Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 106720 |
| Name | oriT_pSal-3973_DHA_CMY  |
| Organism | Salmonella enterica subsp. enterica serovar Anatum strain Sal-3973 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP045467 (78419..78507 [-], 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_pSal-3973_DHA_CMY
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4441 | GenBank | WP_165885255 |
| Name | nikB_GER12_RS22890_pSal-3973_DHA_CMY |
UniProt ID | _ |
| 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_165885255.1 IncI1-type relaxase NikB [Salmonella enterica]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHAFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHAFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 1970 | GenBank | WP_001283947 |
| Name | WP_001283947_pSal-3973_DHA_CMY |
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
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A142CMC2 |
T4CP
| ID | 4473 | GenBank | WP_011264051 |
| Name | trbC_GER12_RS22895_pSal-3973_DHA_CMY |
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_011264051.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 83886..127380
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| GER12_RS22895 (GER12_23280) | 81602..83893 | - | 2292 | WP_011264051 | F-type conjugative transfer protein TrbC | - |
| GER12_RS22900 (GER12_23285) | 83886..84956 | - | 1071 | WP_011264050 | IncI1-type conjugal transfer protein TrbB | trbB |
| GER12_RS22905 (GER12_23290) | 84975..86183 | - | 1209 | WP_011264049 | IncI1-type conjugal transfer protein TrbA | trbA |
| GER12_RS22910 (GER12_23295) | 86490..87272 | - | 783 | WP_023063753 | protein FinQ | - |
| GER12_RS22915 (GER12_23300) | 87468..87785 | + | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| GER12_RS22920 (GER12_23305) | 87782..88315 | - | 534 | WP_001221666 | lipocalin family protein | - |
| GER12_RS22925 (GER12_23310) | 88409..89554 | - | 1146 | WP_000976514 | extended-spectrum class C beta-lactamase CMY-2 | - |
| GER12_RS22930 (GER12_23315) | 89878..91140 | - | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| GER12_RS22935 (GER12_23320) | 91293..91667 | - | 375 | WP_223349261 | hypothetical protein | - |
| GER12_RS22940 (GER12_23325) | 91988..92140 | + | 153 | WP_001387489 | Hok/Gef family protein | - |
| GER12_RS22945 (GER12_23330) | 92212..92463 | - | 252 | WP_001291964 | hypothetical protein | - |
| GER12_RS23940 | 92964..93059 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| GER12_RS22955 | 93124..93300 | - | 177 | WP_001054897 | hypothetical protein | - |
| GER12_RS22960 (GER12_23340) | 93692..93901 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| GER12_RS22965 (GER12_23345) | 93973..94635 | - | 663 | WP_000644796 | plasmid IncI1-type surface exclusion protein ExcA | - |
| GER12_RS22970 (GER12_23350) | 94706..96874 | - | 2169 | WP_023518847 | DotA/TraY family protein | traY |
| GER12_RS22975 (GER12_23355) | 96971..97555 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| GER12_RS22980 (GER12_23360) | 97584..98786 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| GER12_RS22985 (GER12_23365) | 98753..99367 | - | 615 | WP_000337398 | IncI1-type conjugal transfer protein TraV | traV |
| GER12_RS22990 (GER12_23370) | 99367..102411 | - | 3045 | WP_021265678 | IncI1-type conjugal transfer protein TraU | traU |
| GER12_RS22995 (GER12_23375) | 102501..103301 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| GER12_RS23000 (GER12_23380) | 103285..103473 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| GER12_RS23005 (GER12_23385) | 103537..103941 | - | 405 | WP_000086958 | IncI1-type conjugal transfer protein TraR | traR |
| GER12_RS23010 (GER12_23390) | 103992..104519 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| GER12_RS23015 (GER12_23395) | 104519..105223 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| GER12_RS23020 (GER12_23400) | 105223..106512 | - | 1290 | WP_165885256 | conjugal transfer protein TraO | traO |
| GER12_RS23025 (GER12_23405) | 106515..107498 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| GER12_RS23030 (GER12_23410) | 107509..108201 | - | 693 | WP_000138550 | DotI/IcmL family type IV secretion protein | traM |
| GER12_RS23035 (GER12_23415) | 108198..108545 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| GER12_RS23040 (GER12_23420) | 108563..112330 | - | 3768 | WP_001141527 | LPD7 domain-containing protein | - |
| GER12_RS23045 (GER12_23425) | 112419..112970 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| GER12_RS23050 (GER12_23430) | 112985..113275 | - | 291 | WP_001299214 | hypothetical protein | traK |
| GER12_RS23055 (GER12_23435) | 113272..114420 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| GER12_RS23060 (GER12_23440) | 114417..115235 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| GER12_RS23065 (GER12_23445) | 115232..115690 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| GER12_RS23070 (GER12_23450) | 116085..116669 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| GER12_RS23075 (GER12_23455) | 116729..117931 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| GER12_RS23080 (GER12_23460) | 118016..118840 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| GER12_RS23085 (GER12_23465) | 118991..120145 | - | 1155 | WP_001139957 | site-specific integrase | - |
| GER12_RS23090 (GER12_23485) | 121337..121585 | + | 249 | WP_001349157 | hypothetical protein | - |
| GER12_RS23095 (GER12_23490) | 121582..122874 | - | 1293 | WP_001417545 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| GER12_RS23100 (GER12_23495) | 122874..123530 | - | 657 | WP_001193553 | prepilin peptidase | - |
| GER12_RS23105 (GER12_23500) | 123515..124075 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| GER12_RS23110 (GER12_23505) | 124085..124699 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| GER12_RS23115 (GER12_23510) | 124717..125814 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| GER12_RS23120 (GER12_23515) | 125827..127380 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| GER12_RS23125 (GER12_23520) | 127391..127843 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| GER12_RS23130 (GER12_23525) | 127830..129125 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| GER12_RS23135 (GER12_23530) | 129118..130800 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| GER12_RS23140 (GER12_23535) | 130814..131251 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| GER12_RS23145 (GER12_23540) | 131251..132318 | - | 1068 | WP_001302629 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 7157 | GenBank | NZ_CP045467 |
| Plasmid name | pSal-3973_DHA_CMY | Incompatibility group | IncI1 |
| Plasmid size | 195486 bp | Coordinate of oriT [Strand] | 78419..78507 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Anatum strain Sal-3973 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |