Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200418 |
| Name | oriT_Tn6954  |
| Organism | Alcaligenes faecalis strain GZAF3 prolyl aminopeptidase and tRNA (guanosine(46)-N7)-methyltransferase TrmB genes |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | KY623658 (51735..52206 [-], 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_Tn6954
GGGAACTGCTGGACCAACTCGGCGTAGCACTCCAGCGGAGCGCGATAGAGGATGGCGAACTGCTTGCGCGACAGCGATGTGCGCTGCCAGATGTGTTCCAGCAGCTTTTGCCGGCGCGGTATCGCCAGTAGGGATGCGGCCGACTCGGGCCGCAGCAGCCCTTTCGGAAGATCAGTGGCTGGCGTTGGCGACGGAGCGGCAGCGACCGAGGCCCGTTTTCGCTGGAACAGGGAGAGCATGAGGGTGTCCTGATGGCGGGCCGACCGGGAGGCCTTTTTGCTTTTTCGAGGTAGGGCCTTTCCCCTTGCACTCCATTCCCTTCCCCTTTCGGCCTTTTGGCCCTTAACAGCCTTTGGGTATAGGGCGCCAGGCGTTGATCGTCCACCACCAATGCGGGTTGCAGCGGGGCCGGATTGATGCGGGAAGGCGGGCTGTTCCCAGCCTACGATGGGCCGATTCTTGGACTCGGGAG
GGGAACTGCTGGACCAACTCGGCGTAGCACTCCAGCGGAGCGCGATAGAGGATGGCGAACTGCTTGCGCGACAGCGATGTGCGCTGCCAGATGTGTTCCAGCAGCTTTTGCCGGCGCGGTATCGCCAGTAGGGATGCGGCCGACTCGGGCCGCAGCAGCCCTTTCGGAAGATCAGTGGCTGGCGTTGGCGACGGAGCGGCAGCGACCGAGGCCCGTTTTCGCTGGAACAGGGAGAGCATGAGGGTGTCCTGATGGCGGGCCGACCGGGAGGCCTTTTTGCTTTTTCGAGGTAGGGCCTTTCCCCTTGCACTCCATTCCCTTCCCCTTTCGGCCTTTTGGCCCTTAACAGCCTTTGGGTATAGGGCGCCAGGCGTTGATCGTCCACCACCAATGCGGGTTGCAGCGGGGCCGGATTGATGCGGGAAGGCGGGCTGTTCCCAGCCTACGATGGGCCGATTCTTGGACTCGGGAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 14446 | GenBank | ASD48373 |
| Name | TraI_2_-_Tn6954 |
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
>ASD48373.1 relaxase [Alcaligenes faecalis]
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 | 16985 | GenBank | ASD48376 |
| Name | t4cp2_-_Tn6954 |
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
>ASD48376.1 conjugative coupling factor TraD, PFGI-1 class [Alcaligenes faecalis]
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: 28908..50484
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_26 | 23975..25030 | + | 1056 | ASD48364 | helicase | - |
| Locus_27 | 25629..27347 | + | 1719 | ASD48372 | group II intron reverse transcriptase/maturase | - |
| Locus_28 | 27415..28674 | + | 1260 | ASD48367 | DNA topoisomerase III | - |
| Locus_29 | 28908..29486 | + | 579 | ASD48340 | integrating conjugative element protein pill, pfgi-1 | tfc2 |
| Locus_30 | 29483..30124 | + | 642 | ASD48344 | hypothetical protein | - |
| Locus_31 | 30139..30876 | + | 738 | ASD48350 | integrating conjugative element protein | tfc3 |
| Locus_32 | 30858..31463 | + | 606 | ASD48343 | lytic transglycosylase | virB1 |
| Locus_33 | 31460..32008 | + | 549 | ASD48337 | integrating conjugative element protein | tfc5 |
| Locus_34 | 32013..34199 | + | 2187 | ASD48376 | conjugative coupling factor TraD, PFGI-1 class | - |
| Locus_35 | 34196..34945 | + | 750 | ASD48351 | integrating conjugative element membrane protein | tfc7 |
| Locus_36 | 34946..36316 | - | 1371 | ASD48399 | hypothetical protein | - |
| Locus_37 | 36478..36858 | + | 381 | ASD48325 | RAQPRD family plasmid | tfc8 |
| Locus_38 | 36855..37088 | + | 234 | ASD48315 | integrating conjugative element protein | tfc9 |
| Locus_39 | 37105..37464 | + | 360 | ASD48323 | integrating conjugative element membrane protein | tfc10 |
| Locus_40 | 37477..37887 | + | 411 | ASD48328 | hypothetical protein | tfc11 |
| Locus_41 | 37884..38573 | + | 690 | ASD48347 | integrating conjugative element protein | tfc12 |
| Locus_42 | 38570..39502 | + | 933 | ASD48360 | integrating conjugative element protein | tfc13 |
| Locus_43 | 39492..40910 | + | 1419 | ASD48369 | integrating conjugative element protein | tfc14 |
| Locus_44 | 40891..41331 | + | 441 | ASD48331 | conjugal transfer protein | tfc15 |
| Locus_45 | 41331..44201 | + | 2871 | ASD48378 | conjugative transfer ATPase | virb4 |
| Locus_46 | 44217..44969 | + | 753 | ASD48352 | disulfide bond formation protein DsbA | - |
| Locus_47 | 45156..45650 | + | 495 | ASD48334 | DNA repair protein RadC | - |
| Locus_48 | 45794..46240 | + | 447 | ASD48332 | integrating conjugative element protein | tfc24 |
| Locus_49 | 46237..47184 | + | 948 | ASD48361 | integrating conjugative element protein | tfc23 |
| Locus_50 | 47195..48589 | + | 1395 | ASD48368 | integrating conjugative element protein | tfc22 |
| Locus_51 | 48586..48945 | + | 360 | ASD48324 | hypothetical protein | tfc18 |
| Locus_52 | 48961..50484 | + | 1524 | ASD48370 | conjugal transfer protein TraG | tfc19 |
| Locus_53 | 50491..50853 | - | 363 | ASD48386 | hypothetical protein | - |
| Locus_54 | 50881..51339 | - | 459 | ASD48389 | toxin YhaV | - |
| Locus_55 | 51339..51656 | - | 318 | ASD48384 | AbrB family transcriptional regulator | - |
| Locus_56 | 51968..53830 | + | 1863 | ASD48373 | relaxase | - |
| Locus_57 | 53841..54422 | - | 582 | ASD48391 | hypothetical protein | - |
| Locus_58 | 54608..54808 | - | 201 | ASD48379 | hypothetical protein | - |
Host bacterium
| ID | 373 | Element type | ICE (Integrative and conjugative element) |
| Element name | Tn6954 | GenBank | KY623658 |
| Element size | 95872 bp | Coordinate of oriT [Strand] | 51735..52206 [-] |
| Host bacterium | Alcaligenes faecalis strain GZAF3 prolyl aminopeptidase and tRNA (guanosine(46)-N7)-methyltransferase TrmB genes | Coordinate of element | 1..95872 |
Cargo genes
| Drug resistance gene | ant(2'')-Ia, blaVIM-2, dfrA30, dfrB5, qacE, sul1 |
| Virulence gene | - |
| Metal resistance gene | merE, merD, merA, merP, merT, merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |