Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102430
Name   oriT_SMG002F8|unnamed1 in_silico
Organism   Escherichia coli strain SMG002F8
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKVSR010000015 (45096..45447 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_SMG002F8|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1817 GenBank   WP_000987005
Name   traI_ML370_RS20810_SMG002F8|unnamed1 insolico UniProt ID   P14565
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192015.91 Da        Isoelectric Point: 5.8951

>WP_000987005.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQT
LKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

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

(575-625)

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

(633-712)


  Protein structure


Source ID Structure
PDB 2Q7T
PDB 2Q7U
PDB 1P4D
PDB 2A0I
PDB 2L8B
PDB 3FLD
AlphaFold DB P14565


Auxiliary protein

ID   738 GenBank   WP_001369361
Name   WP_001369361_SMG002F8|unnamed1 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   739 GenBank   WP_001151524
Name   WP_001151524_SMG002F8|unnamed1 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   1406 GenBank   WP_000009350
Name   traD_ML370_RS20825_SMG002F8|unnamed1 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81488.99 Da        Isoelectric Point: 5.0504

>WP_000009350.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWIKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCSEQLWSAFVLAAVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  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.



ID   1407 GenBank   WP_242431603
Name   traC_ML370_RS20915_SMG002F8|unnamed1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99164.84 Da        Isoelectric Point: 5.8486

>WP_242431603.1 type IV secretion system protein TraC [Escherichia coli]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WSMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 19617..46018

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ML370_RS20815 (ML370_20815) 18983..19210 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
ML370_RS20820 (ML370_20820) 19210..19608 + 399 WP_000911324 type II toxin-antitoxin system VapC family toxin -
ML370_RS20825 (ML370_20825) 19617..21770 - 2154 WP_000009350 type IV conjugative transfer system coupling protein TraD virb4
ML370_RS20830 (ML370_20830) 22023..22754 - 732 WP_000850422 conjugal transfer complement resistance protein TraT -
ML370_RS20835 (ML370_20835) 22779..23300 - 522 WP_000632670 conjugal transfer entry exclusion protein TraS -
ML370_RS20840 (ML370_20840) 23333..26149 - 2817 WP_001007055 conjugal transfer mating-pair stabilization protein TraG traG
ML370_RS20845 (ML370_20845) 26146..27519 - 1374 WP_021553026 conjugal transfer pilus assembly protein TraH traH
ML370_RS20850 (ML370_20850) 27519..27899 - 381 WP_001366201 F-type conjugal transfer protein TrbF -
ML370_RS20855 (ML370_20855) 27886..28227 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
ML370_RS20860 (ML370_20860) 28157..28702 - 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ML370_RS20865 (ML370_20865) 28689..28973 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
ML370_RS20870 (ML370_20870) 29054..29368 + 315 WP_000415566 protein ArtA -
ML370_RS20875 (ML370_20875) 29370..29717 - 348 WP_001287913 conjugal transfer protein TrbA -
ML370_RS20880 (ML370_20880) 29733..30476 - 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
ML370_RS20885 (ML370_20885) 30469..30726 - 258 WP_000864318 conjugal transfer protein TrbE -
ML370_RS20890 (ML370_20890) 30753..32561 - 1809 WP_040073647 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ML370_RS20895 (ML370_20895) 32558..33196 - 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
ML370_RS20900 (ML370_20900) 33205..34197 - 993 WP_000830185 conjugal transfer pilus assembly protein TraU traU
ML370_RS20905 (ML370_20905) 34194..34826 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
ML370_RS20910 (ML370_20910) 34823..35209 - 387 WP_000099690 type-F conjugative transfer system protein TrbI -
ML370_RS20915 (ML370_20915) 35206..37833 - 2628 WP_242431603 type IV secretion system protein TraC virb4
ML370_RS20920 (ML370_20920) 37993..38214 - 222 WP_001278689 conjugal transfer protein TraR -
ML370_RS20925 (ML370_20925) 38349..38864 - 516 WP_000809843 type IV conjugative transfer system lipoprotein TraV traV
ML370_RS20930 (ML370_20930) 38861..39112 - 252 WP_001038342 conjugal transfer protein TrbG -
ML370_RS20935 (ML370_20935) 39124..39321 - 198 WP_001324648 conjugal transfer protein TrbD -
ML370_RS20940 (ML370_20940) 39308..39898 - 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
ML370_RS20945 (ML370_20945) 39888..41315 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
ML370_RS20950 (ML370_20950) 41315..42043 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ML370_RS20955 (ML370_20955) 42030..42596 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
ML370_RS20960 (ML370_20960) 42618..42929 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
ML370_RS20965 (ML370_20965) 42944..43309 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
ML370_RS20970 (ML370_20970) 43342..43737 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
ML370_RS20975 (ML370_20975) 43836..44525 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
ML370_RS20980 (ML370_20980) 44712..45095 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
ML370_RS20985 (ML370_20985) 45416..46018 + 603 WP_000243701 transglycosylase SLT domain-containing protein virB1
ML370_RS20990 (ML370_20990) 46314..47135 - 822 WP_001234417 DUF932 domain-containing protein -
ML370_RS20995 (ML370_20995) 47254..47541 - 288 WP_000107542 hypothetical protein -
ML370_RS21000 (ML370_21000) 47566..47772 - 207 WP_000547965 hypothetical protein -
ML370_RS21005 (ML370_21005) 47842..48138 + 297 Protein_60 hypothetical protein -
ML370_RS21010 (ML370_21010) 48439..48564 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
ML370_RS21015 (ML370_21015) 48506..48655 - 150 Protein_62 DUF5431 family protein -
ML370_RS21020 (ML370_21020) 48829..49591 - 763 Protein_63 plasmid SOS inhibition protein A -
ML370_RS21025 (ML370_21025) 49588..50022 - 435 WP_000845928 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   2874 GenBank   NZ_JAKVSR010000015
Plasmid name   SMG002F8|unnamed1 Incompatibility group   IncFIC
Plasmid size   93128 bp Coordinate of oriT [Strand]   45096..45447 [-]
Host baterium   Escherichia coli strain SMG002F8

Cargo genes

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