Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105387
Name   oriT_p21978-2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Reading strain CVM 21978
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051450 (50914..51002 [-], 89 nt)
oriT length   89 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 89 nt

>oriT_p21978-2
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3676 GenBank   WP_001306778
Name   nikB_HFQ72_RS24060_p21978-2 insolico UniProt ID   Q79VV7
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104010.41 Da        Isoelectric Point: 7.4265

>WP_001306778.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB Q79VV7


Auxiliary protein

ID   1662 GenBank   WP_001283947
Name   WP_001283947_p21978-2 insolico UniProt ID   A0A142CMC2
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


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

>WP_001283947.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A142CMC2


T4CP

ID   3654 GenBank   WP_001289276
Name   trbC_HFQ72_RS24065_p21978-2 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86941.11 Da        Isoelectric Point: 6.7713

>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56380..90532

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFQ72_RS24065 (HFQ72_24065) 54096..56387 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
HFQ72_RS24070 (HFQ72_24070) 56380..57450 - 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
HFQ72_RS24075 (HFQ72_24075) 57469..58677 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
HFQ72_RS24080 (HFQ72_24080) 58969..59121 + 153 WP_001303307 Hok/Gef family protein -
HFQ72_RS24085 (HFQ72_24085) 59193..59444 - 252 WP_001291965 hypothetical protein -
HFQ72_RS24090 (HFQ72_24090) 60368..60544 - 177 WP_001054900 hypothetical protein -
HFQ72_RS24095 (HFQ72_24095) 60753..60962 - 210 WP_001140545 hemolysin expression modulator Hha -
HFQ72_RS24100 (HFQ72_24100) 61060..61674 - 615 WP_000578649 plasmid IncI1-type surface exclusion protein ExcA -
HFQ72_RS24105 (HFQ72_24105) 61750..63918 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
HFQ72_RS24110 (HFQ72_24110) 64015..64599 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
HFQ72_RS24115 (HFQ72_24115) 64628..65830 - 1203 WP_001189159 IncI1-type conjugal transfer protein TraW traW
HFQ72_RS24120 (HFQ72_24120) 65797..66411 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
HFQ72_RS24125 (HFQ72_24125) 66411..69455 - 3045 WP_001024752 IncI1-type conjugal transfer protein TraU traU
HFQ72_RS24130 (HFQ72_24130) 69545..70345 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HFQ72_RS24135 (HFQ72_24135) 70329..70517 - 189 WP_001277255 putative conjugal transfer protein TraS -
HFQ72_RS24140 (HFQ72_24140) 70581..70985 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
HFQ72_RS24145 (HFQ72_24145) 71036..71563 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HFQ72_RS24150 (HFQ72_24150) 71563..72267 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HFQ72_RS24155 (HFQ72_24155) 72267..73556 - 1290 WP_001271997 conjugal transfer protein TraO traO
HFQ72_RS24160 (HFQ72_24160) 73559..74542 - 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
HFQ72_RS24165 (HFQ72_24165) 74553..75245 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HFQ72_RS24170 (HFQ72_24170) 75242..75589 - 348 WP_001055900 conjugal transfer protein traL
HFQ72_RS24175 (HFQ72_24175) 75607..79374 - 3768 WP_001141534 LPD7 domain-containing protein -
HFQ72_RS24180 (HFQ72_24180) 79464..80015 - 552 WP_000014584 phospholipase D family protein -
HFQ72_RS24185 (HFQ72_24185) 80030..80320 - 291 WP_001299214 hypothetical protein traK
HFQ72_RS24190 (HFQ72_24190) 80317..81465 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HFQ72_RS24195 (HFQ72_24195) 81462..82280 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
HFQ72_RS24200 (HFQ72_24200) 82277..82735 - 459 WP_052892363 IncI1-type conjugal transfer lipoprotein TraH -
HFQ72_RS24205 (HFQ72_24205) 83130..83714 - 585 WP_000977522 histidine phosphatase family protein -
HFQ72_RS24210 (HFQ72_24210) 83774..84976 - 1203 WP_000976353 conjugal transfer protein TraF -
HFQ72_RS24215 (HFQ72_24215) 85062..85886 - 825 WP_001238927 conjugal transfer protein TraE traE
HFQ72_RS24220 (HFQ72_24220) 86037..87191 - 1155 WP_001139958 site-specific integrase -
HFQ72_RS25620 87504..87647 - 144 WP_341466071 shufflon protein C' -
HFQ72_RS24225 (HFQ72_24225) 87997..89331 - 1335 WP_024132209 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HFQ72_RS24230 (HFQ72_24230) 89331..89987 - 657 WP_001389386 prepilin peptidase -
HFQ72_RS24235 (HFQ72_24235) 89972..90532 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HFQ72_RS24240 (HFQ72_24240) 90542..91156 - 615 WP_000959786 type 4 pilus major pilin -
HFQ72_RS24245 (HFQ72_24245) 91174..92271 - 1098 WP_001208805 type II secretion system F family protein -

Host bacterium

ID   5825 GenBank   NZ_CP051450
Plasmid name   p21978-2 Incompatibility group   IncI1
Plasmid size   93550 bp Coordinate of oriT [Strand]   50914..51002 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Reading strain CVM 21978

Cargo genes

Drug resistance gene   -
Virulence gene   faeC, faeD, faeE, faeF, faeH, faeI, faeJ
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -