Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 106777 |
| Name | oriT_pCF1807-2  |
| Organism | Citrobacter freundii strain CF1807 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP110892 (210279..210383 [+], 105 nt) |
| oriT length | 105 nt |
| IRs (inverted repeats) | 56..61, 74..79 (TGGAAT..ATTCCA) 1..6, 8..13 (AATTTG..CAAATT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 105 nt
>oriT_pCF1807-2
AATTTGACAAATTCCAAAGATGGGTTAGCCTAGTGACAGAACTAGATTCCAATATTGGAATAATCAGCTTTAAATTCCAGATAGATAGTTATGTGGATAGGAATT
AATTTGACAAATTCCAAAGATGGGTTAGCCTAGTGACAGAACTAGATTCCAATATTGGAATAATCAGCTTTAAATTCCAGATAGATAGTTATGTGGATAGGAATT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 4515 | GenBank | WP_071687470 |
| Name | traD_OQW59_RS02200_pCF1807-2 |
UniProt ID | _ |
| Length | 688 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 688 a.a. Molecular weight: 78277.09 Da Isoelectric Point: 5.2390
>WP_071687470.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Citrobacter]
MSLNPRDLTQGGQVAFMRLKMFLQINNLISYYVIMGTVLFGLAVVLMRMSIQNLTNGIIYWFVRFMSPFT
ERMVSQPVYNIRYYEHTLQYSARQILSDNYTVYCGQLLKQELVIAGCASLLVAFLATLAVYWYLGRTGRQ
QSEDEIIGGRVLSESPKDVARLLKKRGEASDIRIDDLPLKLDSEIQNFAMHGTVSTGKSTLMRKILKQLR
DRGDLVIIYDKGCTFVEDFYDESRDEVLNALDSRCPNWDLWEECRTISELENASTTLIPASSGEDPFWQG
SARTIFAEGAERMRKDEGRSYNKFLRTLLAIQLDQLRAFLAGTPASTLVDGKIEKTAISIRSVLTNYVKA
MRYLQGIDRPGREKFTIREWMKGQADKSKNGWLFITSDEQNHESLKPLISLWLSIAATSLLAMGPNRQRR
VWFFYDELASLHKLSTLPRIISEARKFGGCFALGFQNFAQMENIYGPKGAAEIFDLLNTKFFFRSPSAQI
AKFVEEDIGETRRLKFSEQTSFGHEQVRDGISFGKEEERVSIVSYSDVQSLNDLQCFVTLPGSYPVVKLT
MKYDAMPKVADALLLRDVQTSLDKNIEDELVRRTEEERLSLDGLFTPVTPVPESASASSGGTERDIEQDL
PREMPPGLNGDGEVVDFAAYEAWEQGQHQTRDMTRREEVNINHATDKTHEIDGDREVY
MSLNPRDLTQGGQVAFMRLKMFLQINNLISYYVIMGTVLFGLAVVLMRMSIQNLTNGIIYWFVRFMSPFT
ERMVSQPVYNIRYYEHTLQYSARQILSDNYTVYCGQLLKQELVIAGCASLLVAFLATLAVYWYLGRTGRQ
QSEDEIIGGRVLSESPKDVARLLKKRGEASDIRIDDLPLKLDSEIQNFAMHGTVSTGKSTLMRKILKQLR
DRGDLVIIYDKGCTFVEDFYDESRDEVLNALDSRCPNWDLWEECRTISELENASTTLIPASSGEDPFWQG
SARTIFAEGAERMRKDEGRSYNKFLRTLLAIQLDQLRAFLAGTPASTLVDGKIEKTAISIRSVLTNYVKA
MRYLQGIDRPGREKFTIREWMKGQADKSKNGWLFITSDEQNHESLKPLISLWLSIAATSLLAMGPNRQRR
VWFFYDELASLHKLSTLPRIISEARKFGGCFALGFQNFAQMENIYGPKGAAEIFDLLNTKFFFRSPSAQI
AKFVEEDIGETRRLKFSEQTSFGHEQVRDGISFGKEEERVSIVSYSDVQSLNDLQCFVTLPGSYPVVKLT
MKYDAMPKVADALLLRDVQTSLDKNIEDELVRRTEEERLSLDGLFTPVTPVPESASASSGGTERDIEQDL
PREMPPGLNGDGEVVDFAAYEAWEQGQHQTRDMTRREEVNINHATDKTHEIDGDREVY
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 62421..86899
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| OQW59_RS02030 (OQW59_02025) | 58777..59211 | + | 435 | WP_114141097 | conjugation system SOS inhibitor PsiB | - |
| OQW59_RS02035 (OQW59_02030) | 59208..59936 | + | 729 | WP_265970002 | plasmid SOS inhibition protein A | - |
| OQW59_RS02040 (OQW59_02035) | 59933..60259 | + | 327 | WP_265970003 | theronine dehydrogenase | - |
| OQW59_RS02045 (OQW59_02040) | 60370..60825 | + | 456 | WP_131341794 | conjugation system SOS inhibitor PsiB family protein | - |
| OQW59_RS02050 (OQW59_02045) | 60841..61143 | - | 303 | WP_127663649 | hypothetical protein | - |
| OQW59_RS02055 (OQW59_02050) | 61278..61487 | + | 210 | WP_071687494 | hypothetical protein | - |
| OQW59_RS02060 (OQW59_02055) | 61506..61628 | + | 123 | WP_256259396 | hypothetical protein | - |
| OQW59_RS02065 (OQW59_02060) | 61880..62410 | + | 531 | WP_071687493 | antirestriction protein | - |
| OQW59_RS02070 (OQW59_02065) | 62421..62876 | - | 456 | WP_071687492 | transglycosylase SLT domain-containing protein | virB1 |
| OQW59_RS02075 (OQW59_02070) | 63345..63728 | + | 384 | WP_071687491 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| OQW59_RS02080 (OQW59_02075) | 64235..64516 | + | 282 | WP_071687490 | conjugal transfer protein TraJ | - |
| OQW59_RS02085 (OQW59_02080) | 64733..64900 | + | 168 | WP_164845037 | hypothetical protein | - |
| OQW59_RS02090 (OQW59_02085) | 65006..65365 | + | 360 | WP_071687489 | type IV conjugative transfer system pilin TraA | - |
| OQW59_RS02095 (OQW59_02090) | 65368..65673 | + | 306 | WP_071687511 | type IV conjugative transfer system protein TraL | traL |
| OQW59_RS02100 (OQW59_02095) | 65693..66256 | + | 564 | WP_071687488 | type IV conjugative transfer system protein TraE | traE |
| OQW59_RS02105 (OQW59_02100) | 66246..66986 | + | 741 | WP_071687487 | type-F conjugative transfer system secretin TraK | traK |
| OQW59_RS02110 (OQW59_02105) | 66973..68334 | + | 1362 | WP_265970005 | F-type conjugal transfer pilus assembly protein TraB | traB |
| OQW59_RS02115 (OQW59_02110) | 68446..68670 | + | 225 | WP_071687485 | TraR/DksA C4-type zinc finger protein | - |
| OQW59_RS02120 (OQW59_02115) | 68719..68859 | + | 141 | WP_250323569 | hypothetical protein | - |
| OQW59_RS02125 (OQW59_02120) | 68843..69259 | + | 417 | WP_071687483 | hypothetical protein | - |
| OQW59_RS02130 (OQW59_02125) | 69268..69702 | + | 435 | WP_224776423 | hypothetical protein | - |
| OQW59_RS02135 (OQW59_02130) | 69720..70361 | + | 642 | WP_071687481 | type IV conjugative transfer system lipoprotein TraV | traV |
| OQW59_RS02140 (OQW59_02135) | 70372..72963 | + | 2592 | WP_265970008 | type IV secretion system protein TraC | virb4 |
| OQW59_RS02145 (OQW59_02140) | 72960..73424 | + | 465 | WP_071687479 | type-F conjugative transfer system protein TrbI | - |
| OQW59_RS02150 (OQW59_02145) | 73424..74059 | + | 636 | WP_071687478 | type-F conjugative transfer system protein TraW | traW |
| OQW59_RS02155 (OQW59_02150) | 74056..75051 | + | 996 | WP_071687477 | conjugal transfer pilus assembly protein TraU | traU |
| OQW59_RS02160 (OQW59_02155) | 75070..75684 | + | 615 | WP_071687476 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| OQW59_RS02165 (OQW59_02160) | 75681..77510 | + | 1830 | WP_265970012 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| OQW59_RS02170 (OQW59_02165) | 77507..78283 | + | 777 | WP_265970013 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| OQW59_RS02175 (OQW59_02170) | 78308..78919 | + | 612 | WP_071446641 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| OQW59_RS02180 (OQW59_02175) | 78919..80280 | + | 1362 | WP_071687474 | conjugal transfer pilus assembly protein TraH | traH |
| OQW59_RS02185 (OQW59_02180) | 80282..83176 | + | 2895 | WP_071687473 | conjugal transfer mating-pair stabilization protein TraG | traG |
| OQW59_RS02190 (OQW59_02185) | 83186..83761 | + | 576 | WP_071687472 | conjugal transfer protein TraS | - |
| OQW59_RS02195 (OQW59_02190) | 83945..84682 | + | 738 | WP_071687471 | conjugal transfer complement resistance protein TraT | - |
| OQW59_RS02200 (OQW59_02195) | 84833..86899 | + | 2067 | WP_071687470 | type IV conjugative transfer system coupling protein TraD | virb4 |
| OQW59_RS02205 (OQW59_02200) | 86899..89868 | + | 2970 | Protein_123 | MobF family relaxase | - |
Host bacterium
| ID | 7214 | GenBank | NZ_CP110892 |
| Plasmid name | pCF1807-2 | Incompatibility group | IncA/C2 |
| Plasmid size | 211224 bp | Coordinate of oriT [Strand] | 210279..210383 [+] |
| Host baterium | Citrobacter freundii strain CF1807 |
Cargo genes
| Drug resistance gene | blaNDM-1, aac(3)-IId, blaTEM-1B |
| Virulence gene | htpB |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |