Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100881 |
| Name | oriT_pAS1  |
| Organism | Pseudomonas frederiksbergensis strain AS1 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP018320 (51065..51492 [-], 428 nt) |
| oriT length | 428 nt |
| IRs (inverted repeats) | IR1: 121..126, 127..132 (ATACAT..ATGTAT) IR2: 137..142, 144..149 (CATGAA..TTCATG) IR3: 162..170, 174..182 (AAGCCGCTC..GCGCGGCTT) |
| Location of nic site | 213..214 |
| Conserved sequence flanking the nic site |
_ |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 428 nt
>oriT_pAS1
GGTGGTCCTCTCTGAGCCAAATATGGGACTAATTCAGGATAACGATAACTTCCGAAATAGCGTATAGCAAATGCAATACATAAAATGCTTGATTTTATTGGTCTAAATGATAATTTTGTAATACATATGTATAGCGCATGAAATTCATGAATTTGCTCTGTAAGCCGCTCCCAGCGCGGCTTTAACCTACCGCTAGGGGGGTGCGTGTTGTGTATTGAGACTTTGACCCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGTCAGGCCGCAGGCCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCAGGAAGGGTGCTAAGAGAGTGCAAGAGGGGTGCAACTTGACTACAGGTAGGGGGCGATTAAGATGCACCTAGAGTGCAATAGGGGTGCAGATAGGGTGCAAA
GGTGGTCCTCTCTGAGCCAAATATGGGACTAATTCAGGATAACGATAACTTCCGAAATAGCGTATAGCAAATGCAATACATAAAATGCTTGATTTTATTGGTCTAAATGATAATTTTGTAATACATATGTATAGCGCATGAAATTCATGAATTTGCTCTGTAAGCCGCTCCCAGCGCGGCTTTAACCTACCGCTAGGGGGGTGCGTGTTGTGTATTGAGACTTTGACCCTGTTAAGGGGAAAAGTTGAAGCTCTTGTTAAGGGCGTATCCACTAGTCAGGCCGCAGGCCGTAGGGGGGTAGCACAGATGGTATGCAGAAAGGGTGCAGGAAGGGTGCTAAGAGAGTGCAAGAGGGGTGCAACTTGACTACAGGTAGGGGGCGATTAAGATGCACCTAGAGTGCAATAGGGGTGCAGATAGGGTGCAAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 952 | GenBank | WP_011117450 |
| Name | TraC_pAS1 |
UniProt ID | A0A1H4IBZ5 |
| Length | 981 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 981 a.a. Molecular weight: 108969.65 Da Isoelectric Point: 9.9827
>WP_011117450.1 MULTISPECIES: MobF family relaxase [Pseudomonas]
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLDGPIDQKELAKLFDGKLPNGELMPKP
VNKETGQIVNRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQTRRKEHGKSMLER
TGNLIIGKFRHELSRAKDPQLHTHAVVMNATRRADGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGY
EIRVLDKDGNFELAHISRDQIEAFSSRSKVIEEALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVK
EYWVIKARDLGIEFGGRSQLDNREYGRRSESIHAEHNLPEGITAGQAVVQYAINHLTEREQVVGESDLRT
AALRRAVGLASPSEVDDEIKRLVKQGTLIESPPTYTMATGKDGTALSPAGWRALLKEQKGWTDKEAQQYV
KMAITRGSLVEAEKRYTTQRALKREKAILAIERSGRGLVAPLLSKEQVAKALEGSTLSAGQYQAVEVIVS
TSNRFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERTTTTDAVFRVVALAPYGNQVTALKNEGLDAHTL
ASFFHTKDKKLDERTIVVLDEAGVVGARQMEHLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGM
QTARIKEIQRQKNQELKIAVQHAADGNPGKSLEHVNHVEEFREPGQRHQAIVRDYMSLTPEERKEVLIVA
GTNKDRKQINAMTRESLGLVGNGKELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRTGLSRGELYTV
DQALPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNANG
VIELASLKEKDGTPERVVALPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSRTTSQNLWYVAISRA
RHEARIYTDSIAGLPAAIANRYDKTTALSLQQARERQRNESIKPRTVLDGKALERKQRSALDGPSAGKSG
V
MFNVTSIKGSNQYAAAGYYTAADDYYAKESPGEWQGIGAELLGLDGPIDQKELAKLFDGKLPNGELMPKP
VNKETGQIVNRRMGLDLTFSAPKSVSMQALIAGDKDVVAAHDRAVTKAMEHVEKLAQTRRKEHGKSMLER
TGNLIIGKFRHELSRAKDPQLHTHAVVMNATRRADGKWRAIHNDDIFKIQPQIDAMYKGELAKELRELGY
EIRVLDKDGNFELAHISRDQIEAFSSRSKVIEEALAKDGKTRSNATALEKQIIAMATRPRKDERDRHLVK
EYWVIKARDLGIEFGGRSQLDNREYGRRSESIHAEHNLPEGITAGQAVVQYAINHLTEREQVVGESDLRT
AALRRAVGLASPSEVDDEIKRLVKQGTLIESPPTYTMATGKDGTALSPAGWRALLKEQKGWTDKEAQQYV
KMAITRGSLVEAEKRYTTQRALKREKAILAIERSGRGLVAPLLSKEQVAKALEGSTLSAGQYQAVEVIVS
TSNRFVGIQGDAGTGKTYSVDRAVKLIESVNNAMTERTTTTDAVFRVVALAPYGNQVTALKNEGLDAHTL
ASFFHTKDKKLDERTIVVLDEAGVVGARQMEHLMRIIEQSGARLVQLGDTKQTEAIEAGKPFAQLQQNGM
QTARIKEIQRQKNQELKIAVQHAADGNPGKSLEHVNHVEEFREPGQRHQAIVRDYMSLTPEERKEVLIVA
GTNKDRKQINAMTRESLGLVGNGKELPTLNRVDTTQAERRYAPSYKKGMIVQPEKDYIRTGLSRGELYTV
DQALPGNVLVVKDKNGNRVEFNPRKLTKLSVYNLEKPEFSVGDLVRITRNDQKLDLTNGDRMRVVGNANG
VIELASLKEKDGTPERVVALPTNRPLHLEHAYSATVHSAQGLTNDRVMISINTKSRTTSQNLWYVAISRA
RHEARIYTDSIAGLPAAIANRYDKTTALSLQQARERQRNESIKPRTVLDGKALERKQRSALDGPSAGKSG
V
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A1H4IBZ5 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 51878..80364
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PFAS1_RS28935 (PFAS1_28875) | 46947..47276 | + | 330 | WP_011117442 | TrfB-related DNA-binding protein | - |
| PFAS1_RS28940 (PFAS1_28880) | 47269..47541 | + | 273 | WP_019694539 | hypothetical protein | - |
| PFAS1_RS28945 (PFAS1_28885) | 47808..48071 | + | 264 | WP_019694540 | hypothetical protein | - |
| PFAS1_RS28950 (PFAS1_28890) | 48581..49366 | - | 786 | WP_011117444 | SprT-like domain-containing protein | - |
| PFAS1_RS28955 (PFAS1_28895) | 49503..49889 | - | 387 | WP_019694541 | hypothetical protein | - |
| PFAS1_RS28960 (PFAS1_28900) | 49893..50612 | - | 720 | WP_011117446 | StbB family protein | - |
| PFAS1_RS28965 (PFAS1_28905) | 50609..51064 | - | 456 | WP_011117447 | hypothetical protein | - |
| PFAS1_RS28970 (PFAS1_28910) | 51493..51885 | + | 393 | WP_011117448 | hypothetical protein | - |
| PFAS1_RS28975 (PFAS1_28915) | 51878..53434 | + | 1557 | WP_011117449 | type IV secretion system DNA-binding domain-containing protein | virb4 |
| PFAS1_RS28980 (PFAS1_28920) | 53445..56390 | + | 2946 | WP_011117450 | MobF family relaxase | - |
| PFAS1_RS28985 (PFAS1_28925) | 56467..57048 | + | 582 | WP_011117451 | hypothetical protein | - |
| PFAS1_RS28990 (PFAS1_28930) | 57377..58015 | - | 639 | WP_011117452 | hypothetical protein | - |
| PFAS1_RS28995 (PFAS1_28935) | 58063..58545 | - | 483 | WP_011117453 | hypothetical protein | - |
| PFAS1_RS29000 (PFAS1_28940) | 58560..59165 | - | 606 | WP_011117454 | phospholipase D family protein | - |
| PFAS1_RS29005 (PFAS1_28945) | 59155..59484 | - | 330 | WP_011117455 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| PFAS1_RS29010 (PFAS1_28950) | 59514..60419 | - | 906 | WP_011117456 | lytic transglycosylase domain-containing protein | virB1 |
| PFAS1_RS29015 (PFAS1_28955) | 60403..61431 | - | 1029 | WP_011117457 | P-type DNA transfer ATPase VirB11 | virB11 |
| PFAS1_RS29020 (PFAS1_28960) | 61441..62724 | - | 1284 | WP_011117458 | TrbI/VirB10 family protein | virB10 |
| PFAS1_RS29025 (PFAS1_28965) | 62727..63518 | - | 792 | WP_011117459 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| PFAS1_RS29030 (PFAS1_28970) | 63543..64208 | - | 666 | WP_011117460 | type IV secretion system protein | virB8 |
| PFAS1_RS29035 (PFAS1_28975) | 64212..65075 | - | 864 | WP_011117461 | type IV secretion system protein | virB6 |
| PFAS1_RS29040 (PFAS1_28980) | 65063..65467 | - | 405 | WP_011117462 | hypothetical protein | - |
| PFAS1_RS29045 (PFAS1_28985) | 65460..65672 | - | 213 | WP_011117463 | hypothetical protein | - |
| PFAS1_RS29050 (PFAS1_28990) | 65700..66389 | - | 690 | WP_011117464 | type IV secretion system protein | virB5 |
| PFAS1_RS29055 (PFAS1_28995) | 66386..69028 | - | 2643 | WP_019694561 | hypothetical protein | virb4 |
| PFAS1_RS29065 (PFAS1_29005) | 69354..69815 | - | 462 | WP_011117467 | TrbC/VirB2 family protein | virB2 |
| PFAS1_RS29075 (PFAS1_29015) | 70753..71526 | + | 774 | WP_019694514 | ParA family protein | - |
| PFAS1_RS29080 (PFAS1_29020) | 71540..72466 | + | 927 | WP_011117385 | ParB/RepB/Spo0J family partition protein | - |
| PFAS1_RS29085 (PFAS1_29025) | 72463..72804 | + | 342 | WP_011117386 | TrfB-related DNA-binding protein | - |
| PFAS1_RS29090 (PFAS1_29030) | 72809..73114 | + | 306 | WP_011117387 | hypothetical protein | - |
| PFAS1_RS29095 (PFAS1_29035) | 73215..73535 | + | 321 | WP_012727769 | hypothetical protein | - |
| PFAS1_RS29100 (PFAS1_29040) | 73803..74432 | + | 630 | WP_011117388 | recombinase family protein | - |
| PFAS1_RS29105 (PFAS1_29045) | 74880..75449 | + | 570 | WP_011117389 | replication protein | - |
| PFAS1_RS29110 (PFAS1_29050) | 75489..76250 | + | 762 | WP_011117390 | hypothetical protein | - |
| PFAS1_RS30260 (PFAS1_29055) | 76703..76891 | + | 189 | WP_052014790 | hypothetical protein | - |
| PFAS1_RS30140 (PFAS1_29060) | 77050..78318 | + | 1269 | Protein_90 | DUF1173 family protein | - |
| PFAS1_RS29125 (PFAS1_29065) | 78362..78757 | + | 396 | WP_011117394 | hypothetical protein | - |
| PFAS1_RS29825 (PFAS1_29070) | 78754..80364 | - | 1611 | WP_228409389 | Y-family DNA polymerase | traN |
| PFAS1_RS29135 (PFAS1_29075) | 81000..81407 | + | 408 | WP_011117396 | hypothetical protein | - |
Host bacterium
| ID | 1340 | GenBank | NZ_CP018320 |
| Plasmid name | pAS1 | Incompatibility group | _ |
| Plasmid size | 81841 bp | Coordinate of oriT [Strand] | 51065..51492 [-] |
| Host baterium | Pseudomonas frederiksbergensis strain AS1 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | nahAa, nahA2, nahAc, nahB, nahF, nahC, nahE, nahD, nagJ, nahJ, nahK, nahM, nahO, nahL, nahN, nahI, nahH, nahAb, nahG |
| Symbiosis gene | - |
| Anti-CRISPR | - |