Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 121972 |
| Name | oriT_78-ME|p7ME01  |
| Organism | Cycloclasticus zancles 78-ME |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NC_021918 (32236..32341 [+], 106 nt) |
| oriT length | 106 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 106 nt
>oriT_78-ME|p7ME01
AGCCTCGCAGAGCAAGATGCCCCGTTGAGCGCCCCCGGCGCGAATAAGGGTGAGTGAAGTAGGAGCCGCCAACTTGTTGGTGGGCCTACTTCACCCATCTTGCCCG
AGCCTCGCAGAGCAAGATGCCCCGTTGAGCGCCCCCGGCGCGAATAAGGGTGAGTGAAGTAGGAGCCGCCAACTTGTTGGTGGGCCTACTTCACCCATCTTGCCCG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 13847 | GenBank | WP_041933078 |
| Name | traI_CYCME_RS12720_78-ME|p7ME01 |
UniProt ID | _ |
| Length | 762 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 762 a.a. Molecular weight: 84439.96 Da Isoelectric Point: 10.7212
>WP_041933078.1 TraI/MobA(P) family conjugative relaxase [Cycloclasticus zancles]
MIAKHVPMRSLKKSDFAGLVKYVTDEQSKTERLGLVNATNCEADTMQAVIGEVLATQQLNTRAEGDKTFH
LIVGFPPGENPSEAVLKDIEERLCAGLGFGEHQRVSAVHHDTDHMHIHIAINKIHPTRNTIHEPYQSYKK
LADMCEMLEEEHGLQRVNHKSARTLSQGRANDMEQHAGIESLVSWIKRECLEEIRTAKTWEELHQVMGDN
GLDIRQRANGFVIESEDGTQVKASTVARDLSKSKLESRLGAFEETAAQAERKAKRRYDKRPTRFKVNTTE
LYARYQEEQKNLTAARKVEWNNARGKKDRRIEAAKRSNRLRRSAIKLMGGDRLSKKILYAQAHKALKDEI
QSINKEHKRERQELYEQYKRRAWADWLKQQALDGDKKALEALRAREQAKGLQGDTIKGEGGAKPGHASVT
DNITKKGTIIFRTGSGAVRDDGDKLQVSRAATGDAVTEALRMAMERYGNRITVTGSPRFKAQVIVAAATS
NLPITFADAGLERRRQQLLQQENSHDRRNEQAGRGNERGRANRRSNGRVERGPADDNGRGRGTADSRAAT
TGRAGDSQRGRGQSVSTGSTNAGRRNDAGNGSRPILNKPHVGRIGGKPPSFAKNRLRTLSSLGVVRFARG
GEVLLPGNAPGELEHQGAKPDNQLRWGVSGSGGITPDQTSAADKYIAEREAKRLKGFDIPKHSRYTNQDG
AVTHGGIRNVQGQSLALLNRGDEVLVLPIDKATAQRMKRVRIGEAVTVTPQGSLKRSKGRSR
MIAKHVPMRSLKKSDFAGLVKYVTDEQSKTERLGLVNATNCEADTMQAVIGEVLATQQLNTRAEGDKTFH
LIVGFPPGENPSEAVLKDIEERLCAGLGFGEHQRVSAVHHDTDHMHIHIAINKIHPTRNTIHEPYQSYKK
LADMCEMLEEEHGLQRVNHKSARTLSQGRANDMEQHAGIESLVSWIKRECLEEIRTAKTWEELHQVMGDN
GLDIRQRANGFVIESEDGTQVKASTVARDLSKSKLESRLGAFEETAAQAERKAKRRYDKRPTRFKVNTTE
LYARYQEEQKNLTAARKVEWNNARGKKDRRIEAAKRSNRLRRSAIKLMGGDRLSKKILYAQAHKALKDEI
QSINKEHKRERQELYEQYKRRAWADWLKQQALDGDKKALEALRAREQAKGLQGDTIKGEGGAKPGHASVT
DNITKKGTIIFRTGSGAVRDDGDKLQVSRAATGDAVTEALRMAMERYGNRITVTGSPRFKAQVIVAAATS
NLPITFADAGLERRRQQLLQQENSHDRRNEQAGRGNERGRANRRSNGRVERGPADDNGRGRGTADSRAAT
TGRAGDSQRGRGQSVSTGSTNAGRRNDAGNGSRPILNKPHVGRIGGKPPSFAKNRLRTLSSLGVVRFARG
GEVLLPGNAPGELEHQGAKPDNQLRWGVSGSGGITPDQTSAADKYIAEREAKRLKGFDIPKHSRYTNQDG
AVTHGGIRNVQGQSLALLNRGDEVLVLPIDKATAQRMKRVRIGEAVTVTPQGSLKRSKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 7681 | GenBank | WP_020933266 |
| Name | WP_020933266_78-ME|p7ME01 |
UniProt ID | S5U131 |
| Length | 129 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 129 a.a. Molecular weight: 14470.73 Da Isoelectric Point: 8.9047
>WP_020933266.1 conjugal transfer transcriptional regulator TraJ [Cycloclasticus zancles]
MSNEIETDKEKKVTRKSSPPIKVYCLPEEKLRIEAQAERAGMSAARYLREVGQGYQIKGVVDFEQVRELA
RINGDLGRLGGLLKLWLTDDVRTAQFGQSTILAVLSKIEATQEEMGKVMTKVVMPRSES
MSNEIETDKEKKVTRKSSPPIKVYCLPEEKLRIEAQAERAGMSAARYLREVGQGYQIKGVVDFEQVRELA
RINGDLGRLGGLLKLWLTDDVRTAQFGQSTILAVLSKIEATQEEMGKVMTKVVMPRSES
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | S5U131 |
T4CP
| ID | 16212 | GenBank | WP_041933079 |
| Name | t4cp2_CYCME_RS12590_78-ME|p7ME01 |
UniProt ID | _ |
| Length | 845 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 845 a.a. Molecular weight: 94128.86 Da Isoelectric Point: 6.4267
>WP_041933079.1 VirB4 family type IV secretion/conjugal transfer ATPase [Cycloclasticus zancles]
MIQSISFAIAVCGAALLLILFARIRAVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVCKNGAFMASWL
YKGDDNASSTDEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPKYSDRNTSAFTDPVSAAIDEERRQLF
EGLGAMYEGYFVLTLTWFPPLLAQRKFVELMFDDDAEIVGKKARTKGLISQFKREISGIENRLTTAVKLT
RLRGQKIVNEDGSKVTHDDFLSWLQFCVTGVSHPVQLPNNPMYMDAYIGGQEMWGGVVPKVGRKFIQVVS
IEGFPLESHPGILSALAELPVEYRWSSRFIFMDQHESIKHLDKFRKKWKQKVRGFFDQVFNTNSGNVDQD
ALSMVQDAESAIAEVNSGLVAVGYYTSVVVLMDESRDRLEQSARQVEKSINRLGFAARTETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTIWTGNADAPCPMYPPLSPALMHCVTSGSTPFRLNLHVRDLGH
TFMFGPTGAGKSTHLALIAAQLRRYAGMSIYAFDKGMSMYPLTKAVGGLHFSVGADDDRLSFCPLQYLET
KNDRAWAMEWIDTILALNGVNSTPAQRNEIAHAIVSMHESGARTLSEFSLTIQDESIREAIRQYTVDGSM
GHLLDADEDGLSLTDFTTFEIEELMNLGEKFALPVLLYLFRRIERSLKGQPAVIILDEAWLMLGHPAFRE
KIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMGLNARQID
ILATAVPKRQYYYVSENGRRLYDLALGPLALSFVGASDKESVAAIKQLEAKFGEQWVHEWLAGRGLKLDN
YLEAA
MIQSISFAIAVCGAALLLILFARIRAVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVCKNGAFMASWL
YKGDDNASSTDEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPKYSDRNTSAFTDPVSAAIDEERRQLF
EGLGAMYEGYFVLTLTWFPPLLAQRKFVELMFDDDAEIVGKKARTKGLISQFKREISGIENRLTTAVKLT
RLRGQKIVNEDGSKVTHDDFLSWLQFCVTGVSHPVQLPNNPMYMDAYIGGQEMWGGVVPKVGRKFIQVVS
IEGFPLESHPGILSALAELPVEYRWSSRFIFMDQHESIKHLDKFRKKWKQKVRGFFDQVFNTNSGNVDQD
ALSMVQDAESAIAEVNSGLVAVGYYTSVVVLMDESRDRLEQSARQVEKSINRLGFAARTETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTIWTGNADAPCPMYPPLSPALMHCVTSGSTPFRLNLHVRDLGH
TFMFGPTGAGKSTHLALIAAQLRRYAGMSIYAFDKGMSMYPLTKAVGGLHFSVGADDDRLSFCPLQYLET
KNDRAWAMEWIDTILALNGVNSTPAQRNEIAHAIVSMHESGARTLSEFSLTIQDESIREAIRQYTVDGSM
GHLLDADEDGLSLTDFTTFEIEELMNLGEKFALPVLLYLFRRIERSLKGQPAVIILDEAWLMLGHPAFRE
KIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMGLNARQID
ILATAVPKRQYYYVSENGRRLYDLALGPLALSFVGASDKESVAAIKQLEAKFGEQWVHEWLAGRGLKLDN
YLEAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 16213 | GenBank | WP_020933264 |
| Name | t4cp2_CYCME_RS12715_78-ME|p7ME01 |
UniProt ID | _ |
| Length | 635 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 635 a.a. Molecular weight: 69841.69 Da Isoelectric Point: 7.3426
>WP_020933264.1 type IV secretory system conjugative DNA transfer family protein [Cycloclasticus zancles]
MKPKINNAVGPQVRDRKPKKQRLLPALGAVSVLGGLQAATQFFAYTFNYQDNLGSHISHVYAPWSILSWA
GDWYSIYPDEFMRSGSIGMVVTTVGLLGVAIAKVVTSNSSKASEYLHGSARWAEKKDIQAAGLLPRGRTA
LEVVTGKDPATSTGVYVGGWEDKDGNFFYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPQSSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSNGGVCWNPLDEIRIATEYEVGDVQNLATLIVDPDGKGMDSHWQ
KTSYALLVGVILHALYKAKNEGTPASLPVVDAMLADPERDTGELWMEMATYGHVDGQNHPAVGSAARDMM
DRPEEEGGSVLSTAKSYLALYRDPVVARNVSKSEFRIKDLMNNDDPVSLYIVTQPNDKARLRPLVRVLTN
MIIRLLADEMSFEKGRPVAHYKHRLLAMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDLNQLKSRET
GYGPDETITSNCHVQNAYPPNRIETAEHLSRLTGQTTVVKEQITTSGRRTSAMLGQVSRTIQEVQRPLLT
PDECLRMPGPTKNAAGDIEKAGDMVIYVAGYPAVYGKQPLYFKDPVFQARASVDAPKISDKLRIVEEPEG
EGVTI
MKPKINNAVGPQVRDRKPKKQRLLPALGAVSVLGGLQAATQFFAYTFNYQDNLGSHISHVYAPWSILSWA
GDWYSIYPDEFMRSGSIGMVVTTVGLLGVAIAKVVTSNSSKASEYLHGSARWAEKKDIQAAGLLPRGRTA
LEVVTGKDPATSTGVYVGGWEDKDGNFFYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPQSSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSNGGVCWNPLDEIRIATEYEVGDVQNLATLIVDPDGKGMDSHWQ
KTSYALLVGVILHALYKAKNEGTPASLPVVDAMLADPERDTGELWMEMATYGHVDGQNHPAVGSAARDMM
DRPEEEGGSVLSTAKSYLALYRDPVVARNVSKSEFRIKDLMNNDDPVSLYIVTQPNDKARLRPLVRVLTN
MIIRLLADEMSFEKGRPVAHYKHRLLAMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDLNQLKSRET
GYGPDETITSNCHVQNAYPPNRIETAEHLSRLTGQTTVVKEQITTSGRRTSAMLGQVSRTIQEVQRPLLT
PDECLRMPGPTKNAAGDIEKAGDMVIYVAGYPAVYGKQPLYFKDPVFQARASVDAPKISDKLRIVEEPEG
EGVTI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 4350..15154
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CYCME_RS12545 (CYCME_3001) | 59..355 | - | 297 | WP_020933234 | hypothetical protein | - |
| CYCME_RS12560 (CYCME_3003) | 2091..3221 | - | 1131 | WP_020933236 | plasmid replication initiator TrfA | - |
| CYCME_RS12565 (CYCME_3004) | 3268..3615 | - | 348 | WP_020933237 | single-stranded DNA-binding protein | - |
| CYCME_RS12570 (CYCME_3005) | 3714..4097 | + | 384 | WP_020933238 | transcriptional regulator | - |
| CYCME_RS12575 (CYCME_3006) | 4350..5309 | + | 960 | WP_020933239 | P-type conjugative transfer ATPase TrbB | virB11 |
| CYCME_RS12580 (CYCME_3007) | 5336..5761 | + | 426 | WP_020933240 | IncP-type conjugal transfer pilin TrbC | virB2 |
| CYCME_RS12585 (CYCME_3008) | 5764..6075 | + | 312 | WP_020933241 | conjugal transfer protein TrbD | virB3 |
| CYCME_RS12590 (CYCME_3009) | 6075..8612 | + | 2538 | WP_041933079 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| CYCME_RS12595 (CYCME_3010) | 8612..9394 | + | 783 | WP_020933243 | conjugal transfer protein TrbF | virB8 |
| CYCME_RS12600 (CYCME_3011) | 9412..10317 | + | 906 | WP_020933244 | P-type conjugative transfer protein TrbG | virB9 |
| CYCME_RS12605 (CYCME_3012) | 10320..10835 | + | 516 | WP_020933245 | conjugal transfer protein TrbH | - |
| CYCME_RS12610 (CYCME_3013) | 10839..12263 | + | 1425 | WP_020933246 | TrbI/VirB10 family protein | virB10 |
| CYCME_RS12615 (CYCME_3014) | 12282..13049 | + | 768 | WP_020933247 | P-type conjugative transfer protein TrbJ | virB5 |
| CYCME_RS12620 (CYCME_3015) | 13059..13286 | + | 228 | WP_020933248 | entry exclusion lipoprotein TrbK | - |
| CYCME_RS12625 (CYCME_3016) | 13298..15154 | + | 1857 | WP_020933249 | P-type conjugative transfer protein TrbL | virB6 |
| CYCME_RS12630 (CYCME_3017) | 15174..15656 | + | 483 | WP_020933250 | hypothetical protein | - |
| CYCME_RS12635 (CYCME_3018) | 15670..16302 | + | 633 | WP_041933081 | muramidase | - |
| CYCME_RS12640 (CYCME_3019) | 16299..17027 | + | 729 | WP_020933252 | TraX family protein | - |
| CYCME_RS12645 (CYCME_3020) | 17041..17466 | + | 426 | WP_020933253 | OmpA family protein | - |
| CYCME_RS12650 (CYCME_3021) | 17485..17754 | + | 270 | WP_014579500 | hypothetical protein | - |
| CYCME_RS12655 (CYCME_3022) | 17779..18033 | + | 255 | WP_020933254 | hypothetical protein | - |
| CYCME_RS12660 (CYCME_3023) | 18038..18547 | + | 510 | WP_020933255 | hypothetical protein | - |
| CYCME_RS12665 (CYCME_3024) | 18554..18937 | + | 384 | WP_041933077 | helix-turn-helix domain-containing protein | - |
| CYCME_RS12670 (CYCME_3025) | 18958..19581 | - | 624 | WP_020933257 | recombinase family protein | - |
| CYCME_RS12675 (CYCME_3026) | 19590..19862 | - | 273 | WP_020933258 | hypothetical protein | - |
Host bacterium
| ID | 22399 | GenBank | NC_021918 |
| Plasmid name | 78-ME|p7ME01 | Incompatibility group | - |
| Plasmid size | 42347 bp | Coordinate of oriT [Strand] | 32236..32341 [+] |
| Host baterium | Cycloclasticus zancles 78-ME |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |