   _
Length   773 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 773 a.a.        Molecular weight: 86126.05 Da        Isoelectric Point: 5.1241

>WP_119173778.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKARPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPDDAGSHAGEQHEPVKQSE
PAGDPVSPVPVKAPSAAKTSVAAEPVKSPETPQPVVPATRVTTVPLIRTKPASAANGTAVATGGATAHSG
GTEQELKPQPADTGQEMMPAGMNEDGEIEDMAAYDAWLAGEQTQREMQRREEVNINHSHRHDEQDDVEIG
GNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40061..67596

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AM363_RS02520 (AM363_02530) 40061..42382 - 2322 WP_119173778 type IV conjugative transfer system coupling protein TraD virb4
AM363_RS02525 (AM363_02535) 42454..42717 - 264 WP_162906117 hypothetical protein -
AM363_RS29685 42738..43430 - 693 WP_162762153 hypothetical protein -
AM363_RS02535 (AM363_02545) 43677..44348 - 672 WP_088883382 hypothetical protein -
AM363_RS02540 (AM363_02550) 44365..47190 - 2826 WP_119173780 conjugal transfer mating-pair stabilization protein TraG traG
AM363_RS02545 (AM363_02555) 47190..48560 - 1371 WP_004159274 conjugal transfer pilus assembly protein TraH traH
AM363_RS02550 (AM363_02560) 48547..48975 - 429 WP_015065560 hypothetical protein -
AM363_RS02555 (AM363_02565) 48968..49540 - 573 WP_023292147 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AM363_RS02560 (AM363_02570) 49512..49751 - 240 WP_004152687 type-F conjugative transfer system pilin chaperone TraQ -
AM363_RS02565 (AM363_02575) 49762..50514 - 753 WP_117072077 type-F conjugative transfer system pilin assembly protein TraF traF
AM363_RS02570 (AM363_02580) 50535..50861 - 327 WP_119173781 hypothetical protein -
AM363_RS02575 (AM363_02585) 50872..51099 - 228 WP_012540032 conjugal transfer protein TrbE -
AM363_RS02580 (AM363_02590) 51089..51370 - 282 WP_012540038 hypothetical protein -
AM363_RS02585 (AM363_02595) 51403..53358 - 1956 WP_060598862 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AM363_RS02590 (AM363_02600) 53417..54064 - 648 WP_039698503 type-F conjugative transfer system pilin assembly protein TrbC trbC
AM363_RS02595 (AM363_02605) 54209..54811 - 603 WP_022631520 hypothetical protein -
AM363_RS02605 (AM363_02615) 55532..56080 - 549 WP_022631518 hypothetical protein -
AM363_RS02610 (AM363_02620) 56095..57054 - 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
AM363_RS02615 (AM363_02625) 57098..57724 - 627 WP_020314628 type-F conjugative transfer system protein TraW traW
AM363_RS02620 (AM363_02630) 57724..58113 - 390 WP_060446931 type-F conjugative transfer system protein TrbI -
AM363_RS02625 (AM363_02635) 58113..60752 - 2640 WP_020323518 type IV secretion system protein TraC virb4
AM363_RS02630 (AM363_02640) 60824..61222 - 399 WP_162906118 hypothetical protein -
AM363_RS02635 (AM363_02645) 61230..61520 - 291 WP_020323516 hypothetical protein -
AM363_RS02640 (AM363_02650) 61517..61921 - 405 WP_049246239 hypothetical protein -
AM363_RS02645 (AM363_02655) 61988..62299 - 312 WP_100698965 hypothetical protein -
AM363_RS02650 (AM363_02660) 62300..62518 - 219 WP_119173783 hypothetical protein -
AM363_RS02655 (AM363_02665) 62542..62826 - 285 WP_119173789 hypothetical protein -
AM363_RS02660 (AM363_02670) 62831..63241 - 411 WP_020805613 hypothetical protein -
AM363_RS02665 (AM363_02675) 63373..63942 - 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
AM363_RS02670 (AM363_02680) 63965..64561 - 597 WP_023316398 conjugal transfer pilus-stabilizing protein TraP -
AM363_RS02675 (AM363_02685) 64554..65978 - 1425 WP_119173784 F-type conjugal transfer pilus assembly protein TraB traB
AM363_RS02680 (AM363_02690) 65978..66718 - 741 WP_119173785 type-F conjugative transfer system secretin TraK traK
AM363_RS02685 (AM363_02695) 66705..67271 - 567 WP_020316627 type IV conjugative transfer system protein TraE traE
AM363_RS02690 (AM363_02700) 67291..67596 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
AM363_RS02695 (AM363_02705) 67610..67978 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
AM363_RS02705 (AM363_02715) 68332..69033 - 702 WP_022644938 hypothetical protein -
AM363_RS02710 (AM363_02720) 69268..69660 - 393 WP_022644939 conjugal transfer relaxosome DNA-binding protein TraM -
AM363_RS02715 (AM363_02725) 70166..70573 + 408 WP_109043189 transglycosylase SLT domain-containing protein -
AM363_RS02720 (AM363_02730) 70611..71138 - 528 WP_109043195 antirestriction protein -
AM363_RS02725 (AM363_02735) 71551..71697 - 147 WP_109043194 succinate dehydrogenase flavoprotein subunit -
AM363_RS02730 (AM363_02740) 71790..72137 - 348 WP_109043188 hypothetical protein -
AM363_RS02735 (AM363_02745) 72204..72584 - 381 WP_119173786 hypothetical protein -

Host bacterium

ID   20890 GenBank   NZ_CP032181
Plasmid name   AR_0116|unnamed3 Incompatibility group   -
Plasmid size   81323 bp Coordinate of oriT [Strand]   69973..70021 [+]
Host baterium   Citrobacter freundii strain AR_0116

Cargo genes

Drug resistance gene   blaKPC-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -