Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 104340 |
| Name | oriT_pNDM-IMP-2  |
| Organism | Klebsiella variicola strain SHET-01 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP050682 (89821..89870 [+], 50 nt) |
| oriT length | 50 nt |
| IRs (inverted repeats) | 7..14, 17..24 (GCAAAATT..AATTTTGC) |
| Location of nic site | 33..34 |
| Conserved sequence flanking the nic site |
GGTGTGGTGA |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 50 nt
>oriT_pNDM-IMP-2
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3177 | GenBank | WP_274757505 |
| Name | traI_HCO75_RS28615_pNDM-IMP-2 |
UniProt ID | _ |
| Length | 1753 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1753 a.a. Molecular weight: 190333.43 Da Isoelectric Point: 6.4385
>WP_274757505.1 conjugative transfer relaxase/helicase TraI [Klebsiella variicola]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
VVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYASQLAFGKIYREVLKPLTE
KLGYETEVTGKHGMWEFKGVPVEPFSTRTKEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVARQVP
FSDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAANNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGLLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QAQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPAQEKAIE
KALSEGETLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTVHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILE
PRNDRALKTADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAITGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
VVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYASQLAFGKIYREVLKPLTE
KLGYETEVTGKHGMWEFKGVPVEPFSTRTKEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVARQVP
FSDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAANNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGLLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTI
QAQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPAQEKAIE
KALSEGETLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTVHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILE
PRNDRALKTADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAITGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTL
GGD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 3091 | GenBank | WP_274757506 |
| Name | traD_HCO75_RS28620_pNDM-IMP-2 |
UniProt ID | _ |
| Length | 769 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 769 a.a. Molecular weight: 85824.81 Da Isoelectric Point: 5.0080
>WP_274757506.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLLYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDTPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRSLDARVDARLSALLEAREAEGSLARVLFTPDAPASGPADTDSHTGEQPEPITQPA
PAEVTVSPAPVKAPPTTKSPVAEPSVRATEPPVLRVTTVPLIKPKAATAAAAASTASSAVTPAAAAGGTE
QELAQQSAERGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHSRDEQDDVEIGGNF
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLLYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTVWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDTPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRSLDARVDARLSALLEAREAEGSLARVLFTPDAPASGPADTDSHTGEQPEPITQPA
PAEVTVSPAPVKAPPTTKSPVAEPSVRATEPPVLRVTTVPLIKPKAATAAAAASTASSAVTPAAAAGGTE
QELAQQSAERGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHSRDEQDDVEIGGNF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 61158..87434
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HCO75_RS28620 (HCO75_28915) | 61158..63467 | - | 2310 | WP_274757506 | type IV conjugative transfer system coupling protein TraD | virb4 |
| HCO75_RS28625 (HCO75_28920) | 63690..64376 | - | 687 | WP_145940812 | tetratricopeptide repeat protein | - |
| HCO75_RS28630 (HCO75_28925) | 64409..65047 | - | 639 | WP_145940811 | hypothetical protein | - |
| HCO75_RS28635 (HCO75_28930) | 65072..67924 | - | 2853 | WP_274757507 | conjugal transfer mating-pair stabilization protein TraG | traG |
| HCO75_RS28640 (HCO75_28935) | 67924..69273 | - | 1350 | WP_040107994 | conjugal transfer pilus assembly protein TraH | traH |
| HCO75_RS28645 (HCO75_28940) | 69739..70287 | - | 549 | WP_040107946 | hypothetical protein | - |
| HCO75_RS28650 (HCO75_28945) | 70277..70852 | - | 576 | WP_274757508 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| HCO75_RS28655 (HCO75_28950) | 70824..71063 | - | 240 | WP_004152687 | type-F conjugative transfer system pilin chaperone TraQ | - |
| HCO75_RS28660 (HCO75_28955) | 71074..71826 | - | 753 | WP_040107944 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| HCO75_RS28665 (HCO75_28960) | 71847..72173 | - | 327 | WP_040107943 | hypothetical protein | - |
| HCO75_RS28670 (HCO75_28965) | 72184..72411 | - | 228 | WP_040107941 | conjugal transfer protein TrbE | - |
| HCO75_RS28675 (HCO75_28970) | 72401..72682 | - | 282 | WP_040107939 | hypothetical protein | - |
| HCO75_RS28680 (HCO75_28975) | 72715..74670 | - | 1956 | WP_040107938 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| HCO75_RS28685 (HCO75_28980) | 74736..75374 | - | 639 | WP_040107937 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| HCO75_RS28690 (HCO75_28985) | 75387..76376 | - | 990 | WP_274757490 | conjugal transfer pilus assembly protein TraU | traU |
| HCO75_RS28695 (HCO75_28990) | 76373..76762 | - | 390 | WP_040107935 | hypothetical protein | - |
| HCO75_RS28700 (HCO75_28995) | 76804..77430 | - | 627 | WP_231669556 | type-F conjugative transfer system protein TraW | traW |
| HCO75_RS28705 (HCO75_29000) | 77430..77819 | - | 390 | WP_040107933 | type-F conjugative transfer system protein TrbI | - |
| HCO75_RS28710 (HCO75_29005) | 77819..80458 | - | 2640 | WP_040107932 | type IV secretion system protein TraC | virb4 |
| HCO75_RS28715 (HCO75_29010) | 80530..80928 | - | 399 | WP_162493351 | hypothetical protein | - |
| HCO75_RS28720 | 80936..81259 | - | 324 | WP_040107930 | hypothetical protein | - |
| HCO75_RS28725 (HCO75_29020) | 81302..81706 | - | 405 | WP_032740694 | hypothetical protein | - |
| HCO75_RS28730 (HCO75_29025) | 81773..82084 | - | 312 | WP_040107929 | hypothetical protein | - |
| HCO75_RS28735 (HCO75_29030) | 82085..82303 | - | 219 | WP_004195468 | hypothetical protein | - |
| HCO75_RS28740 (HCO75_29035) | 82327..82617 | - | 291 | WP_040107928 | hypothetical protein | - |
| HCO75_RS28745 | 82646..83044 | - | 399 | WP_227514785 | hypothetical protein | - |
| HCO75_RS28750 (HCO75_29045) | 83199..83768 | - | 570 | WP_071983369 | type IV conjugative transfer system lipoprotein TraV | traV |
| HCO75_RS28755 (HCO75_29050) | 83788..83949 | - | 162 | WP_158514515 | hypothetical protein | - |
| HCO75_RS28760 (HCO75_29055) | 83986..84399 | - | 414 | Protein_72 | conjugal transfer pilus-stabilizing protein TraP | - |
| HCO75_RS28765 (HCO75_29060) | 84392..85816 | - | 1425 | WP_040107926 | F-type conjugal transfer pilus assembly protein TraB | traB |
| HCO75_RS28770 (HCO75_29065) | 85816..86556 | - | 741 | WP_040107925 | type-F conjugative transfer system secretin TraK | traK |
| HCO75_RS28775 (HCO75_29070) | 86543..87109 | - | 567 | WP_040107924 | type IV conjugative transfer system protein TraE | traE |
| HCO75_RS28780 (HCO75_29075) | 87129..87434 | - | 306 | WP_004178059 | type IV conjugative transfer system protein TraL | traL |
| HCO75_RS28785 (HCO75_29080) | 87448..87816 | - | 369 | WP_040107923 | type IV conjugative transfer system pilin TraA | - |
| HCO75_RS28790 (HCO75_29085) | 87878..88084 | - | 207 | WP_172412524 | TraY domain-containing protein | - |
| HCO75_RS28795 (HCO75_29090) | 88217..88936 | - | 720 | WP_158514514 | conjugal transfer protein TrbJ | - |
| HCO75_RS28800 (HCO75_29095) | 89136..89552 | - | 417 | WP_074181767 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| HCO75_RS28805 (HCO75_29100) | 90015..90422 | + | 408 | WP_223170089 | transglycosylase SLT domain-containing protein | - |
| HCO75_RS28810 (HCO75_29105) | 90460..90990 | - | 531 | WP_023292160 | antirestriction protein | - |
Host bacterium
| ID | 4779 | GenBank | NZ_CP050682 |
| Plasmid name | pNDM-IMP-2 | Incompatibility group | IncFII |
| Plasmid size | 144371 bp | Coordinate of oriT [Strand] | 89821..89870 [+] |
| Host baterium | Klebsiella variicola strain SHET-01 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |