Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100032 |
| Name | oriT_pEK204  |
| Organism | Escherichia coli strain C |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | EU935740 (36439..36540 [-], 102 nt) |
| oriT length | 102 nt |
| IRs (inverted repeats) | 8..bp: 26..33, 37..44 (GTCGGGGC..GCCCTGAC) 17..bp: 51..67, 74..90 (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC) |
| Location of nic site | 98..99 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | minimal oriT sequence |
oriT sequence
Download Length: 102 nt
ACTCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Woodford N et al. (2009) Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone. Antimicrob Agents Chemother. 53(10):4472-82. [PMID:19687243]
Relaxase
| ID | 31 | GenBank | ACQ42157 |
| Name | NikB_pEK204 |
UniProt ID | C7SA36 |
| Length | 899 a.a. | PDB ID | |
| Note | relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104070.55 Da Isoelectric Point: 7.3623
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | C7SA36 |
Reference
[1] Woodford N et al. (2009) Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone. Antimicrob Agents Chemother. 53(10):4472-82. [PMID:19687243]
Auxiliary protein
| ID | 48 | GenBank | ACQ42156 |
| Name | NikA_pEK204 |
UniProt ID | C7SA35 |
| Length | 110 a.a. | PDB ID | _ |
| Note | plasmid mobilization protein | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12613.57 Da Isoelectric Point: 10.7463
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | C7SA35 |
Reference
[1] Woodford N et al. (2009) Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone. Antimicrob Agents Chemother. 53(10):4472-82. [PMID:19687243]
T4CP
| ID | 31 | GenBank | ACQ42158 |
| Name | TrbC_pEK204 |
UniProt ID | C7SA37 |
| Length | 763 a.a. | PDB ID | _ |
| Note | Type IV Secretion System Coupling Protein | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86911.02 Da Isoelectric Point: 6.7713
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | C7SA37 |
Reference
[1] Woodford N et al. (2009) Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone. Antimicrob Agents Chemother. 53(10):4472-82. [PMID:19687243]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 41898..83669
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_44 | 39614..41905 | - | 2292 | ACQ42158 | IcmO-like type IV secretion system protein | - |
| Locus_45 | 41898..42968 | - | 1071 | ACQ42159 | protein-disulfide | trbB |
| Locus_46 | 42987..44195 | - | 1209 | ACQ42160 | TrbA protein | trbA |
| Locus_47 | 44502..45431 | - | 930 | ACQ42161 | FinQ | - |
| Locus_48 | 45769..46053 | + | 285 | ACQ42162 | post-segregation killing protein | - |
| Locus_49 | 45908..46060 | + | 153 | ACQ42163 | post-segregation killing protein | - |
| Locus_50 | 47893..48555 | - | 663 | ACQ42164 | surface exclusion protein | - |
| Locus_51 | 48626..50863 | - | 2238 | ACQ42165 | TraY | traY |
| Locus_52 | 50891..51475 | - | 585 | ACQ42166 | TraX protein | - |
| Locus_53 | 51504..52706 | - | 1203 | ACQ42167 | TraW protein | traW |
| Locus_54 | 52673..53287 | - | 615 | ACQ42168 | TraV protein | traV |
| Locus_55 | 53287..56331 | - | 3045 | ACQ42169 | TraU protein | traU |
| Locus_56 | 56421..57221 | - | 801 | ACQ42170 | TraT protein | traT |
| Locus_57 | 57205..57393 | - | 189 | ACQ42171 | TraS protein | - |
| Locus_58 | 57457..57861 | - | 405 | ACQ42172 | TraR protein | traR |
| Locus_59 | 57912..58439 | - | 528 | ACQ42173 | TraQ protein | traQ |
| Locus_60 | 58439..59143 | - | 705 | ACQ42174 | TraP protein | traP |
| Locus_61 | 59143..60432 | - | 1290 | ACQ42175 | TraO protein | traO |
| Locus_62 | 60435..61418 | - | 984 | ACQ42176 | TraN protein | traN |
| Locus_63 | 61429..62121 | - | 693 | ACQ42177 | TraM protein | traM |
| Locus_64 | 62118..62465 | - | 348 | ACQ42178 | TraL protein | traL |
| Locus_65 | 62483..66250 | - | 3768 | ACQ42179 | SogL protein | - |
| Locus_66 | 62483..65017 | - | 2535 | ACQ42180 | SogS protein | - |
| Locus_67 | 66340..66891 | - | 552 | ACQ42181 | EDTA-resistant nuclease | - |
| Locus_68 | 66906..67196 | - | 291 | ACQ42182 | TraK protein | traK |
| Locus_69 | 67193..68341 | - | 1149 | ACQ42183 | TraJ protein | virB11 |
| Locus_70 | 68338..69156 | - | 819 | ACQ42184 | TraI protein | traI |
| Locus_71 | 69153..69611 | - | 459 | ACQ42185 | TraH protein | - |
| Locus_72 | 70005..70589 | - | 585 | ACQ42186 | TraG protein | - |
| Locus_73 | 70649..71851 | - | 1203 | ACQ42187 | TraF protein | - |
| Locus_74 | 71937..72761 | - | 825 | ACQ42188 | TraE protein | traE |
| Locus_75 | 72912..74066 | - | 1155 | ACQ42189 | shufflon-specific DNA recombinase | - |
| Locus_76 | 75447..77060 | + | 1614 | ACQ42190 | IS66 transposase | - |
| Locus_77 | 77739..79163 | - | 1425 | ACQ42191 | type IV prepilin | - |
| Locus_78 | 79163..79819 | - | 657 | ACQ42192 | prepilin peptidase | - |
| Locus_79 | 79804..80364 | - | 561 | ACQ42193 | PilT | virB1 |
| Locus_80 | 80374..80988 | - | 615 | ACQ42194 | type IV prepilin | - |
| Locus_81 | 81006..82103 | - | 1098 | ACQ42195 | integral membrane protein | - |
| Locus_82 | 82116..83669 | - | 1554 | ACQ42196 | nucleotide-binding protein | virB11 |
| Locus_83 | 83680..84132 | - | 453 | ACQ42197 | PilP | - |
| Locus_84 | 84119..85414 | - | 1296 | ACQ42198 | PilO | - |
| Locus_85 | 85407..87089 | - | 1683 | ACQ42199 | lipoprotein | - |
| Locus_86 | 87103..87540 | - | 438 | ACQ42200 | PilM | - |
| Locus_87 | 87540..88607 | - | 1068 | ACQ42201 | lipoprotein | - |
Host bacterium
| ID | 31 | GenBank | EU935740 |
| Plasmid name | pEK204 | Incompatibility group | IncI1 |
| Plasmid size | 93732 bp | Coordinate of oriT [Strand] | 36439..36540 [-] |
| Host baterium | Escherichia coli strain C |
Cargo genes
| Drug resistance gene | beta-lactamases: CTX-M-3 enzyme and TEM-1 enzyme (resistance genes: blaCTX-M-3 and blaTEM-1) |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |