Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102417
Name   oriT_SMG002F9|unnamed2 in_silico
Organism   Escherichia coli strain SMG002F9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKVSS010000026 (6685..6808 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_SMG002F9|unnamed2
GGTTGGTGGTTCTCACCACTAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1810 GenBank   WP_053001887
Name   traI_ML382_RS20300_SMG002F9|unnamed2 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: 192126.75 Da        Isoelectric Point: 5.8440

>WP_053001887.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFADLGREINT
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQEAIQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGIRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DSKTEQAVREIAGQERDRSAISEREAALPESVLRESQREREAVREVARENLLQERLQQMEQDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-627)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   729 GenBank   WP_000124981
Name   WP_000124981_SMG002F9|unnamed2 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   730 GenBank   WP_001254386
Name   WP_001254386_SMG002F9|unnamed2 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   1394 GenBank   WP_001064268
Name   traC_ML382_RS20205_SMG002F9|unnamed2 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: 99248.97 Da        Isoelectric Point: 6.0801

>WP_001064268.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNKARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.



ID   1395 GenBank   WP_001360340
Name   traD_ML382_RS20295_SMG002F9|unnamed2 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: 82860.46 Da        Isoelectric Point: 5.0524

>WP_001360340.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
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: 6113..32776

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ML382_RS20085 (ML382_20080) 2079..2513 + 435 WP_096309212 conjugation system SOS inhibitor PsiB -
ML382_RS20090 (ML382_20085) 2510..3272 + 763 Protein_2 plasmid SOS inhibition protein A -
ML382_RS20095 (ML382_20090) 3241..3429 - 189 WP_001299721 hypothetical protein -
ML382_RS20100 (ML382_20095) 3451..3600 + 150 Protein_4 plasmid maintenance protein Mok -
ML382_RS20105 (ML382_20100) 3542..3667 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
ML382_RS20110 (ML382_20105) 3887..4117 + 231 WP_072279680 hypothetical protein -
ML382_RS20115 (ML382_20110) 4115..4288 - 174 Protein_7 hypothetical protein -
ML382_RS20120 (ML382_20115) 4358..4564 + 207 WP_000547968 hypothetical protein -
ML382_RS20125 (ML382_20120) 4589..4876 + 288 WP_000107548 hypothetical protein -
ML382_RS20130 (ML382_20125) 4995..5816 + 822 WP_052953840 DUF932 domain-containing protein -
ML382_RS20135 (ML382_20130) 6113..6760 - 648 WP_001567347 transglycosylase SLT domain-containing protein virB1
ML382_RS20140 (ML382_20135) 7037..7420 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
ML382_RS20145 (ML382_20140) 7611..8297 + 687 WP_000332484 PAS domain-containing protein -
ML382_RS20150 (ML382_20145) 8391..8618 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
ML382_RS20155 (ML382_20150) 8652..9014 + 363 WP_033566647 type IV conjugative transfer system pilin TraA -
ML382_RS20160 (ML382_20155) 9019..9330 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
ML382_RS20165 (ML382_20160) 9352..9918 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
ML382_RS20170 (ML382_20165) 9905..10633 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ML382_RS20175 (ML382_20170) 10633..12060 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
ML382_RS20180 (ML382_20175) 12050..12622 + 573 WP_000002780 conjugal transfer pilus-stabilizing protein TraP -
ML382_RS20185 (ML382_20180) 12619..12936 + 318 WP_001057292 conjugal transfer protein TrbD virb4
ML382_RS20190 (ML382_20185) 12933..13184 + 252 WP_001038341 conjugal transfer protein TrbG -
ML382_RS20195 (ML382_20190) 13181..13696 + 516 WP_032178525 type IV conjugative transfer system lipoprotein TraV traV
ML382_RS20200 (ML382_20195) 13830..14051 + 222 WP_001278689 conjugal transfer protein TraR -
ML382_RS20205 (ML382_20200) 14211..16838 + 2628 WP_001064268 type IV secretion system protein TraC virb4
ML382_RS20210 (ML382_20205) 16835..17221 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
ML382_RS20215 (ML382_20210) 17218..17850 + 633 WP_104159822 type-F conjugative transfer system protein TraW traW
ML382_RS20220 (ML382_20215) 17847..18839 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
ML382_RS20225 (ML382_20220) 18865..19326 + 462 WP_000277845 hypothetical protein -
ML382_RS20230 (ML382_20225) 19356..19808 + 453 WP_000069427 hypothetical protein -
ML382_RS20235 (ML382_20230) 19836..20474 + 639 WP_001104248 type-F conjugative transfer system pilin assembly protein TrbC trbC
ML382_RS20240 (ML382_20235) 20471..22279 + 1809 WP_000821818 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ML382_RS20245 (ML382_20240) 22306..22563 + 258 WP_000864325 conjugal transfer protein TrbE -
ML382_RS20250 (ML382_20245) 22556..23299 + 744 WP_021553228 type-F conjugative transfer system pilin assembly protein TraF traF
ML382_RS20255 (ML382_20250) 23315..23662 + 348 WP_053001888 conjugal transfer protein TrbA -
ML382_RS20260 (ML382_20255) 23781..24065 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
ML382_RS20265 (ML382_20260) 24052..24597 + 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ML382_RS20270 (ML382_20265) 24527..24889 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
ML382_RS20275 (ML382_20270) 24889..26262 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
ML382_RS20280 (ML382_20275) 26259..29084 + 2826 WP_001554363 conjugal transfer mating-pair stabilization protein TraG traG
ML382_RS20285 (ML382_20280) 29081..29590 + 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
ML382_RS20290 (ML382_20285) 29604..30335 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
ML382_RS20295 (ML382_20290) 30587..32776 + 2190 WP_001360340 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2861 GenBank   NZ_JAKVSS010000026
Plasmid name   SMG002F9|unnamed2 Incompatibility group   IncFII
Plasmid size   61709 bp Coordinate of oriT [Strand]   6685..6808 [+]
Host baterium   Escherichia coli strain SMG002F9

Cargo genes

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