Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 110309 |
| Name | oriT_pLDNY1  |
| Organism | Fluoribacter dumoffii NY 23 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CM001374 (28854..28886 [+], 33 nt) |
| oriT length | 33 nt |
| IRs (inverted repeats) | 3..9, 13..19 (ACGTTGC..GCAACGT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 33 nt
>oriT_pLDNY1
GCACGTTGCAACGCAACGTATAAGCGCGCACTT
GCACGTTGCAACGCAACGTATAAGCGCGCACTT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 7646 | GenBank | WP_081466373 |
| Name | traD_KYQ_RS18480_pLDNY1 |
UniProt ID | _ |
| Length | 621 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 621 a.a. Molecular weight: 70581.77 Da Isoelectric Point: 6.8930
>WP_081466373.1 type IV conjugative transfer system coupling protein TraD [Fluoribacter dumoffii]
MRKQPNFKHYTRGGIISFHNVRMWDQITLTLMFLCLFLWVILTGIITWLVISAENLHQAIAYYYALFLSL
VGQKHTFALSFHGKEYHQSVEAILHYPYYAENAKHVINSLGRATLSAFAVAFLSGLGIAIYFIKRGKEQS
ESQFVRGSQLKNSNEVKKQILHDKAHSDITIDTFPLIKDSEVQHVLVHGTVGTGKSQLIMKIMDCLRKRG
DRVIVYDKGCSFIPHYYQDDSDVILNPFDKRCANWDMWLEAPRDSDFENMAESSIPMHGESDPFWVNASR
TVFSCLGSVMRHHSDRSVEKLLKLILTDEFSDLEEYLQGTPAATLVSSKIEKTAISIRATLTSYLKSFSA
LADLNQEGKPPFSIRDYILDEQQKGWLFISSNGETHKSLKPLISMWLAQASLALLSLAPDRNRRIWFICD
ELPSLHKLPLLGETIAEVRKFGGCFLLGMQSFSQLTKVYGQAGGREIFDLLNTRFFFRSPSSDMARLVAS
ELGEEEIEESRENYSYGANSIRDGISLGAQRVTRPIVSYPQIMELKDLHCFVRLPGHYPITQLTLDLGFR
TIKTNGFIERNMPTTFNFSQLTSIDEDWESGTDGHVGSKQPNKNKINAEHLCIEELNLESL
MRKQPNFKHYTRGGIISFHNVRMWDQITLTLMFLCLFLWVILTGIITWLVISAENLHQAIAYYYALFLSL
VGQKHTFALSFHGKEYHQSVEAILHYPYYAENAKHVINSLGRATLSAFAVAFLSGLGIAIYFIKRGKEQS
ESQFVRGSQLKNSNEVKKQILHDKAHSDITIDTFPLIKDSEVQHVLVHGTVGTGKSQLIMKIMDCLRKRG
DRVIVYDKGCSFIPHYYQDDSDVILNPFDKRCANWDMWLEAPRDSDFENMAESSIPMHGESDPFWVNASR
TVFSCLGSVMRHHSDRSVEKLLKLILTDEFSDLEEYLQGTPAATLVSSKIEKTAISIRATLTSYLKSFSA
LADLNQEGKPPFSIRDYILDEQQKGWLFISSNGETHKSLKPLISMWLAQASLALLSLAPDRNRRIWFICD
ELPSLHKLPLLGETIAEVRKFGGCFLLGMQSFSQLTKVYGQAGGREIFDLLNTRFFFRSPSSDMARLVAS
ELGEEEIEESRENYSYGANSIRDGISLGAQRVTRPIVSYPQIMELKDLHCFVRLPGHYPITQLTLDLGFR
TIKTNGFIERNMPTTFNFSQLTSIDEDWESGTDGHVGSKQPNKNKINAEHLCIEELNLESL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 7435..25407
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| KYQ_RS16965 | 2459..3163 | + | 705 | WP_019350370 | methyltransferase domain-containing protein | - |
| KYQ_RS16970 | 3156..4094 | + | 939 | WP_019350371 | queuosine precursor transporter | - |
| KYQ_RS16975 | 4066..4758 | - | 693 | WP_019350372 | helix-turn-helix transcriptional regulator | - |
| KYQ_RS16980 | 4911..5153 | + | 243 | WP_019350373 | TraY domain-containing protein | - |
| KYQ_RS18695 | 5131..6222 | + | 1092 | WP_019350374 | replication protein | - |
| KYQ_RS16990 | 6273..7016 | + | 744 | WP_019350375 | complement resistance protein TraT | - |
| KYQ_RS16995 | 7134..7421 | + | 288 | WP_019350376 | hypothetical protein | - |
| KYQ_RS17000 | 7435..7731 | + | 297 | WP_012187514 | type IV conjugative transfer system protein TraL | traL |
| KYQ_RS17005 | 7742..8311 | + | 570 | WP_012187515 | type IV conjugative transfer system protein TraE | traE |
| KYQ_RS17010 | 8304..9023 | + | 720 | WP_019350377 | type-F conjugative transfer system secretin TraK | traK |
| KYQ_RS17015 | 9016..10389 | + | 1374 | WP_019350378 | TrbI/VirB10 family protein | traB |
| KYQ_RS17020 | 10449..10676 | + | 228 | WP_231294685 | conjugal transfer protein | traV |
| KYQ_RS17025 | 10667..13264 | + | 2598 | WP_019350380 | type IV secretion system protein TraC | virb4 |
| KYQ_RS17030 | 13255..13590 | + | 336 | WP_019350381 | type-F conjugative transfer system protein TrbI | - |
| KYQ_RS17035 | 13587..14222 | + | 636 | WP_029489086 | type-F conjugative transfer system protein TraW | traW |
| KYQ_RS17040 | 14212..15195 | + | 984 | WP_019350383 | conjugal transfer pilus assembly protein TraU | traU |
| KYQ_RS17045 | 15208..15630 | + | 423 | WP_019350384 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| KYQ_RS17050 | 15623..17311 | + | 1689 | WP_019350385 | conjugal transfer protein TraN | traN |
| KYQ_RS17055 | 17304..18053 | + | 750 | WP_019350386 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| KYQ_RS17060 | 18050..18559 | + | 510 | WP_231294687 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| KYQ_RS17065 | 18559..19923 | + | 1365 | WP_019350388 | conjugal transfer protein TraH | traH |
| KYQ_RS17070 | 19934..22747 | + | 2814 | WP_019350389 | conjugal transfer mating-pair stabilization protein TraG | traG |
| KYQ_RS17075 | 22749..23549 | + | 801 | WP_019350390 | hypothetical protein | - |
| KYQ_RS18480 | 23542..25407 | + | 1866 | WP_081466373 | type IV conjugative transfer system coupling protein TraD | virb4 |
| KYQ_RS17085 | 25492..26109 | - | 618 | WP_019350392 | hypothetical protein | - |
| KYQ_RS17090 | 26119..28923 | - | 2805 | WP_231294689 | Ti-type conjugative transfer relaxase TraA | - |
| KYQ_RS18485 | 29013..29303 | + | 291 | WP_012187532 | hypothetical protein | - |
| KYQ_RS19220 | 29324..29581 | + | 258 | WP_035749192 | hypothetical protein | - |
| KYQ_RS18490 | 29589..29828 | + | 240 | WP_035749195 | hypothetical protein | - |
Host bacterium
| ID | 10744 | GenBank | NZ_CM001374 |
| Plasmid name | pLDNY1 | Incompatibility group | - |
| Plasmid size | 81759 bp | Coordinate of oriT [Strand] | 28854..28886 [+] |
| Host baterium | Fluoribacter dumoffii NY 23 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIB |