Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122055
Name   oriT_pSY_CA01_mcr-3.5 in_silico
Organism   Citrobacter amalonaticus strain SY_CA35
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JALNMK010000021 (40112..40463 [+], 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_CA01_mcr-3.5
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13915 GenBank   WP_065800510
Name   traI_MYG01_RS22970_pSY_CA01_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   7729 GenBank   WP_001151524
Name   WP_001151524_pSY_CA01_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   7730 GenBank   WP_053320748
Name   WP_053320748_pSY_CA01_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   16308 GenBank   WP_001064265
Name   traC_MYG01_RS22890_pSY_CA01_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 39541..61083

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MYG01_RS22780 (MYG01_22785) 35508..35942 + 435 WP_000845934 conjugation system SOS inhibitor PsiB -
MYG01_RS22785 (MYG01_22790) 35939..36701 + 763 Protein_48 plasmid SOS inhibition protein A -
MYG01_RS22790 (MYG01_22795) 36880..37029 + 150 Protein_49 plasmid maintenance protein Mok -
MYG01_RS22795 (MYG01_22800) 36971..37096 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
MYG01_RS22800 (MYG01_22805) 37316..37546 + 231 WP_001426396 hypothetical protein -
MYG01_RS22805 (MYG01_22810) 37544..37717 - 174 Protein_52 hypothetical protein -
MYG01_RS22810 (MYG01_22815) 37787..37993 + 207 WP_000547968 hypothetical protein -
MYG01_RS22815 (MYG01_22820) 38018..38305 + 288 WP_065800506 hypothetical protein -
MYG01_RS22820 (MYG01_22825) 38423..39244 + 822 WP_001234469 DUF932 domain-containing protein -
MYG01_RS22825 (MYG01_22830) 39541..40131 - 591 WP_165899088 transglycosylase SLT domain-containing protein virB1
MYG01_RS22830 (MYG01_22835) 40464..40847 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
MYG01_RS22835 (MYG01_22840) 41034..41723 + 690 WP_000283380 conjugal transfer transcriptional regulator TraJ -
MYG01_RS22840 (MYG01_22845) 41822..42217 + 396 WP_053320748 conjugal transfer relaxosome DNA-bindin protein TraY -
MYG01_RS22845 (MYG01_22850) 42250..42612 + 363 WP_000994784 type IV conjugative transfer system pilin TraA -
MYG01_RS22850 (MYG01_22855) 42617..42928 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
MYG01_RS22855 (MYG01_22860) 42950..43516 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
MYG01_RS22860 (MYG01_22865) 43503..44231 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
MYG01_RS22865 (MYG01_22870) 44231..45658 + 1428 WP_000146672 F-type conjugal transfer pilus assembly protein TraB traB
MYG01_RS22870 (MYG01_22875) 45648..46235 + 588 WP_053320746 conjugal transfer pilus-stabilizing protein TraP -
MYG01_RS22875 (MYG01_22880) 46222..46542 + 321 WP_001057285 conjugal transfer protein TrbD -
MYG01_RS22880 (MYG01_22885) 46539..47054 + 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
MYG01_RS22885 (MYG01_22890) 47189..47410 + 222 WP_001278692 conjugal transfer protein TraR -
MYG01_RS22890 (MYG01_22895) 47570..50197 + 2628 WP_001064265 type IV secretion system protein TraC virb4
MYG01_RS22895 (MYG01_22900) 50194..50580 + 387 WP_000099687 type-F conjugative transfer system protein TrbI -
MYG01_RS22900 (MYG01_22905) 50577..51209 + 633 WP_001749440 type-F conjugative transfer system protein TraW traW
MYG01_RS22905 (MYG01_22910) 51206..52198 + 993 WP_053320745 conjugal transfer pilus assembly protein TraU traU
MYG01_RS22910 (MYG01_22915) 52207..52845 + 639 WP_000777691 type-F conjugative transfer system pilin assembly protein TrbC trbC
MYG01_RS22915 (MYG01_22920) 52842..54650 + 1809 WP_065800507 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MYG01_RS22920 (MYG01_22925) 54677..54934 + 258 WP_000864353 conjugal transfer protein TrbE -
MYG01_RS22925 (MYG01_22930) 54927..55670 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
MYG01_RS22930 (MYG01_22935) 55831..56067 + 237 WP_001346259 type-F conjugative transfer system pilin chaperone TraQ -
MYG01_RS22935 (MYG01_22940) 56054..56599 + 546 WP_065800508 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MYG01_RS22940 (MYG01_22945) 56529..56891 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
MYG01_RS22945 (MYG01_22950) 56891..58264 + 1374 WP_065800514 conjugal transfer pilus assembly protein TraH traH
MYG01_RS22950 (MYG01_22955) 58261..61083 + 2823 WP_053320755 conjugal transfer mating-pair stabilization protein TraG traG
MYG01_RS22955 (MYG01_22960) 61098..61601 + 504 WP_053320762 surface exclusion protein -
MYG01_RS22960 (MYG01_22965) 61633..62364 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
MYG01_RS22965 (MYG01_22970) 62617..64916 + 2300 Protein_84 type IV conjugative transfer system coupling protein TraD -

Host bacterium

ID   22482 GenBank   NZ_JALNMK010000021
Plasmid name   pSY_CA01_mcr-3.5 Incompatibility group   IncFII
Plasmid size   80445 bp Coordinate of oriT [Strand]   40112..40463 [+]
Host baterium   Citrobacter amalonaticus strain SY_CA35

Cargo genes

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