Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120226
Name   oriT_Dcc0527|unnamed4 in_silico
Organism   Cronobacter malonaticus strain Dcc0527
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP141996 (55333..55413 [-], 81 nt)
oriT length   81 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..13, 21..26  (TGATTT..AAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 81 nt

>oriT_Dcc0527|unnamed4
AATTACATGATTTAAAACGCAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12725 GenBank   WP_324688948
Name   traI_U9L39_RS21880_Dcc0527|unnamed4 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: 192040.64 Da        Isoelectric Point: 5.9775

>WP_324688948.1 conjugative transfer relaxase/helicase TraI [Cronobacter malonaticus]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRQEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREINA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYTLIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQEAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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   7178 GenBank   WP_021559009
Name   WP_021559009_Dcc0527|unnamed4 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14493.50 Da        Isoelectric Point: 5.0120

>WP_021559009.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISISGTASMLLELGLRVHQAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSVEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   7179 GenBank   WP_000089265
Name   WP_000089265_Dcc0527|unnamed4 insolico UniProt ID   A0A1E5M428
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8472.68 Da        Isoelectric Point: 9.9218

>WP_000089265.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLSRFPDFYNLDAIKEGTGETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A1E5M428


T4CP

ID   14938 GenBank   WP_021519755
Name   traC_U9L39_RS21770_Dcc0527|unnamed4 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: 99327.25 Da        Isoelectric Point: 6.5173

>WP_021519755.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVKASWLAKKNQARIDDVVNFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLFPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-763)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   14939 GenBank   WP_034169381
Name   traD_U9L39_RS21875_Dcc0527|unnamed4 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83846.52 Da        Isoelectric Point: 5.2346

>WP_034169381.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 366..21323

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U9L39_RS21755 (U9L39_21755) 49..366 + 318 WP_024189706 conjugal transfer protein TrbD -
U9L39_RS21760 (U9L39_21760) 366..881 + 516 WP_021519754 type IV conjugative transfer system lipoprotein TraV traV
U9L39_RS21765 (U9L39_21765) 1016..1237 + 222 WP_001278689 conjugal transfer protein TraR -
U9L39_RS21770 (U9L39_21770) 1397..4024 + 2628 WP_021519755 type IV secretion system protein TraC virb4
U9L39_RS21775 (U9L39_21775) 4021..4407 + 387 WP_000214096 type-F conjugative transfer system protein TrbI -
U9L39_RS21780 (U9L39_21780) 4404..5036 + 633 WP_062873969 type-F conjugative transfer system protein TraW traW
U9L39_RS21785 (U9L39_21785) 5033..6025 + 993 WP_021559016 conjugal transfer pilus assembly protein TraU traU
U9L39_RS21790 (U9L39_21790) 6055..6360 + 306 WP_122987481 hypothetical protein -
U9L39_RS21795 (U9L39_21795) 6369..7007 + 639 WP_032083946 type-F conjugative transfer system pilin assembly protein TrbC trbC
U9L39_RS21800 (U9L39_21800) 7004..7384 + 381 WP_324688930 hypothetical protein -
U9L39_RS21805 (U9L39_21805) 7620..9482 + 1863 WP_226149361 type-F conjugative transfer system mating-pair stabilization protein TraN traN
U9L39_RS21810 (U9L39_21810) 9509..9766 + 258 WP_000864336 conjugal transfer protein TrbE -
U9L39_RS21815 (U9L39_21815) 9759..10502 + 744 WP_130570191 type-F conjugative transfer system pilin assembly protein TraF traF
U9L39_RS21820 (U9L39_21820) 10663..10899 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
U9L39_RS21825 (U9L39_21825) 10886..11431 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
U9L39_RS21830 (U9L39_21830) 11421..11735 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
U9L39_RS21835 (U9L39_21835) 11689..12081 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
U9L39_RS21840 (U9L39_21840) 12068..12241 + 174 Protein_18 conjugal transfer protein TraH -
U9L39_RS21845 (U9L39_21845) 12268..12660 + 393 WP_000660703 F-type conjugal transfer protein TrbF -
U9L39_RS21850 (U9L39_21850) 12647..14020 + 1374 WP_001137363 conjugal transfer pilus assembly protein TraH traH
U9L39_RS21855 (U9L39_21855) 14017..16836 + 2820 WP_032214174 conjugal transfer mating-pair stabilization protein TraG traG
U9L39_RS21860 (U9L39_21860) 16855..17352 + 498 WP_000605862 entry exclusion protein -
U9L39_RS21865 (U9L39_21865) 17385..18116 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
U9L39_RS21870 (U9L39_21870) 18319..19056 + 738 WP_000199911 hypothetical protein -
U9L39_RS21875 (U9L39_21875) 19107..21323 + 2217 WP_034169381 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   20655 GenBank   NZ_CP141996
Plasmid name   Dcc0527|unnamed4 Incompatibility group   -
Plasmid size   61266 bp Coordinate of oriT [Strand]   55333..55413 [-]
Host baterium   Cronobacter malonaticus strain Dcc0527

Cargo genes

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