Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101159
Name   oriT_pSS20EcIncFII in_silico
Organism   Escherichia coli strain EcSS20
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SDDW01000022 (24372..24495 [+], 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_pSS20EcIncFII
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1156 GenBank   WP_129015002
Name   traI_ERL57_RS20135_pSS20EcIncFII 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: 191766.43 Da        Isoelectric Point: 5.7960

>WP_129015002.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQDGMTFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQILITDSGQRTGTGSALMSMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNMRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(968-1156)

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   415 GenBank   WP_001151562
Name   WP_001151562_pSS20EcIncFII 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   416 GenBank   WP_001254388
Name   WP_001254388_pSS20EcIncFII 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   733 GenBank   WP_001526033
Name   traC_ERL57_RS20020_pSS20EcIncFII 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: 99213.73 Da        Isoelectric Point: 5.8465

>WP_001526033.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGINLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(468-764)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   734 GenBank   WP_096988748
Name   traD_ERL57_RS20130_pSS20EcIncFII insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82758.29 Da        Isoelectric Point: 5.1008

>WP_096988748.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGHQGKQ
QSENEVTGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPVSSVINDKKSDAGVSVPAGGIEQELNMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
IQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 23800..53511

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ERL57_RS19895 (ERL57_19895) 20041..20475 + 435 WP_129014999 conjugation system SOS inhibitor PsiB -
ERL57_RS19900 (ERL57_19900) 20472..21234 + 763 Protein_28 plasmid SOS inhibition protein A -
ERL57_RS24610 21203..21391 - 189 WP_001336239 hypothetical protein -
ERL57_RS24990 21413..21562 + 150 Protein_30 plasmid maintenance protein Mok -
ERL57_RS19905 (ERL57_19905) 21504..21629 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
ERL57_RS24995 (ERL57_19910) 21849..22079 + 231 WP_071593758 hypothetical protein -
ERL57_RS19915 (ERL57_19915) 22077..22274 - 198 Protein_33 hypothetical protein -
ERL57_RS19920 (ERL57_19920) 22276..22563 + 288 WP_000107535 hypothetical protein -
ERL57_RS19925 (ERL57_19925) 22684..23505 + 822 WP_001234469 DUF932 domain-containing protein -
ERL57_RS19935 (ERL57_19935) 23800..24402 - 603 WP_077539848 transglycosylase SLT domain-containing protein virB1
ERL57_RS19940 (ERL57_19940) 24733..25116 + 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
ERL57_RS19945 (ERL57_19945) 25310..25996 + 687 WP_000332499 PAS domain-containing protein -
ERL57_RS19950 (ERL57_19950) 26090..26317 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
ERL57_RS19955 (ERL57_19955) 26351..26710 + 360 WP_016239104 type IV conjugative transfer system pilin TraA -
ERL57_RS19960 (ERL57_19960) 26725..27036 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
ERL57_RS19965 (ERL57_19965) 27058..27624 + 567 WP_016239103 type IV conjugative transfer system protein TraE traE
ERL57_RS19970 (ERL57_19970) 27611..28339 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ERL57_RS19975 (ERL57_19975) 28339..29766 + 1428 WP_129015000 F-type conjugal transfer pilus assembly protein TraB traB
ERL57_RS19980 (ERL57_19980) 29756..30346 + 591 WP_001535745 conjugal transfer pilus-stabilizing protein TraP -
ERL57_RS19985 (ERL57_19985) 30333..30653 + 321 WP_001057298 conjugal transfer protein TrbD virb4
ERL57_RS19990 (ERL57_19990) 30646..30897 + 252 WP_001038333 conjugal transfer protein TrbG -
ERL57_RS19995 (ERL57_19995) 30894..31409 + 516 WP_032234029 type IV conjugative transfer system lipoprotein TraV traV
ERL57_RS20000 (ERL57_20000) 31544..31765 + 222 WP_001278689 conjugal transfer protein TraR -
ERL57_RS20005 (ERL57_20005) 31758..32234 + 477 WP_109547838 hypothetical protein -
ERL57_RS20010 (ERL57_20010) 32315..32533 + 219 WP_000556751 hypothetical protein -
ERL57_RS20015 (ERL57_20015) 32561..32908 + 348 WP_000836682 hypothetical protein -
ERL57_RS20020 (ERL57_20020) 33034..35664 + 2631 WP_001526033 type IV secretion system protein TraC virb4
ERL57_RS20025 (ERL57_20025) 35661..36047 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
ERL57_RS20030 (ERL57_20030) 36044..36676 + 633 WP_001526032 type-F conjugative transfer system protein TraW traW
ERL57_RS20035 (ERL57_20035) 36673..37665 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
ERL57_RS20040 (ERL57_20040) 37692..38000 + 309 WP_000412445 hypothetical protein -
ERL57_RS20045 (ERL57_20045) 38063..38581 + 519 WP_000009085 hypothetical protein -
ERL57_RS20050 (ERL57_20050) 38608..39246 + 639 WP_109547839 type-F conjugative transfer system pilin assembly protein TrbC trbC
ERL57_RS20055 (ERL57_20055) 39243..39614 + 372 WP_000056340 hypothetical protein -
ERL57_RS20060 (ERL57_20060) 39639..40061 + 423 WP_001229306 HNH endonuclease signature motif containing protein -
ERL57_RS20065 (ERL57_20065) 40058..41908 + 1851 WP_109547840 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ERL57_RS20070 (ERL57_20070) 41935..42192 + 258 WP_129015006 conjugal transfer protein TrbE -
ERL57_RS20075 (ERL57_20075) 42185..42928 + 744 WP_001030385 type-F conjugative transfer system pilin assembly protein TraF traF
ERL57_RS20080 (ERL57_20080) 42942..43286 + 345 WP_096979571 conjugal transfer protein TrbA -
ERL57_RS20085 (ERL57_20085) 43405..43689 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
ERL57_RS20090 (ERL57_20090) 43676..44221 + 546 WP_129015001 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ERL57_RS20095 (ERL57_20095) 44151..44498 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
ERL57_RS20100 (ERL57_20100) 44479..44871 + 393 WP_000660700 F-type conjugal transfer protein TrbF -
ERL57_RS20105 (ERL57_20105) 44858..46231 + 1374 WP_021563037 conjugal transfer pilus assembly protein TraH traH
ERL57_RS20110 (ERL57_20110) 46228..49050 + 2823 WP_109547842 conjugal transfer mating-pair stabilization protein TraG traG
ERL57_RS20115 (ERL57_20115) 49066..49551 + 486 WP_020241360 surface exclusion inner membrane protein -
ERL57_RS20120 (ERL57_20120) 49600..50331 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
ERL57_RS20125 (ERL57_20125) 50534..51271 + 738 WP_032301641 hypothetical protein -
ERL57_RS20130 (ERL57_20130) 51322..53511 + 2190 WP_096988748 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1603 GenBank   NZ_SDDW01000022
Plasmid name   pSS20EcIncFII Incompatibility group   IncFII
Plasmid size   66445 bp Coordinate of oriT [Strand]   24372..24495 [+]
Host baterium   Escherichia coli strain EcSS20

Cargo genes

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