Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 104964 |
| Name | oriT_pNB5_3  |
| Organism | Klebsiella pneumoniae strain NB5 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP092654 (142273..142322 [+], 50 nt) |
| oriT length | 50 nt |
| IRs (inverted repeats) | 7..14, 17..24 (GCAAAATT..AATTTTGC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 50 nt
>oriT_pNB5_3
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3489 | GenBank | WP_004153029 |
| Name | traI_MJ642_RS02420_pNB5_3 |
UniProt ID | A0A422WEA5 |
| Length | 1753 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1753 a.a. Molecular weight: 190808.90 Da Isoelectric Point: 6.2081
>WP_004153029.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRLVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKKAEQTAREMAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRLVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKKAEQTAREMAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 3438 | GenBank | WP_004152630 |
| Name | traD_MJ642_RS02425_pNB5_3 |
UniProt ID | _ |
| Length | 769 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 769 a.a. Molecular weight: 85951.02 Da Isoelectric Point: 5.0632
>WP_004152630.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIPRRLDTRVDARLSALLEEREAEGSLARALFTPDAPASGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAAEPSVRATEPPVLRVTTVPLIKPKAAAAAAAASTASSAGIPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIPRRLDTRVDARLSALLEEREAEGSLARALFTPDAPASGPADTDSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAAEPSVRATEPPVLRVTTVPLIKPKAAAAAAAASTASSAGIPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 112619..142880
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| MJ642_RS02425 | 112619..114928 | - | 2310 | WP_004152630 | type IV conjugative transfer system coupling protein TraD | virb4 |
| MJ642_RS02430 | 115288..116019 | - | 732 | WP_004152629 | conjugal transfer complement resistance protein TraT | - |
| MJ642_RS02435 | 116209..116736 | - | 528 | WP_004153030 | hypothetical protein | - |
| MJ642_RS02440 | 116880..117577 | + | 698 | WP_095033700 | IS1-like element IS1B family transposase | - |
| MJ642_RS02445 | 117588..120368 | - | 2781 | WP_137922717 | conjugal transfer mating-pair stabilization protein TraG | traG |
| MJ642_RS02450 | 120368..121738 | - | 1371 | WP_004178055 | conjugal transfer pilus assembly protein TraH | traH |
| MJ642_RS02455 | 121725..122153 | - | 429 | WP_004152689 | hypothetical protein | - |
| MJ642_RS02460 | 122146..122718 | - | 573 | WP_004152688 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| MJ642_RS02465 | 122690..122929 | - | 240 | WP_004152687 | type-F conjugative transfer system pilin chaperone TraQ | - |
| MJ642_RS02470 | 122940..123692 | - | 753 | WP_004152686 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| MJ642_RS02475 | 123713..124039 | - | 327 | WP_004152685 | hypothetical protein | - |
| MJ642_RS29245 | 124085..124270 | - | 186 | WP_004152684 | hypothetical protein | - |
| MJ642_RS02480 | 124267..124503 | - | 237 | WP_004152683 | conjugal transfer protein TrbE | - |
| MJ642_RS02485 | 124535..126490 | - | 1956 | WP_004153093 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| MJ642_RS02490 | 126538..127176 | - | 639 | WP_004152682 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| MJ642_RS02495 | 127189..128148 | - | 960 | WP_015065634 | conjugal transfer pilus assembly protein TraU | traU |
| MJ642_RS02500 | 128192..128818 | - | 627 | WP_004152590 | type-F conjugative transfer system protein TraW | traW |
| MJ642_RS02505 | 128818..129207 | - | 390 | WP_004152591 | type-F conjugative transfer system protein TrbI | - |
| MJ642_RS02510 | 129207..131846 | - | 2640 | WP_004152592 | type IV secretion system protein TraC | virb4 |
| MJ642_RS02515 | 131918..132316 | - | 399 | WP_004153071 | hypothetical protein | - |
| MJ642_RS02520 | 132612..133016 | - | 405 | WP_004152594 | hypothetical protein | - |
| MJ642_RS02525 | 133083..133400 | - | 318 | WP_004152595 | hypothetical protein | - |
| MJ642_RS02530 | 133401..133619 | - | 219 | WP_004171484 | hypothetical protein | - |
| MJ642_RS02535 | 133643..133933 | - | 291 | WP_004152596 | hypothetical protein | - |
| MJ642_RS02540 | 133938..134348 | - | 411 | WP_004152597 | lipase chaperone | - |
| MJ642_RS02545 | 134480..135049 | - | 570 | WP_004152598 | type IV conjugative transfer system lipoprotein TraV | traV |
| MJ642_RS02550 | 135072..135668 | - | 597 | WP_004152599 | conjugal transfer pilus-stabilizing protein TraP | - |
| MJ642_RS02555 | 135661..137086 | - | 1426 | Protein_140 | F-type conjugal transfer pilus assembly protein TraB | - |
| MJ642_RS02560 | 137086..137826 | - | 741 | WP_004152601 | type-F conjugative transfer system secretin TraK | traK |
| MJ642_RS02565 | 137813..138379 | - | 567 | WP_004152602 | type IV conjugative transfer system protein TraE | traE |
| MJ642_RS02570 | 138399..138704 | - | 306 | WP_004178059 | type IV conjugative transfer system protein TraL | traL |
| MJ642_RS02575 | 138718..139086 | - | 369 | WP_004178060 | type IV conjugative transfer system pilin TraA | - |
| MJ642_RS02580 | 139140..139511 | - | 372 | WP_004208838 | TraY domain-containing protein | - |
| MJ642_RS02585 | 139595..140290 | - | 696 | WP_004178061 | transcriptional regulator TraJ family protein | - |
| MJ642_RS02590 | 140504..140662 | - | 159 | Protein_147 | relaxosome protein TraM | - |
| MJ642_RS02595 | 140695..141663 | + | 969 | WP_072198477 | IS5 family transposase | - |
| MJ642_RS02600 | 141725..141967 | - | 243 | Protein_149 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| MJ642_RS02605 | 142395..142880 | + | 486 | WP_004178063 | transglycosylase SLT domain-containing protein | virB1 |
| MJ642_RS02610 | 142913..143242 | - | 330 | WP_011977736 | DUF5983 family protein | - |
| MJ642_RS02615 | 143275..144096 | - | 822 | WP_004178064 | DUF932 domain-containing protein | - |
| MJ642_RS02620 | 144930..145343 | - | 414 | WP_004152722 | helix-turn-helix domain-containing protein | - |
| MJ642_RS02625 | 145344..145622 | - | 279 | WP_004152721 | helix-turn-helix transcriptional regulator | - |
| MJ642_RS02630 | 145612..145932 | - | 321 | WP_004152720 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| MJ642_RS02635 | 146013..146237 | - | 225 | WP_004152719 | hypothetical protein | - |
| MJ642_RS02640 | 146248..146460 | - | 213 | WP_004152718 | hypothetical protein | - |
| MJ642_RS02645 | 146521..146877 | - | 357 | WP_004152717 | hypothetical protein | - |
| MJ642_RS02650 | 147513..147863 | - | 351 | WP_137922726 | hypothetical protein | - |
Host bacterium
| ID | 5402 | GenBank | NZ_CP092654 |
| Plasmid name | pNB5_3 | Incompatibility group | IncFIB |
| Plasmid size | 171047 bp | Coordinate of oriT [Strand] | 142273..142322 [+] |
| Host baterium | Klebsiella pneumoniae strain NB5 |
Cargo genes
| Drug resistance gene | aph(3')-Ia, mph(A) |
| Virulence gene | - |
| Metal resistance gene | silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIE9 |