Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114377
Name   oriT_pSa21-TC-CIP in_silico
Organism   Salmonella sp. strain Sa21
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH884651 (35315..35403 [+], 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_pSa21-TC-CIP
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9218 GenBank   WP_052971501
Name   nikB_HXI94_RS00165_pSa21-TC-CIP insolico UniProt ID   A0A3G2C959
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103896.37 Da        Isoelectric Point: 7.4198

>WP_052971501.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMEGK
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 A0A3G2C959


Auxiliary protein

ID   5404 GenBank   WP_001283947
Name   WP_001283947_pSa21-TC-CIP 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   10684 GenBank   WP_176705461
Name   trbC_HXI94_RS00160_pSa21-TC-CIP 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: 86954.10 Da        Isoelectric Point: 6.7713

>WP_176705461.1 F-type conjugative transfer protein TrbC [Salmonella sp.]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMARLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTAKTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 501..29937

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXI94_RS00010 (GPNKGMII_00136) 501..1325 + 825 WP_058649947 conjugal transfer protein TraE traE
HXI94_RS00015 (GPNKGMII_00137) 1411..2613 + 1203 WP_000976353 conjugal transfer protein TraF -
HXI94_RS00020 (GPNKGMII_00138) 2673..3257 + 585 WP_000977520 histidine phosphatase family protein -
HXI94_RS00025 (GPNKGMII_00139) 3652..4110 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HXI94_RS00030 (GPNKGMII_00140) 4107..4925 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
HXI94_RS00035 (GPNKGMII_00141) 4922..6070 + 1149 WP_001024976 plasmid transfer ATPase TraJ virB11
HXI94_RS00040 (GPNKGMII_00142) 6067..6357 + 291 WP_001299214 hypothetical protein traK
HXI94_RS00045 (GPNKGMII_00143) 6372..6923 + 552 WP_000014584 phospholipase D family protein -
HXI94_RS00050 (GPNKGMII_00144) 7014..10781 + 3768 WP_058649948 LPD7 domain-containing protein -
HXI94_RS00055 (GPNKGMII_00145) 10799..11146 + 348 WP_001055900 conjugal transfer protein traL
HXI94_RS00060 (GPNKGMII_00146) 11143..11835 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HXI94_RS00065 (GPNKGMII_00147) 11846..12832 + 987 WP_176705460 IncI1-type conjugal transfer protein TraN traN
HXI94_RS00070 (GPNKGMII_00148) 12835..14124 + 1290 WP_001271991 conjugal transfer protein TraO traO
HXI94_RS00075 (GPNKGMII_00149) 14124..14828 + 705 WP_001493811 IncI1-type conjugal transfer protein TraP traP
HXI94_RS00080 (GPNKGMII_00150) 14828..15355 + 528 WP_001055569 conjugal transfer protein TraQ traQ
HXI94_RS00085 (GPNKGMII_00151) 15406..15810 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
HXI94_RS00090 (GPNKGMII_00152) 15874..16062 + 189 WP_001277255 putative conjugal transfer protein TraS -
HXI94_RS00095 (GPNKGMII_00153) 16046..16846 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HXI94_RS00100 (GPNKGMII_00154) 16936..19980 + 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
HXI94_RS00105 (GPNKGMII_00155) 19980..20594 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
HXI94_RS00110 (GPNKGMII_00156) 20561..21763 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
HXI94_RS00115 (GPNKGMII_00157) 21792..22376 + 585 WP_052896781 IncI1-type conjugal transfer protein TraX -
HXI94_RS00120 (GPNKGMII_00158) 22473..24641 + 2169 WP_176705467 DotA/TraY family protein traY
HXI94_RS00125 (GPNKGMII_00159) 24715..25365 + 651 WP_001178506 plasmid IncI1-type surface exclusion protein ExcA -
HXI94_RS00130 (GPNKGMII_00160) 25437..25646 - 210 WP_000062603 HEAT repeat domain-containing protein -
HXI94_RS00135 (GPNKGMII_00161) 26038..26214 + 177 WP_001054898 hypothetical protein -
HXI94_RS00690 (GPNKGMII_00162) 26279..26374 - 96 WP_001303310 DinQ-like type I toxin DqlB -
HXI94_RS00140 (GPNKGMII_00163) 26873..27124 + 252 WP_001291964 hypothetical protein -
HXI94_RS00145 (GPNKGMII_00164) 27196..27348 - 153 WP_001331364 Hok/Gef family protein -
HXI94_RS00150 (GPNKGMII_00165) 27640..28848 + 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
HXI94_RS00155 (GPNKGMII_00166) 28867..29937 + 1071 WP_000151579 IncI1-type conjugal transfer protein TrbB trbB
HXI94_RS00160 (GPNKGMII_00167) 29930..32221 + 2292 WP_176705461 F-type conjugative transfer protein TrbC -

Host bacterium

ID   14812 GenBank   NZ_MH884651
Plasmid name   pSa21-TC-CIP Incompatibility group   IncX1
Plasmid size   115480 bp Coordinate of oriT [Strand]   35315..35403 [+]
Host baterium   Salmonella sp. strain Sa21

Cargo genes

Drug resistance gene   qnrS1, tet(A), aph(6)-Id, aph(3'')-Ib
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -