Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102441
Name   oriT_p49141_IncFII in_silico
Organism   Citrobacter freundii strain CF49141
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAFIQF010000006 (83467..83590 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_p49141_IncFII
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1825 GenBank   WP_206151347
Name   traI_JYQ93_RS25450_p49141_IncFII insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191691.44 Da        Isoelectric Point: 5.8498

>WP_206151347.1 conjugative transfer relaxase/helicase TraI [Citrobacter freundii]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFPPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTEAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDEPRTAEKLARHPSFTVVSDQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGTSETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGRGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

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

(575-626)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   742 GenBank   WP_001151562
Name   WP_001151562_p49141_IncFII insolico UniProt ID   A0A7I0KNG1
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14420.36 Da        Isoelectric Point: 4.8624

>WP_001151562.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVHEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0KNG1

ID   743 GenBank   WP_001254388
Name   WP_001254388_p49141_IncFII insolico UniProt ID   W9A0Z2
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB W9A0Z2


T4CP

ID   1412 GenBank   WP_000069772
Name   traC_JYQ93_RS26055_p49141_IncFII insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99344.15 Da        Isoelectric Point: 6.4096

>WP_000069772.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   1413 GenBank   WP_024623315
Name   traD_JYQ93_RS26165_p49141_IncFII insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 83140.79 Da        Isoelectric Point: 5.1657

>WP_024623315.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 82895..112378

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JYQ93_RS25945 (JYQ93_25945) 79137..79571 + 435 WP_016239106 conjugation system SOS inhibitor PsiB -
JYQ93_RS25950 (JYQ93_25950) 79568..80330 + 763 Protein_105 plasmid SOS inhibition protein A -
JYQ93_RS28565 80509..80658 + 150 Protein_106 plasmid maintenance protein Mok -
JYQ93_RS25955 (JYQ93_25955) 80600..80725 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
JYQ93_RS28570 80945..81175 + 231 WP_071593758 hypothetical protein -
JYQ93_RS25960 (JYQ93_25960) 81173..81370 - 198 Protein_109 hypothetical protein -
JYQ93_RS25965 (JYQ93_25965) 81372..81659 + 288 WP_000107535 hypothetical protein -
JYQ93_RS25970 (JYQ93_25970) 81779..82600 + 822 WP_001234469 DUF932 domain-containing protein -
JYQ93_RS25975 (JYQ93_25975) 82895..83497 - 603 WP_077539848 transglycosylase SLT domain-containing protein virB1
JYQ93_RS25980 (JYQ93_25980) 83828..84211 + 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
JYQ93_RS25985 (JYQ93_25985) 84405..85091 + 687 WP_016230906 PAS domain-containing protein -
JYQ93_RS25990 (JYQ93_25990) 85185..85412 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
JYQ93_RS25995 (JYQ93_25995) 85446..85805 + 360 WP_001098994 type IV conjugative transfer system pilin TraA -
JYQ93_RS26000 (JYQ93_26000) 85820..86131 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
JYQ93_RS26005 (JYQ93_26005) 86153..86719 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
JYQ93_RS26010 (JYQ93_26010) 86706..87434 + 729 WP_001617735 type-F conjugative transfer system secretin TraK traK
JYQ93_RS26015 (JYQ93_26015) 87434..88861 + 1428 WP_001617736 F-type conjugal transfer pilus assembly protein TraB traB
JYQ93_RS26020 (JYQ93_26020) 88851..89441 + 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
JYQ93_RS26025 (JYQ93_26025) 89428..89748 + 321 WP_001057307 conjugal transfer protein TrbD -
JYQ93_RS26030 (JYQ93_26030) 89745..90260 + 516 WP_000809883 type IV conjugative transfer system lipoprotein TraV traV
JYQ93_RS26035 (JYQ93_26035) 90395..90616 + 222 WP_001278689 conjugal transfer protein TraR -
JYQ93_RS26040 (JYQ93_26040) 90609..91085 + 477 WP_032180036 hypothetical protein -
JYQ93_RS26045 (JYQ93_26045) 91184..91402 + 219 WP_016230909 hypothetical protein -
JYQ93_RS26050 (JYQ93_26050) 91430..91777 + 348 WP_000836682 hypothetical protein -
JYQ93_RS26055 (JYQ93_26055) 91903..94533 + 2631 WP_000069772 type IV secretion system protein TraC virb4
JYQ93_RS26060 (JYQ93_26060) 94530..94916 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
JYQ93_RS26065 (JYQ93_26065) 94913..95545 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
JYQ93_RS26070 (JYQ93_26070) 95542..96534 + 993 WP_000830849 conjugal transfer pilus assembly protein TraU traU
JYQ93_RS26075 (JYQ93_26075) 96561..96869 + 309 WP_000412445 hypothetical protein -
JYQ93_RS26080 (JYQ93_26080) 96932..97450 + 519 WP_000009085 hypothetical protein -
JYQ93_RS26085 (JYQ93_26085) 97477..98115 + 639 WP_000087533 type-F conjugative transfer system pilin assembly protein TrbC trbC
JYQ93_RS26090 (JYQ93_26090) 98112..98483 + 372 WP_000056339 hypothetical protein -
JYQ93_RS26095 (JYQ93_26095) 98509..98931 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
JYQ93_RS26100 (JYQ93_26100) 98928..100778 + 1851 WP_042024687 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JYQ93_RS26105 (JYQ93_26105) 100805..101062 + 258 WP_000864353 conjugal transfer protein TrbE -
JYQ93_RS26110 (JYQ93_26110) 101055..101798 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
JYQ93_RS26115 (JYQ93_26115) 101812..102156 + 345 WP_000556796 conjugal transfer protein TrbA -
JYQ93_RS26120 (JYQ93_26120) 102275..102559 + 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
JYQ93_RS26125 (JYQ93_26125) 102546..103091 + 546 WP_032268350 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JYQ93_RS26130 (JYQ93_26130) 103021..103368 + 348 WP_071840683 P-type conjugative transfer protein TrbJ -
JYQ93_RS26135 (JYQ93_26135) 103349..103741 + 393 WP_014106973 F-type conjugal transfer protein TrbF -
JYQ93_RS26140 (JYQ93_26140) 103728..105101 + 1374 WP_014106974 conjugal transfer pilus assembly protein TraH traH
JYQ93_RS26145 (JYQ93_26145) 105098..107920 + 2823 WP_016235414 conjugal transfer mating-pair stabilization protein TraG traG
JYQ93_RS26150 (JYQ93_26150) 107936..108421 + 486 WP_077507647 surface exclusion protein -
JYQ93_RS26155 (JYQ93_26155) 108470..109201 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
JYQ93_RS26160 (JYQ93_26160) 109404..110183 + 780 WP_137444669 hypothetical protein -
JYQ93_RS26165 (JYQ93_26165) 110180..112378 + 2199 WP_024623315 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2885 GenBank   NZ_JAFIQF010000006
Plasmid name   p49141_IncFII Incompatibility group   IncFII
Plasmid size   117298 bp Coordinate of oriT [Strand]   83467..83590 [+]
Host baterium   Citrobacter freundii strain CF49141

Cargo genes

Drug resistance gene   mph(A), dfrA14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -