Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100028
Name   oriT_R621a in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_015965 (37332..37414 [-], 83 nt)
oriT length   83 nt
IRs (inverted repeats)      8..bp: 6..13, 17..24  (GTCGGGGC..GCCCTGAC)
  17..bp: 31..754..70  (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC)
Location of nic site      78..79
Conserved sequence flanking the
  nic site    		  CATCCTG|T
Note   minimal oriT sequence

  oriT sequence  


Download         Length: 83 nt

>oriT_R621a
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Takahashi H et al. (2011) The genome sequence of the incompatibility group I纬 plasmid R621a: evolution of IncI plasmids. Plasmid. 66(2):112-21. [PMID:21763721]


Relaxase

ID   27 GenBank   YP_004823733
Name   NikB_R621a insolico UniProt ID   G2HK77
Length   899 a.a. PDB ID   
Note   NikB relaxase

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104019.46 Da        Isoelectric Point: 7.3526

>YP_004823733.1 NikB relaxase (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
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 G2HK77

  Reference


[1] Takahashi H et al. (2011) The genome sequence of the incompatibility group I纬 plasmid R621a: evolution of IncI plasmids. Plasmid. 66(2):112-21. [PMID:21763721]


Auxiliary protein

ID   41 GenBank   YP_004823732
Name   NikA_R621a insolico UniProt ID   Q79VV8
Length   111 a.a. PDB ID   _
Note   NikA oriT-specific DNA-binding protein

  Auxiliary protein sequence


Download         Length: 111 a.a.        Molecular weight: 12613.57 Da        Isoelectric Point: 10.7463

>YP_004823732.1 NikA oriT-specific DNA-binding protein (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q79VV8

  Reference


[1] Takahashi H et al. (2011) The genome sequence of the incompatibility group I纬 plasmid R621a: evolution of IncI plasmids. Plasmid. 66(2):112-21. [PMID:21763721]


T4CP

ID   27 GenBank   YP_004823734
Name   TrbC_R621a insolico UniProt ID   G2HK78
Length   763 a.a. PDB ID   _
Note   TrbC transfer protein

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86914.98 Da        Isoelectric Point: 6.6402

>YP_004823734.1 TrbC transfer protein (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTMITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLNTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure


Source ID Structure
AlphaFold DB G2HK78

  Reference


[1] Takahashi H et al. (2011) The genome sequence of the incompatibility group I纬 plasmid R621a: evolution of IncI plasmids. Plasmid. 66(2):112-21. [PMID:21763721]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42792..83793

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXF67_RS00250 (R621a_p053) 40508..42799 - 2292 WP_014065723 F-type conjugative transfer protein TrbC -
HXF67_RS00255 (R621a_p054) 42792..43862 - 1071 WP_014065724 IncI1-type conjugal transfer protein TrbB trbB
HXF67_RS00260 (R621a_p055) 43881..45089 - 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
HXF67_RS00265 (R621a_p056) 45396..46175 - 780 WP_275542888 protein FinQ -
HXF67_RS00270 (R621a_p058) 46802..46954 + 153 WP_001331364 Hok/Gef family protein -
HXF67_RS00275 47026..47277 - 252 WP_001291963 hypothetical protein -
HXF67_RS00545 47778..47873 + 96 WP_000609148 DinQ-like type I toxin DqlB -
HXF67_RS00285 47938..48114 - 177 WP_001054900 hypothetical protein -
HXF67_RS00290 48481..48690 + 210 WP_000062603 HEAT repeat domain-containing protein -
HXF67_RS00295 (R621a_p059) 48762..49376 - 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
HXF67_RS00300 (R621a_p060) 49452..51620 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
HXF67_RS00305 (R621a_p061) 51717..52301 - 585 WP_001037993 IncI1-type conjugal transfer protein TraX -
HXF67_RS00310 (R621a_p062) 52330..53532 - 1203 WP_014065727 IncI1-type conjugal transfer protein TraW traW
HXF67_RS00315 (R621a_p063) 53499..54113 - 615 WP_014065728 IncI1-type conjugal transfer protein TraV traV
HXF67_RS00320 (R621a_p064) 54113..57157 - 3045 WP_014065729 IncI1-type conjugal transfer protein TraU traU
HXF67_RS00330 (R621a_p067) 58583..59383 - 801 WP_001493813 IncI1-type conjugal transfer protein TraT traT
HXF67_RS00335 (R621a_p068) 59367..59555 - 189 WP_001277255 putative conjugal transfer protein TraS -
HXF67_RS00340 (R621a_p069) 59619..60023 - 405 WP_000086964 IncI1-type conjugal transfer protein TraR traR
HXF67_RS00345 (R621a_p070) 60074..60601 - 528 WP_001493812 conjugal transfer protein TraQ traQ
HXF67_RS00350 (R621a_p071) 60601..61305 - 705 WP_001493811 IncI1-type conjugal transfer protein TraP traP
HXF67_RS00355 (R621a_p072) 61305..62594 - 1290 WP_014065730 conjugal transfer protein TraO traO
HXF67_RS00360 (R621a_p073) 62597..63580 - 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
HXF67_RS00365 (R621a_p074) 63591..64283 - 693 WP_000138551 DotI/IcmL family type IV secretion protein traM
HXF67_RS00370 (R621a_p075) 64280..64627 - 348 WP_001493810 hypothetical protein traL
HXF67_RS00375 (R621a_p076) 64645..68412 - 3768 WP_014065731 LPD7 domain-containing protein -
HXF67_RS00380 (R621a_p078) 68502..69053 - 552 WP_012783942 phospholipase D family protein -
HXF67_RS00385 (R621a_p079) 69068..69358 - 291 WP_014065733 hypothetical protein traK
HXF67_RS00390 (R621a_p080) 69355..70503 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HXF67_RS00395 (R621a_p081) 70500..71318 - 819 WP_014065734 IncI1-type conjugal transfer lipoprotein TraI traI
HXF67_RS00400 (R621a_p082) 71315..71773 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HXF67_RS00405 (R621a_p083) 72167..72751 - 585 WP_000977522 histidine phosphatase family protein -
HXF67_RS00410 (R621a_p084) 72811..74013 - 1203 WP_014065735 conjugal transfer protein TraF -
HXF67_RS00415 (R621a_p085) 74099..74923 - 825 WP_014065736 conjugal transfer protein TraE traE
HXF67_RS00420 (R621a_p086) 75074..76228 - 1155 WP_001139955 site-specific integrase -
HXF67_RS00425 (R621a_p087) 76212..76538 + 327 WP_001213803 hypothetical protein -
HXF67_RS00430 (R621a_p089) 76833..77090 - 258 WP_001302706 hypothetical protein -
HXF67_RS00435 (R621a_p091) 77403..77558 - 156 WP_001302705 hypothetical protein -
HXF67_RS00550 77641..77865 + 225 Protein_89 hypothetical protein -
HXF67_RS00445 (R621a_p093) 77862..79286 - 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HXF67_RS00450 (R621a_p095) 79286..79942 - 657 WP_001193553 prepilin peptidase -
HXF67_RS00455 (R621a_p096) 79927..80487 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HXF67_RS00460 (R621a_p097) 80497..81111 - 615 WP_014065737 type 4 pilus major pilin -
HXF67_RS00465 (R621a_p098) 81130..82227 - 1098 WP_014065738 type II secretion system F family protein -
HXF67_RS00470 (R621a_p099) 82240..83793 - 1554 WP_014065739 ATPase, T2SS/T4P/T4SS family virB11
HXF67_RS00475 (R621a_p100) 83804..84256 - 453 WP_001247870 type IV pilus biogenesis protein PilP -
HXF67_RS00480 (R621a_p101) 84243..85538 - 1296 WP_014065740 type 4b pilus protein PilO2 -
HXF67_RS00485 (R621a_p102) 85531..87213 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HXF67_RS00490 (R621a_p103) 87227..87664 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
HXF67_RS00495 (R621a_p104) 87664..88731 - 1068 WP_014065741 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   27 GenBank   NC_015965
Plasmid name   R621a Incompatibility group   IncI
Plasmid size   93185 bp Coordinate of oriT [Strand]   37332..37414 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

Drug resistance gene   tet(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2