Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103391
Name   oriT_pST1030-1C in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT507879 (81073..81161 [-], 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_pST1030-1C
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2532 GenBank   WP_001405892
Name   nikB_JYH29_RS00540_pST1030-1C insolico UniProt ID   A0A3V4WX06
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103883.32 Da        Isoelectric Point: 7.3373

>WP_001405892.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
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 A0A3V4WX06


Auxiliary protein

ID   1094 GenBank   WP_001283947
Name   WP_001283947_pST1030-1C 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   2307 GenBank   WP_001289282
Name   trbC_JYH29_RS00545_pST1030-1C 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: 86969.12 Da        Isoelectric Point: 6.7713

>WP_001289282.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMARLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
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: 86539..124790

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JYH29_RS00545 (ELPBMBEK_00078) 84255..86546 - 2292 WP_001289282 F-type conjugative transfer protein TrbC -
JYH29_RS00550 (ELPBMBEK_00079) 86539..87609 - 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
JYH29_RS00555 (ELPBMBEK_00080) 87628..88836 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
JYH29_RS00560 (ELPBMBEK_00081) 89128..89280 + 153 WP_001303307 Hok/Gef family protein -
JYH29_RS00565 89352..89585 - 234 WP_072148106 hypothetical protein -
JYH29_RS00815 (ELPBMBEK_00082) 90052..90147 + 96 WP_001303310 DinQ-like type I toxin DqlB -
JYH29_RS00570 (ELPBMBEK_00083) 90212..90388 - 177 WP_001054897 hypothetical protein -
JYH29_RS00575 (ELPBMBEK_00084) 90780..90989 + 210 WP_000062603 HEAT repeat domain-containing protein -
JYH29_RS00580 (ELPBMBEK_00085) 91061..91735 - 675 WP_223866377 plasmid IncI1-type surface exclusion protein ExcA -
JYH29_RS00585 (ELPBMBEK_00086) 91785..93953 - 2169 WP_000698358 DotA/TraY family protein traY
JYH29_RS00590 (ELPBMBEK_00087) 94050..94634 - 585 WP_001037986 IncI1-type conjugal transfer protein TraX -
JYH29_RS00595 (ELPBMBEK_00088) 94663..95865 - 1203 WP_001189159 IncI1-type conjugal transfer protein TraW traW
JYH29_RS00600 (ELPBMBEK_00089) 95832..96446 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
JYH29_RS00605 (ELPBMBEK_00090) 96446..99490 - 3045 WP_001024752 IncI1-type conjugal transfer protein TraU traU
JYH29_RS00610 (ELPBMBEK_00091) 99580..100380 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
JYH29_RS00615 (ELPBMBEK_00092) 100364..100552 - 189 WP_001277255 putative conjugal transfer protein TraS -
JYH29_RS00620 (ELPBMBEK_00093) 100616..101020 - 405 WP_000086959 IncI1-type conjugal transfer protein TraR traR
JYH29_RS00625 (ELPBMBEK_00094) 101071..101598 - 528 WP_001055569 conjugal transfer protein TraQ traQ
JYH29_RS00630 (ELPBMBEK_00095) 101598..102302 - 705 WP_000801919 IncI1-type conjugal transfer protein TraP traP
JYH29_RS00635 (ELPBMBEK_00096) 102302..103591 - 1290 WP_001272000 conjugal transfer protein TraO traO
JYH29_RS00640 (ELPBMBEK_00097) 103594..104577 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
JYH29_RS00645 (ELPBMBEK_00098) 104588..105280 - 693 WP_000138551 DotI/IcmL family type IV secretion protein traM
JYH29_RS00650 (ELPBMBEK_00099) 105277..105624 - 348 WP_001055900 conjugal transfer protein traL
JYH29_RS00655 (ELPBMBEK_00100) 105642..109409 - 3768 WP_204884849 LPD7 domain-containing protein -
JYH29_RS00660 (ELPBMBEK_00101) 109499..110050 - 552 WP_000014584 phospholipase D family protein -
JYH29_RS00665 (ELPBMBEK_00102) 110065..110355 - 291 WP_001299214 hypothetical protein traK
JYH29_RS00670 (ELPBMBEK_00103) 110352..111500 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
JYH29_RS00675 (ELPBMBEK_00104) 111497..112315 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
JYH29_RS00680 (ELPBMBEK_00105) 112312..112770 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
JYH29_RS00685 (ELPBMBEK_00106) 113165..113749 - 585 WP_000977522 histidine phosphatase family protein -
JYH29_RS00690 (ELPBMBEK_00107) 113809..115011 - 1203 WP_000976353 conjugal transfer protein TraF -
JYH29_RS00695 (ELPBMBEK_00108) 115097..115921 - 825 WP_001238929 conjugal transfer protein TraE traE
JYH29_RS00700 (ELPBMBEK_00109) 116072..117226 - 1155 WP_001139958 site-specific integrase -
JYH29_RS00705 118332..118511 - 180 WP_001417544 hypothetical protein -
JYH29_RS00710 118747..118995 + 249 WP_001349157 hypothetical protein -
JYH29_RS00715 (ELPBMBEK_00110) 118992..120284 - 1293 WP_001417545 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
JYH29_RS00720 (ELPBMBEK_00111) 120284..120940 - 657 WP_001193553 prepilin peptidase -
JYH29_RS00725 (ELPBMBEK_00112) 120925..121485 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
JYH29_RS00730 (ELPBMBEK_00113) 121495..122109 - 615 WP_000959786 type 4 pilus major pilin -
JYH29_RS00735 (ELPBMBEK_00114) 122127..123224 - 1098 WP_001208805 type II secretion system F family protein -
JYH29_RS00740 (ELPBMBEK_00115) 123237..124790 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
JYH29_RS00745 (ELPBMBEK_00116) 124801..125253 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
JYH29_RS00750 (ELPBMBEK_00117) 125240..126535 - 1296 WP_000752772 type 4b pilus protein PilO2 -
JYH29_RS00755 (ELPBMBEK_00118) 126528..128210 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
JYH29_RS00760 (ELPBMBEK_00119) 128224..128661 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
JYH29_RS00765 (ELPBMBEK_00120) 128661..129728 - 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   3834 GenBank   NZ_MT507879
Plasmid name   pST1030-1C Incompatibility group   IncI1
Plasmid size   134862 bp Coordinate of oriT [Strand]   81073..81161 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

Drug resistance gene   tet(B), aph(6)-Id, aph(3'')-Ib, sul2, blaTEM-1B, sul3, ant(3'')-Ia, cmlA1, aadA2, dfrA12
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -