Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100033
Name   oriT_pSTM709 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_023915 (_)
oriT length   88 nt
IRs (inverted repeats)      8..bp: 2..9, 13..20  (GTCGGGGC..GCCCTGAC)
  17..bp: 27..43, 50..66  (GTAATTGTAATAGCGTC..GACGGTATTACAATTAC)
Location of nic site      74..75
Conserved sequence flanking the
  nic site    		  CATCCTG|T
Note   _

  oriT sequence  


Download         Length: 88 nt

>oriT_pSTM709
TGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   32 GenBank   YP_009023753
Name   NikB_pSTM709 insolico UniProt ID   X5JA84
Length   899 a.a. PDB ID   
Note   NikB relaxase

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103834.33 Da        Isoelectric Point: 7.3473

>YP_009023753.1 NikB relaxase (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium str. STM709]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure



No available structure.




Auxiliary protein

ID   49 GenBank   YP_009023752
Name   NikA_pSTM709 insolico UniProt ID   X5J9V3
Length   110 a.a. PDB ID   _
Note   NikA oriT-specific DNA binding protein

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12613.57 Da        Isoelectric Point: 10.7463

>YP_009023752.1 NikA oriT-specific DNA binding protein (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium str. STM709]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   32 GenBank   YP_009023754
Name   TrbC_pSTM709 insolico UniProt ID   X5JAP4
Length   763 a.a. PDB ID   _
Note   TrbC transfer protein

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86927.12 Da        Isoelectric Point: 6.7713

>YP_009023754.1 TrbC transfer protein (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium str. STM709]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 49375..89077

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
D645_p16051 47091..49382 - 2292 YP_009023754 TrbC transfer protein -
D645_p16050 49375..50445 - 1071 YP_009023755 IncI1 conjugal transfer protein TrbB trbB
D645_p16049 50464..51672 - 1209 YP_009023756 TrbA transfer protein trbA
D645_p16048 51906..52109 + 204 YP_009023757 post-segregation killing protein -
D645_p16047 51964..52116 + 153 YP_009023758 post-segregation killing protein PndA -
D645_p16046 52800..53582 - 783 YP_009023759 insertion sequence IS100, ATP-binding protein -
D645_p16045 53579..54601 - 1023 YP_009023760 IS100 transposase orfA -
D645_p16044 56171..56833 - 663 YP_009023761 surface exclusion protein ExcA -
D645_p16043 56904..59141 - 2238 YP_009023762 TraY integral membrane protein traY
D645_p16042 59169..59753 - 585 YP_009023763 conjugative transfer protein TraX -
D645_p16040 60950..61564 - 615 YP_009023764 conjugative transfer protein TraV traV
D645_p16039 61564..63591 - 2028 YP_009023765 TraU nucleotide-binding protein traU
D645_p16038 64697..65497 - 801 YP_009023766 conjugative transfer protein TraT traT
D645_p16037 65481..65669 - 189 YP_009023767 conjugal transfer protein TraS -
D645_p16036 65733..66137 - 405 YP_009023768 conjugal transfer protein TraR traR
D645_p16035 66188..66715 - 528 YP_009023769 conjugal transfer protein TraQ traQ
D645_p16034 66715..67419 - 705 YP_009023770 conjugal transfer protein TraP traP
D645_p16033 67419..68708 - 1290 YP_009023771 TraO transfer protein traO
D645_p16032 68711..69694 - 984 YP_009023772 conjugative transfer protein TraN traN
D645_p16031 69705..70397 - 693 YP_009023773 conjugal transfer protein TraM traM
D645_p16030 70394..70741 - 348 YP_009023774 conjugal transfer protein TraL traL
D645_p16028 70759..74562 - 3804 YP_009023775 SogL DNA primase -
D645_p16027 74616..75167 - 552 YP_009023776 EDTA-resistant nuclease -
D645_p16026 75182..75472 - 291 YP_009023777 conjugal protein Trak traK
D645_p16025 75469..76617 - 1149 YP_009023778 plasmid transfer ATPase TraJ virB11
D645_p16024 76614..77432 - 819 YP_009023779 conjugal transfer protein TraI traI
D645_p16023 77429..77887 - 459 YP_009023780 conjugal transfer protein TraH -
D645_p16022 78282..78866 - 585 YP_009023781 conjugal transfer protein TraG -
D645_p16021 78926..80128 - 1203 YP_009023782 conjugal transfer protein TraF -
D645_p16020 80214..81038 - 825 YP_009023783 conjugal transfer protein TraE traE
D645_p16019 81189..82343 - 1155 YP_009023784 Shufflon-specific DNA recombinase -
D645_p16018 83147..84583 - 1437 YP_009023785 type III prepilin -
D645_p16017 84571..85227 - 657 YP_009023786 Type-IV sectretion leader peptidase/N-methyltransferase PilU -
D645_p16016 85212..85772 - 561 YP_009023787 putative transglycosylase PilT virB1
D645_p16015 85782..86396 - 615 YP_009023788 type IV prepilin PilS -
D645_p16014 86414..87511 - 1098 YP_009023789 integral membrane protein PilR -
D645_p16013 87524..89077 - 1554 YP_009023790 ATP-binding protein PilQ virB11
D645_p16012 89088..89540 - 453 YP_009023791 type IV pilus biogenesis protein PilP -
D645_p16011 89527..90822 - 1296 YP_009023792 PilO type IV pilus biogenesis protein -
D645_p16010 90815..92497 - 1683 YP_009023793 PilN type IV pilus secretin -
D645_p16009 92511..92948 - 438 YP_009023794 conjugal transfer protein PilM -
D645_p16008 92948..94015 - 1068 YP_009023795 lipoprotein PilL -

Host bacterium

ID   32 GenBank   NC_023915
Plasmid name   pSTM709 Incompatibility group   IncI1
Plasmid size   99184 bp Coordinate of oriT [Strand]   43906..43949 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

Drug resistance gene   class-C beta-lactamase gene blaCMY-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -