Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114153 |
| Name | oriT_pSFR1-USMARC-69835  |
| Organism | Salmonella enterica subsp. enterica serovar Fresno strain USMARC-69835 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP032445 (30305..30393 [-], 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_pSFR1-USMARC-69835
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9090 | GenBank | WP_001306778 |
| Name | nikB_DZA58_RS24220_pSFR1-USMARC-69835 |
UniProt ID | Q79VV7 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104010.41 Da Isoelectric Point: 7.4265
>WP_001306778.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q79VV7 |
Auxiliary protein
| ID | 5305 | GenBank | WP_001283947 |
| Name | WP_001283947_pSFR1-USMARC-69835 |
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 | 10535 | GenBank | WP_119766336 |
| Name | trbC_DZA58_RS24225_pSFR1-USMARC-69835 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86925.05 Da Isoelectric Point: 6.7738
>WP_119766336.1 F-type conjugative transfer protein TrbC [Salmonella enterica]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRSP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRSP
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: 35771..73817
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| DZA58_RS24225 (DZA58_24225) | 33487..35778 | - | 2292 | WP_119766336 | F-type conjugative transfer protein TrbC | - |
| DZA58_RS24230 (DZA58_24230) | 35771..36841 | - | 1071 | WP_000151582 | IncI1-type conjugal transfer protein TrbB | trbB |
| DZA58_RS24235 (DZA58_24235) | 36860..38068 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| DZA58_RS24240 (DZA58_24240) | 38360..38512 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| DZA58_RS24245 (DZA58_24245) | 38584..38835 | - | 252 | WP_001291965 | hypothetical protein | - |
| DZA58_RS24730 | 39759..39935 | - | 177 | WP_001054900 | hypothetical protein | - |
| DZA58_RS24260 (DZA58_24260) | 40144..40353 | - | 210 | WP_001140545 | hemolysin expression modulator Hha | - |
| DZA58_RS24265 (DZA58_24265) | 40451..41065 | - | 615 | WP_000578649 | plasmid IncI1-type surface exclusion protein ExcA | - |
| DZA58_RS24270 (DZA58_24270) | 41141..43309 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| DZA58_RS24275 (DZA58_24275) | 43406..43990 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| DZA58_RS24280 (DZA58_24280) | 44019..45221 | - | 1203 | WP_001189159 | IncI1-type conjugal transfer protein TraW | traW |
| DZA58_RS24285 (DZA58_24285) | 45188..45802 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| DZA58_RS24290 (DZA58_24290) | 45802..48846 | - | 3045 | WP_001024752 | IncI1-type conjugal transfer protein TraU | traU |
| DZA58_RS24295 (DZA58_24295) | 48936..49736 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| DZA58_RS24300 (DZA58_24300) | 49720..49908 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| DZA58_RS24305 (DZA58_24305) | 49972..50376 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| DZA58_RS24310 (DZA58_24310) | 50427..50954 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| DZA58_RS24315 (DZA58_24315) | 50954..51658 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| DZA58_RS24320 (DZA58_24320) | 51658..52947 | - | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| DZA58_RS24325 (DZA58_24325) | 52950..53933 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| DZA58_RS24330 (DZA58_24330) | 53944..54636 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| DZA58_RS24335 (DZA58_24335) | 54633..54980 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| DZA58_RS24340 (DZA58_24340) | 54998..58765 | - | 3768 | WP_001141534 | LPD7 domain-containing protein | - |
| DZA58_RS24345 (DZA58_24345) | 58855..59406 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| DZA58_RS24350 (DZA58_24350) | 59421..59711 | - | 291 | WP_001299214 | hypothetical protein | traK |
| DZA58_RS24355 (DZA58_24355) | 59708..60856 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| DZA58_RS24360 (DZA58_24360) | 60853..61671 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| DZA58_RS24365 (DZA58_24365) | 61668..62126 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| DZA58_RS24370 (DZA58_24370) | 62521..63105 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| DZA58_RS24375 (DZA58_24375) | 63165..64367 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| DZA58_RS24380 (DZA58_24380) | 64453..65277 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| DZA58_RS24385 (DZA58_24385) | 65428..66582 | - | 1155 | WP_001139958 | tyrosine-type recombinase/integrase | - |
| DZA58_RS24410 (DZA58_24410) | 68019..69311 | - | 1293 | WP_001417545 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| DZA58_RS24415 (DZA58_24415) | 69311..69967 | - | 657 | WP_001389386 | prepilin peptidase | - |
| DZA58_RS24420 (DZA58_24420) | 69952..70512 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| DZA58_RS24425 (DZA58_24425) | 70522..71136 | - | 615 | WP_000959786 | type 4 pilus major pilin | - |
| DZA58_RS24430 (DZA58_24430) | 71154..72251 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| DZA58_RS24435 (DZA58_24435) | 72264..73817 | - | 1554 | WP_000362202 | GspE/PulE family protein | virB11 |
| DZA58_RS24440 (DZA58_24440) | 73828..74280 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| DZA58_RS24445 (DZA58_24445) | 74267..75562 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| DZA58_RS24450 (DZA58_24450) | 75555..77237 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| DZA58_RS24455 (DZA58_24455) | 77251..77688 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| DZA58_RS24460 (DZA58_24460) | 77688..78755 | - | 1068 | WP_001302629 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 14588 | GenBank | NZ_CP032445 |
| Plasmid name | pSFR1-USMARC-69835 | Incompatibility group | IncI1 |
| Plasmid size | 89737 bp | Coordinate of oriT [Strand] | 30305..30393 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Fresno strain USMARC-69835 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |