Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103824 |
| Name | oriT_pR85_2-2  |
| Organism | Klebsiella pneumoniae strain Nord9_R85 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP091585 (21704..21752 [+], 49 nt) |
| oriT length | 49 nt |
| IRs (inverted repeats) | 6..13, 16..23 (GCAAAATT..AATTTTGC) |
| Location of nic site | 32..33 |
| Conserved sequence flanking the nic site |
GGTGTGGTGA |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 49 nt
>oriT_pR85_2-2
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Auxiliary protein
| ID | 1185 | GenBank | WP_020805752 |
| Name | WP_020805752_pR85_2-2 |
UniProt ID | A0A377TIM3 |
| Length | 130 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 130 a.a. Molecular weight: 14772.81 Da Isoelectric Point: 4.5715
>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A377TIM3 |
T4CP
| ID | 2662 | GenBank | WP_032454979 |
| Name | traD_L5468_RS29330_pR85_2-2 |
UniProt ID | _ |
| Length | 770 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 770 a.a. Molecular weight: 86062.11 Da Isoelectric Point: 5.0175
>WP_032454979.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKRPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDEVEIGGNF
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKRPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDEVEIGGNF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2949..22310
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| L5468_RS28735 (L5468_28740) | 1..1105 | - | 1105 | Protein_0 | conjugal transfer protein TraG N-terminal domain-containing protein | - |
| L5468_RS28740 (L5468_28745) | 1105..2483 | - | 1379 | Protein_1 | conjugal transfer pilus assembly protein TraH | - |
| L5468_RS28745 (L5468_28750) | 2461..2904 | - | 444 | Protein_2 | F-type conjugal transfer protein TrbF | - |
| L5468_RS28750 (L5468_28755) | 2949..3506 | - | 558 | WP_004152678 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| L5468_RS28755 (L5468_28760) | 3478..3717 | - | 240 | WP_004144400 | type-F conjugative transfer system pilin chaperone TraQ | - |
| L5468_RS28760 (L5468_28765) | 3728..4480 | - | 753 | WP_009309874 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| L5468_RS28765 (L5468_28770) | 4501..4827 | - | 327 | WP_004194451 | hypothetical protein | - |
| L5468_RS28770 (L5468_28775) | 4840..5088 | - | 249 | WP_004152675 | hypothetical protein | - |
| L5468_RS28775 (L5468_28780) | 5066..5320 | - | 255 | WP_004195500 | conjugal transfer protein TrbE | - |
| L5468_RS28780 (L5468_28785) | 5352..7307 | - | 1956 | WP_009309873 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| L5468_RS28785 (L5468_28790) | 7366..8004 | - | 639 | WP_004193871 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| L5468_RS28790 (L5468_28795) | 8017..9006 | - | 990 | WP_009309872 | conjugal transfer pilus assembly protein TraU | traU |
| L5468_RS28795 (L5468_28800) | 9003..9392 | - | 390 | WP_004194992 | hypothetical protein | - |
| L5468_RS28800 (L5468_28805) | 9434..10060 | - | 627 | WP_004152507 | type-F conjugative transfer system protein TraW | traW |
| L5468_RS28805 (L5468_28810) | 10060..10449 | - | 390 | WP_004167468 | type-F conjugative transfer system protein TrbI | - |
| L5468_RS28810 (L5468_28815) | 10446..13088 | - | 2643 | WP_032454974 | type IV secretion system protein TraC | virb4 |
| L5468_RS28815 (L5468_28820) | 13160..13558 | - | 399 | WP_074184101 | hypothetical protein | - |
| L5468_RS28820 (L5468_28825) | 13936..14340 | - | 405 | WP_004197817 | hypothetical protein | - |
| L5468_RS28825 (L5468_28830) | 14407..14718 | - | 312 | WP_004195240 | hypothetical protein | - |
| L5468_RS28830 (L5468_28835) | 14719..14937 | - | 219 | WP_004195235 | hypothetical protein | - |
| L5468_RS28835 (L5468_28840) | 15043..15453 | - | 411 | WP_004152499 | hypothetical protein | - |
| L5468_RS28840 (L5468_28845) | 15585..16169 | - | 585 | WP_032441881 | type IV conjugative transfer system lipoprotein TraV | traV |
| L5468_RS28845 (L5468_28850) | 16283..17706 | - | 1424 | Protein_22 | F-type conjugal transfer pilus assembly protein TraB | - |
| L5468_RS28850 (L5468_28855) | 17706..18446 | - | 741 | WP_013214019 | type-F conjugative transfer system secretin TraK | traK |
| L5468_RS28855 (L5468_28860) | 18433..18999 | - | 567 | WP_004144423 | type IV conjugative transfer system protein TraE | traE |
| L5468_RS28860 (L5468_28865) | 19019..19324 | - | 306 | WP_004178059 | type IV conjugative transfer system protein TraL | traL |
| L5468_RS28865 (L5468_28870) | 19338..19706 | - | 369 | WP_020316649 | type IV conjugative transfer system pilin TraA | - |
| L5468_RS29685 | 19775..19975 | - | 201 | WP_050442686 | TraY domain-containing protein | - |
| L5468_RS28870 (L5468_28875) | 20059..20763 | - | 705 | WP_050442685 | hypothetical protein | - |
| L5468_RS28875 (L5468_28880) | 21001..21393 | - | 393 | WP_020805752 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| L5468_RS28880 (L5468_28885) | 21825..22310 | + | 486 | WP_001568108 | transglycosylase SLT domain-containing protein | virB1 |
| L5468_RS28885 (L5468_28890) | 22343..22672 | - | 330 | WP_011977736 | DUF5983 family protein | - |
| L5468_RS28890 (L5468_28895) | 22705..23526 | - | 822 | WP_032454971 | DUF932 domain-containing protein | - |
| L5468_RS28895 (L5468_28900) | 24342..24741 | - | 400 | Protein_33 | hypothetical protein | - |
Region 2: 105681..122258
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| L5468_RS29330 (L5468_29335) | 105681..107993 | - | 2313 | WP_032454979 | type IV conjugative transfer system coupling protein TraD | virb4 |
| L5468_RS29335 (L5468_29340) | 108120..108809 | - | 690 | WP_013023831 | hypothetical protein | - |
| L5468_RS29340 (L5468_29345) | 109002..109733 | - | 732 | WP_013023830 | conjugal transfer complement resistance protein TraT | - |
| L5468_RS29345 (L5468_29350) | 109924..110451 | - | 528 | Protein_124 | conjugal transfer protein TraS | - |
| L5468_RS29350 (L5468_29355) | 110454..113303 | - | 2850 | WP_237437286 | conjugal transfer mating-pair stabilization protein TraG | traG |
| L5468_RS29355 (L5468_29360) | 113303..114682 | - | 1380 | WP_011977731 | conjugal transfer pilus assembly protein TraH | traH |
| L5468_RS29360 (L5468_29365) | 114660..115103 | - | 444 | WP_015065638 | F-type conjugal transfer protein TrbF | - |
| L5468_RS29365 (L5468_29370) | 115148..115705 | - | 558 | WP_004152678 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| L5468_RS29370 (L5468_29375) | 115677..115916 | - | 240 | WP_004144400 | type-F conjugative transfer system pilin chaperone TraQ | - |
| L5468_RS29375 (L5468_29380) | 115927..116679 | - | 753 | WP_009309874 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| L5468_RS29380 (L5468_29385) | 116700..117026 | - | 327 | WP_004194451 | hypothetical protein | - |
| L5468_RS29385 (L5468_29390) | 117039..117287 | - | 249 | WP_004152675 | hypothetical protein | - |
| L5468_RS29390 (L5468_29395) | 117265..117519 | - | 255 | WP_004195500 | conjugal transfer protein TrbE | - |
| L5468_RS29395 (L5468_29400) | 117551..119505 | - | 1955 | Protein_134 | type-F conjugative transfer system mating-pair stabilization protein TraN | - |
| L5468_RS29400 (L5468_29405) | 119564..120202 | - | 639 | WP_004193871 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| L5468_RS29405 (L5468_29410) | 120215..121204 | - | 990 | WP_009309872 | conjugal transfer pilus assembly protein TraU | traU |
| L5468_RS29410 (L5468_29415) | 121201..121590 | - | 390 | WP_004194992 | hypothetical protein | - |
| L5468_RS29415 (L5468_29420) | 121632..122258 | - | 627 | WP_004152507 | type-F conjugative transfer system protein TraW | traW |
| L5468_RS29420 (L5468_29425) | 122258..122647 | - | 390 | WP_004167468 | type-F conjugative transfer system protein TrbI | - |
| L5468_RS29425 (L5468_29430) | 122644..123504 | - | 861 | Protein_140 | type IV secretion system protein TraC | - |
| L5468_RS29430 (L5468_29435) | 123687..124386 | - | 700 | Protein_141 | DUF5934 domain-containing protein | - |
Host bacterium
| ID | 4264 | GenBank | NZ_CP091585 |
| Plasmid name | pR85_2-2 | Incompatibility group | IncFII |
| Plasmid size | 124386 bp | Coordinate of oriT [Strand] | 21704..21752 [+] |
| Host baterium | Klebsiella pneumoniae strain Nord9_R85 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |