Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101281
Name   oriT_IncFIB(pN55391) in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain JS5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKCLH010000002 (71966..72054 [+], 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_IncFIB(pN55391)
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1233 GenBank   WP_001299212
Name   nikB_LZ008_RS23580_IncFIB(pN55391) insolico UniProt ID   A0A5T4AK12
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103956.40 Da        Isoelectric Point: 7.2642

>WP_001299212.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWINFYGVTCFHNCTSLETAAADMEYIALQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVSDWLSLHRRLAEDGLYLSQMDGK
YLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
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 A0A5T4AK12


Auxiliary protein

ID   432 GenBank   WP_001283947
Name   WP_001283947_IncFIB(pN55391) 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   844 GenBank   WP_001289276
Name   trbC_LZ008_RS23575_IncFIB(pN55391) 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: 30446..66588

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LZ008_RS23370 (LZ008_23370) 25508..26575 + 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -
LZ008_RS23375 (LZ008_23375) 26575..27012 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
LZ008_RS23380 (LZ008_23380) 27026..28708 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
LZ008_RS23385 (LZ008_23385) 28701..29996 + 1296 WP_001545757 type 4b pilus protein PilO2 -
LZ008_RS23390 (LZ008_23390) 29983..30435 + 453 WP_001247331 type IV pilus biogenesis protein PilP -
LZ008_RS23395 (LZ008_23395) 30446..31999 + 1554 WP_000362206 ATPase, T2SS/T4P/T4SS family virB11
LZ008_RS23400 (LZ008_23400) 32012..33097 + 1086 WP_001208802 type II secretion system F family protein -
LZ008_RS23405 (LZ008_23405) 33114..33728 + 615 WP_000908226 type 4 pilus major pilin -
LZ008_RS23410 (LZ008_23410) 33738..34298 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
LZ008_RS23415 (LZ008_23415) 34283..34939 + 657 WP_001193549 A24 family peptidase -
LZ008_RS23420 (LZ008_23420) 34939..36231 + 1293 WP_001350014 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
LZ008_RS23425 (LZ008_23425) 36287..36412 - 126 Protein_41 transposase -
LZ008_RS23430 (LZ008_23430) 36620..37444 + 825 WP_001238942 conjugal transfer protein TraE traE
LZ008_RS23435 (LZ008_23435) 37530..38732 + 1203 WP_000976348 conjugal transfer protein TraF -
LZ008_RS23440 (LZ008_23440) 38792..39376 + 585 WP_000977522 histidine phosphatase family protein -
LZ008_RS23445 (LZ008_23445) 39771..40229 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
LZ008_RS23450 (LZ008_23450) 40226..41044 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
LZ008_RS23455 (LZ008_23455) 41041..42189 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
LZ008_RS23460 (LZ008_23460) 42186..42476 + 291 WP_001299214 hypothetical protein traK
LZ008_RS23465 (LZ008_23465) 42491..43042 + 552 WP_000014584 phospholipase D family protein -
LZ008_RS23470 (LZ008_23470) 43132..46899 + 3768 WP_001141542 LPD7 domain-containing protein -
LZ008_RS23475 (LZ008_23475) 46917..47264 + 348 WP_001055900 conjugal transfer protein traL
LZ008_RS23480 (LZ008_23480) 47261..47953 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
LZ008_RS23485 (LZ008_23485) 47964..48947 + 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
LZ008_RS23490 (LZ008_23490) 48950..50239 + 1290 WP_001271997 conjugal transfer protein TraO traO
LZ008_RS23495 (LZ008_23495) 50239..50943 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
LZ008_RS23500 (LZ008_23500) 50943..51470 + 528 WP_001055569 conjugal transfer protein TraQ traQ
LZ008_RS23505 (LZ008_23505) 51521..51925 + 405 WP_000086961 IncI1-type conjugal transfer protein TraR traR
LZ008_RS23510 (LZ008_23510) 51989..52177 + 189 WP_001277255 putative conjugal transfer protein TraS -
LZ008_RS23515 (LZ008_23515) 52161..52961 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
LZ008_RS23520 (LZ008_23520) 53051..56095 + 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
LZ008_RS23525 (LZ008_23525) 56095..56709 + 615 WP_000337400 IncI1-type conjugal transfer protein TraV traV
LZ008_RS23530 (LZ008_23530) 56676..57878 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
LZ008_RS23535 (LZ008_23535) 57907..58491 + 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
LZ008_RS23540 (LZ008_23540) 58588..60756 + 2169 WP_000698357 DotA/TraY family protein traY
LZ008_RS23545 (LZ008_23545) 60830..61480 + 651 WP_001178506 plasmid IncI1-type surface exclusion protein ExcA -
LZ008_RS23550 (LZ008_23550) 61552..61761 - 210 WP_000062603 HEAT repeat domain-containing protein -
LZ008_RS23555 (LZ008_23555) 62153..62329 + 177 WP_001054904 hypothetical protein -
LZ008_RS24450 62394..62489 - 96 WP_001303310 DinQ-like type I toxin DqlB -
LZ008_RS23560 (LZ008_23560) 63121..64029 + 909 WP_000055084 hypothetical protein -
LZ008_RS23565 (LZ008_23565) 64291..65499 + 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
LZ008_RS23570 (LZ008_23570) 65518..66588 + 1071 WP_000151577 IncI1-type conjugal transfer protein TrbB trbB
LZ008_RS23575 (LZ008_23575) 66581..68872 + 2292 WP_001289276 F-type conjugative transfer protein TrbC -

Host bacterium

ID   1725 GenBank   NZ_JAKCLH010000002
Plasmid name   IncFIB(pN55391) Incompatibility group   IncFIB
Plasmid size   189906 bp Coordinate of oriT [Strand]   71966..72054 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain JS5

Cargo genes

Drug resistance gene   ant(3'')-Ia, qacE, sul1, tet(A)
Virulence gene   faeI, faeH, faeF, faeE, faeD, faeC
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -