Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200407 |
| Name | oriT_Tn6413  |
| Organism | Pseudomonas aeruginosa strain 6762 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | CP030075 (47353..47824 [-], 472 nt) |
| oriT length | 472 nt |
| IRs (inverted repeats) | 200..205, 219..224 (CAGCGA..TCGCTG) 135..141, 148..154 (TGCGGCC..GGCCGCA) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 472 nt
>oriT_Tn6413
GGGAACTGCTGGACCAACTCGGCGTAGCACTCCAGCGGAGCGCGATAGAGGATGGCGAACTGCTTGCGCGACAGCGATGTGCGCTGCCAGATGTGTTCCAGCAGCTTTTGCCGGCGCGGTATCGCCAGTAGGGATGCGGCCGACTCGGGCCGCAGCAGCCCTTTCGGAAGATCAGTGGCTGGCGTTGGCGACGGAGCGGCAGCGACCGAGGCCCGTTTTCGCTGGAACAGGGAGAGCATGAGGGTGTCCTGATGGCGGGCCGACCGGGAGGCCTTTTTGCTTTTTCGAGGTAGGGCCTTTCCCCTTGCACTCCATTCCCTTCCCCTTTCGGCCTTTTGGCCCTTAACAGCCTTTGGGTATAGGGCGCCAGGCGTTGATCGTCCACCACCAATGCGGGTTGCAGCGGGGCCGGATTGATGCGGGAAGGCGGGCTGTTCCCAGCCTACGATGGGCCGATTCTTGGACTCGGGAG
GGGAACTGCTGGACCAACTCGGCGTAGCACTCCAGCGGAGCGCGATAGAGGATGGCGAACTGCTTGCGCGACAGCGATGTGCGCTGCCAGATGTGTTCCAGCAGCTTTTGCCGGCGCGGTATCGCCAGTAGGGATGCGGCCGACTCGGGCCGCAGCAGCCCTTTCGGAAGATCAGTGGCTGGCGTTGGCGACGGAGCGGCAGCGACCGAGGCCCGTTTTCGCTGGAACAGGGAGAGCATGAGGGTGTCCTGATGGCGGGCCGACCGGGAGGCCTTTTTGCTTTTTCGAGGTAGGGCCTTTCCCCTTGCACTCCATTCCCTTCCCCTTTCGGCCTTTTGGCCCTTAACAGCCTTTGGGTATAGGGCGCCAGGCGTTGATCGTCCACCACCAATGCGGGTTGCAGCGGGGCCGGATTGATGCGGGAAGGCGGGCTGTTCCCAGCCTACGATGGGCCGATTCTTGGACTCGGGAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 14435 | GenBank | AYL28120 |
| Name | TraI_2_DN073_01845_Tn6413 |
UniProt ID | _ |
| Length | 620 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 620 a.a. Molecular weight: 67923.42 Da Isoelectric Point: 7.1518
>AYL28120.1 relaxase [Pseudomonas aeruginosa]
MLSLFQRKRASVAAAPSPTPATDLPKGLLRPESAASLLAIPRRQKLLEHIWQRTSLSRKQFAILYRAPLE
CYAELVQQFPASEAHHHAYPGGMLDHGLEIVAYSLKLRQSHLLPIGANPEDQAAQSEAWTAAVAYAALLH
DIGKIAVDLHVELADGSTWHPWHGPLQQPYRFRYRDDREYRLHSAATGLLHHQLLDRQILDWLSGYPALW
GPLLYVLAGQYEHAGVLGELVVQADRASVALELGGDPARAMVAPKHALQRKLLDGLRYLLKEELKLNQPE
ASDGWLTEDGLWLVSKTVSDKLRAHLLSQGIDGIPANNTAVFNVLQDHGMLKPTPDGKAVWRATVISTTG
WSHSFTLLRLAPALIWESGERPAPFAGTVAIDATLAENDASAPATPPAVVMKPAQEDQGPRPWEGGSAAA
LAPPPTAHQALPDALEDMLTMVGMGDSSGTQQDAEVVSSMTPATRPEASMPAMVTVSPTSMPTAATSPST
ARPSGEHFMTWLQQGIASRRLIINDAKALVHTVSDTAYLVSPGVFQRYAQEHPQVGAFAKQENQQDWRWV
QKRFERLQLHRKQASGLNIWTCEVTGPRKSRKLHGYLLLQPQSVFGDVPPNNPYLAVLPT
MLSLFQRKRASVAAAPSPTPATDLPKGLLRPESAASLLAIPRRQKLLEHIWQRTSLSRKQFAILYRAPLE
CYAELVQQFPASEAHHHAYPGGMLDHGLEIVAYSLKLRQSHLLPIGANPEDQAAQSEAWTAAVAYAALLH
DIGKIAVDLHVELADGSTWHPWHGPLQQPYRFRYRDDREYRLHSAATGLLHHQLLDRQILDWLSGYPALW
GPLLYVLAGQYEHAGVLGELVVQADRASVALELGGDPARAMVAPKHALQRKLLDGLRYLLKEELKLNQPE
ASDGWLTEDGLWLVSKTVSDKLRAHLLSQGIDGIPANNTAVFNVLQDHGMLKPTPDGKAVWRATVISTTG
WSHSFTLLRLAPALIWESGERPAPFAGTVAIDATLAENDASAPATPPAVVMKPAQEDQGPRPWEGGSAAA
LAPPPTAHQALPDALEDMLTMVGMGDSSGTQQDAEVVSSMTPATRPEASMPAMVTVSPTSMPTAATSPST
ARPSGEHFMTWLQQGIASRRLIINDAKALVHTVSDTAYLVSPGVFQRYAQEHPQVGAFAKQENQQDWRWV
QKRFERLQLHRKQASGLNIWTCEVTGPRKSRKLHGYLLLQPQSVFGDVPPNNPYLAVLPT
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 16968 | GenBank | AYL28099 |
| Name | traD_DN073_01735_Tn6413 |
UniProt ID | _ |
| Length | 728 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 728 a.a. Molecular weight: 80922.65 Da Isoelectric Point: 7.3167
>AYL28099.1 conjugative coupling factor TraD, PFGI-1 class [Pseudomonas aeruginosa]
MSGKQPVEVLLRPAVEFYTVAACAGAAFLSLVAPWSLALSPAMGVGSALAFCAYGAIRYRDARVILRYRR
NIRRLPRYVMTSKDVPVSQQRLFVGRGFLWEQKHTHRLMQTYRPEFRRYVELTPAYRLARRLEERLEFAP
FPLSRLPALTGWDVSFNPVRPLPPVGGLPRLHGIEPDEVDVSLPLGERVGHSLVLGTTRVGKTRLAELFV
TQDIRRKNADGEHEVVIVIDPKGDADLLKRVYVEAKRAGREGEFYVFHLGWPDISARYNAVGRFGRISEV
ATRVAGQLSGEGNSAAFREFAWRFVNIIARALVELGQRPDYMLIQRHVINIDALFIEYAQHYFAKTEPKA
WEVIVQIEAKLNEKNIPRNMIGREKRVVALEQYLSQARNYDPVLDGLRSAVRYDKTYFDKIVASLLPLLE
KLTSGKISQLLAPNYSDLADPRPIFDWMQVIRKRAVVYVGLDALSDAEVAAAVGNSMFSDLVSVAGHIYK
HGIDDGLPGASAGTRVPINVHADEFNELMGDEFVPLINKGGGAGLQVTAYTQTLSDIEARIGNRAKAGQV
IGNFNNLFMLRVRETATAELLTRQLPKVEVYTTTIVSGATDSSDIRGATDFTSNTQDRISMSSVPMIEPS
HVVALPKGQCFALLQGGQLWKVRMPLPAPDPDEVMPQDLQQLAGYMRQSYSEATQWWEFTSSPVLQDTAL
PDDLLDEVATADAPASGTGDMARDEAAP
MSGKQPVEVLLRPAVEFYTVAACAGAAFLSLVAPWSLALSPAMGVGSALAFCAYGAIRYRDARVILRYRR
NIRRLPRYVMTSKDVPVSQQRLFVGRGFLWEQKHTHRLMQTYRPEFRRYVELTPAYRLARRLEERLEFAP
FPLSRLPALTGWDVSFNPVRPLPPVGGLPRLHGIEPDEVDVSLPLGERVGHSLVLGTTRVGKTRLAELFV
TQDIRRKNADGEHEVVIVIDPKGDADLLKRVYVEAKRAGREGEFYVFHLGWPDISARYNAVGRFGRISEV
ATRVAGQLSGEGNSAAFREFAWRFVNIIARALVELGQRPDYMLIQRHVINIDALFIEYAQHYFAKTEPKA
WEVIVQIEAKLNEKNIPRNMIGREKRVVALEQYLSQARNYDPVLDGLRSAVRYDKTYFDKIVASLLPLLE
KLTSGKISQLLAPNYSDLADPRPIFDWMQVIRKRAVVYVGLDALSDAEVAAAVGNSMFSDLVSVAGHIYK
HGIDDGLPGASAGTRVPINVHADEFNELMGDEFVPLINKGGGAGLQVTAYTQTLSDIEARIGNRAKAGQV
IGNFNNLFMLRVRETATAELLTRQLPKVEVYTTTIVSGATDSSDIRGATDFTSNTQDRISMSSVPMIEPS
HVVALPKGQCFALLQGGQLWKVRMPLPAPDPDEVMPQDLQQLAGYMRQSYSEATQWWEFTSSPVLQDTAL
PDDLLDEVATADAPASGTGDMARDEAAP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 362398..383974
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| DN073_01690 | 357499..358149 | + | 651 | AYL28090 | hypothetical protein | - |
| DN073_01695 | 358214..359335 | + | 1122 | AYL28091 | class I SAM-dependent methyltransferase | - |
| DN073_01700 | 359436..359747 | + | 312 | AYL28092 | hypothetical protein | - |
| DN073_01705 | 359885..362164 | + | 2280 | AYL28093 | DEAD/DEAH box helicase | - |
| DN073_01710 | 362398..362976 | + | 579 | AYL28094 | integrating conjugative element protein pill, pfgi-1 | tfc2 |
| DN073_01715 | 362973..363614 | + | 642 | AYL28095 | hypothetical protein | - |
| DN073_01720 | 363629..364366 | + | 738 | AYL28096 | TIGR03759 family integrating conjugative element protein | tfc3 |
| DN073_01725 | 364348..364953 | + | 606 | AYL28097 | lytic transglycosylase domain-containing protein | virB1 |
| DN073_01730 | 364950..365498 | + | 549 | AYL28098 | integrating conjugative element protein | tfc5 |
| DN073_01735 | 365503..367689 | + | 2187 | AYL28099 | conjugative coupling factor TraD, PFGI-1 class | - |
| DN073_01740 | 367686..368435 | + | 750 | AYL28100 | TIGR03747 family integrating conjugative element membrane protein | tfc7 |
| DN073_01745 | 368436..369806 | - | 1371 | AYL28101 | hypothetical protein | - |
| DN073_01750 | 369968..370348 | + | 381 | AYL28102 | RAQPRD family plasmid | tfc8 |
| DN073_01755 | 370345..370578 | + | 234 | AYL28103 | TIGR03758 family integrating conjugative element protein | tfc9 |
| DN073_01760 | 370595..370954 | + | 360 | AYL28104 | TIGR03745 family integrating conjugative element membrane protein | tfc10 |
| DN073_01765 | 370967..371377 | + | 411 | AYL28105 | TIGR03750 family conjugal transfer protein | tfc11 |
| DN073_01770 | 371374..372063 | + | 690 | AYL28106 | TIGR03746 family integrating conjugative element protein | tfc12 |
| DN073_01775 | 372060..372992 | + | 933 | AYL28107 | TIGR03749 family integrating conjugative element protein | tfc13 |
| DN073_01780 | 372982..374400 | + | 1419 | AYL28108 | TIGR03752 family integrating conjugative element protein | tfc14 |
| DN073_01785 | 374381..374821 | + | 441 | AYL33750 | TIGR03751 family conjugal transfer lipoprotein | tfc15 |
| DN073_01790 | 374821..377691 | + | 2871 | AYL28109 | conjugative transfer ATPase | virb4 |
| DN073_01795 | 377707..378459 | + | 753 | AYL28110 | disulfide bond formation protein DsbA | - |
| DN073_01800 | 378646..379140 | + | 495 | AYL28111 | DNA repair protein RadC | - |
| DN073_01805 | 379284..379730 | + | 447 | AYL28112 | TIGR03757 family integrating conjugative element protein | tfc24 |
| DN073_01810 | 379727..380674 | + | 948 | AYL28113 | TIGR03756 family integrating conjugative element protein | tfc23 |
| DN073_01815 | 380685..382079 | + | 1395 | AYL28114 | integrating conjugative element protein | tfc22 |
| DN073_01820 | 382076..382435 | + | 360 | AYL28115 | hypothetical protein | tfc18 |
| DN073_01825 | 382451..383974 | + | 1524 | AYL28116 | conjugal transfer protein TraG | tfc19 |
| DN073_01830 | 383981..384343 | - | 363 | AYL28117 | DUF3742 family protein | - |
| DN073_01835 | 384371..384829 | - | 459 | AYL28118 | type II toxin-antitoxin system YhaV family toxin | - |
| DN073_01840 | 384829..385146 | - | 318 | AYL28119 | AbrB family transcriptional regulator | - |
| DN073_01845 | 385458..387320 | + | 1863 | AYL28120 | relaxase | - |
| DN073_01850 | 387331..388065 | - | 735 | Protein_362 | DUF2130 domain-containing protein | - |
| DN073_01855 | 388098..388316 | - | 219 | AYL28121 | hypothetical protein | - |
Host bacterium
| ID | 362 | Element type | ICE (Integrative and conjugative element) |
| Element name | Tn6413 | GenBank | CP030075 |
| Element size | 6714842 bp | Coordinate of oriT [Strand] | 47353..47824 [-] |
| Host bacterium | Pseudomonas aeruginosa strain 6762 | Coordinate of element | 337873..451939 |
Cargo genes
| Drug resistance gene | aadA2, qacE, sul1, msr(E), mph(E), blaVIM-4, aac(6')-Il |
| Virulence gene | - |
| Metal resistance gene | merE, merD, merA, merP, merT, merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |