Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122053
Name   oriT_pSY_CS01_mcr-3.5 in_silico
Organism   Citrobacter sedlakii strain SY_CS04
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JALNML010000026 (39753..40104 [+], 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_pSY_CS01_mcr-3.5
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13914 GenBank   WP_065800510
Name   traI_MYG02_RS23640_pSY_CS01_mcr-3.5 insolico UniProt ID   A0A2Z5TVL6
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191941.80 Da        Isoelectric Point: 6.0531

>WP_065800510.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHTVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGEILLETAISLQKAGLHTPAQQAIHLALPVLENKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESGRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSAWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMTGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETVRRADEIVRKMAENKPDLL
DGRTEQAVREIAGQERDRSAISEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

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   7727 GenBank   WP_001151524
Name   WP_001151524_pSY_CS01_mcr-3.5 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

ID   7728 GenBank   WP_053320748
Name   WP_053320748_pSY_CS01_mcr-3.5 insolico UniProt ID   A0A2K9V2C2
Length   131 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 131 a.a.        Molecular weight: 15211.44 Da        Isoelectric Point: 9.9240

>WP_053320748.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Enterobacteriaceae]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRVGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(70-117)

TraY domain (TraY)

(16-58)


  Protein structure


Source ID Structure
AlphaFold DB A0A2K9V2C2


T4CP

ID   16305 GenBank   WP_001064265
Name   traC_MYG02_RS23560_pSY_CS01_mcr-3.5 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: 99296.07 Da        Isoelectric Point: 6.3032

>WP_001064265.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
AGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.



ID   16306 GenBank   WP_065813483
Name   traD_MYG02_RS23635_pSY_CS01_mcr-3.5 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: 83939.60 Da        Isoelectric Point: 5.1674

>WP_065813483.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWVLGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISKSGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 39182..64474

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MYG02_RS23450 (MYG02_23445) 35149..35583 + 435 WP_000845934 conjugation system SOS inhibitor PsiB -
MYG02_RS23455 (MYG02_23450) 35580..36342 + 763 Protein_48 plasmid SOS inhibition protein A -
MYG02_RS23460 (MYG02_23455) 36521..36670 + 150 Protein_49 plasmid maintenance protein Mok -
MYG02_RS23465 (MYG02_23460) 36612..36737 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
MYG02_RS23470 (MYG02_23465) 36957..37187 + 231 WP_001426396 hypothetical protein -
MYG02_RS23475 (MYG02_23470) 37185..37358 - 174 Protein_52 hypothetical protein -
MYG02_RS23480 (MYG02_23475) 37428..37634 + 207 WP_000547968 hypothetical protein -
MYG02_RS23485 (MYG02_23480) 37659..37946 + 288 WP_065800506 hypothetical protein -
MYG02_RS23490 (MYG02_23485) 38064..38885 + 822 WP_001234469 DUF932 domain-containing protein -
MYG02_RS23495 (MYG02_23490) 39182..39772 - 591 WP_165899088 transglycosylase SLT domain-containing protein virB1
MYG02_RS23500 (MYG02_23495) 40105..40488 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
MYG02_RS23505 (MYG02_23500) 40675..41364 + 690 WP_000283380 conjugal transfer transcriptional regulator TraJ -
MYG02_RS23510 (MYG02_23505) 41463..41858 + 396 WP_053320748 conjugal transfer relaxosome DNA-bindin protein TraY -
MYG02_RS23515 (MYG02_23510) 41891..42253 + 363 WP_000994784 type IV conjugative transfer system pilin TraA -
MYG02_RS23520 (MYG02_23515) 42258..42569 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
MYG02_RS23525 (MYG02_23520) 42591..43157 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
MYG02_RS23530 (MYG02_23525) 43144..43872 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
MYG02_RS23535 (MYG02_23530) 43872..45299 + 1428 WP_000146672 F-type conjugal transfer pilus assembly protein TraB traB
MYG02_RS23540 (MYG02_23535) 45289..45876 + 588 WP_053320746 conjugal transfer pilus-stabilizing protein TraP -
MYG02_RS23545 (MYG02_23540) 45863..46183 + 321 WP_001057285 conjugal transfer protein TrbD -
MYG02_RS23550 (MYG02_23545) 46180..46695 + 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
MYG02_RS23555 (MYG02_23550) 46830..47051 + 222 WP_001278692 conjugal transfer protein TraR -
MYG02_RS23560 (MYG02_23555) 47211..49838 + 2628 WP_001064265 type IV secretion system protein TraC virb4
MYG02_RS23565 (MYG02_23560) 49835..50221 + 387 WP_000099687 type-F conjugative transfer system protein TrbI -
MYG02_RS23570 (MYG02_23565) 50218..50850 + 633 WP_001749440 type-F conjugative transfer system protein TraW traW
MYG02_RS23575 (MYG02_23570) 50847..51839 + 993 WP_053320745 conjugal transfer pilus assembly protein TraU traU
MYG02_RS23580 (MYG02_23575) 51848..52486 + 639 WP_000777691 type-F conjugative transfer system pilin assembly protein TrbC trbC
MYG02_RS23585 (MYG02_23580) 52483..54291 + 1809 WP_065800507 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MYG02_RS23590 (MYG02_23585) 54318..54575 + 258 WP_000864353 conjugal transfer protein TrbE -
MYG02_RS23595 (MYG02_23590) 54568..55311 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
MYG02_RS23600 (MYG02_23595) 55472..55708 + 237 WP_001346259 type-F conjugative transfer system pilin chaperone TraQ -
MYG02_RS23605 (MYG02_23600) 55695..56240 + 546 WP_065800508 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MYG02_RS23610 (MYG02_23605) 56170..56532 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
MYG02_RS23615 (MYG02_23610) 56532..57905 + 1374 WP_065800514 conjugal transfer pilus assembly protein TraH traH
MYG02_RS23620 (MYG02_23615) 57902..60724 + 2823 WP_053320755 conjugal transfer mating-pair stabilization protein TraG traG
MYG02_RS23625 (MYG02_23620) 60739..61242 + 504 WP_053320762 surface exclusion protein -
MYG02_RS23630 (MYG02_23625) 61274..62005 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
MYG02_RS23635 (MYG02_23630) 62258..64474 + 2217 WP_065813483 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   22480 GenBank   NZ_JALNML010000026
Plasmid name   pSY_CS01_mcr-3.5 Incompatibility group   IncFII
Plasmid size   80003 bp Coordinate of oriT [Strand]   39753..40104 [+]
Host baterium   Citrobacter sedlakii strain SY_CS04

Cargo genes

Drug resistance gene   mcr-3.5, mph(A), erm(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -