Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120728
Name   oriT_pKqq_U41_1 in_silico
Organism   Klebsiella quasipneumoniae subsp. quasipneumoniae strain U41
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084790 (166696..166745 [+], 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    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pKqq_U41_1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13068 GenBank   WP_136071125
Name   traI_LGM24_RS27515_pKqq_U41_1 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190712.63 Da        Isoelectric Point: 6.1403

>WP_136071125.1 conjugative transfer relaxase/helicase TraI [Klebsiella quasipneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELLEAAGPDASLKSRDVAALDTRKSKEAIDPAENMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETAMVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLLEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRIWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(970-1156)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(634-713)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)


  Protein structure



No available structure.




T4CP

ID   15337 GenBank   WP_136071126
Name   traD_LGM24_RS27520_pKqq_U41_1 insolico UniProt ID   _
Length   754 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 754 a.a.        Molecular weight: 84334.28 Da        Isoelectric Point: 5.0560

>WP_136071126.1 type IV conjugative transfer system coupling protein TraD [Klebsiella quasipneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPAEVTV
SPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQGQDMLP
AGMNEDGVIEDMQAYAAWLADEQTQRDMQRREEVNINHNHRHDEQDDVEIGGNI

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 136904..167303

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LGM24_RS27520 (LGM24_27520) 136904..139168 - 2265 WP_136071126 type IV conjugative transfer system coupling protein TraD virb4
LGM24_RS27525 (LGM24_27525) 139526..140257 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
LGM24_RS27530 (LGM24_27530) 140447..140974 - 528 WP_029498351 conjugal transfer protein TraS -
LGM24_RS27535 (LGM24_27535) 140980..143829 - 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
LGM24_RS27540 (LGM24_27540) 143829..145208 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
LGM24_RS27545 (LGM24_27545) 145186..145629 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
LGM24_RS27550 (LGM24_27550) 145675..146232 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LGM24_RS27555 (LGM24_27555) 146204..146443 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
LGM24_RS27560 (LGM24_27560) 146454..147206 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
LGM24_RS27565 (LGM24_27565) 147227..147553 - 327 WP_029498361 hypothetical protein -
LGM24_RS27570 (LGM24_27570) 147566..147814 - 249 WP_004152675 hypothetical protein -
LGM24_RS27575 (LGM24_27575) 147792..148046 - 255 WP_015065558 conjugal transfer protein TrbE -
LGM24_RS27580 (LGM24_27580) 148078..150033 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LGM24_RS27585 (LGM24_27585) 150092..150739 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
LGM24_RS27590 (LGM24_27590) 150818..150994 - 177 WP_162866177 hypothetical protein -
LGM24_RS27595 (LGM24_27595) 151015..152004 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
LGM24_RS27600 (LGM24_27600) 152001..152402 - 402 WP_023158005 hypothetical protein -
LGM24_RS27605 (LGM24_27605) 152437..153072 - 636 WP_020325113 type-F conjugative transfer system protein TraW traW
LGM24_RS27610 (LGM24_27610) 153072..153461 - 390 WP_029498365 type-F conjugative transfer system protein TrbI -
LGM24_RS27615 (LGM24_27615) 153461..156100 - 2640 WP_029498367 type IV secretion system protein TraC virb4
LGM24_RS27620 (LGM24_27620) 156172..156570 - 399 WP_023158008 hypothetical protein -
LGM24_RS29955 156578..156772 - 195 WP_327021880 hypothetical protein -
LGM24_RS27625 (LGM24_27625) 156754..157734 - 981 WP_048293623 IS5-like element ISKpn26 family transposase -
LGM24_RS27630 (LGM24_27630) 157775..158167 - 393 WP_226650004 hypothetical protein -
LGM24_RS27635 (LGM24_27635) 158210..158614 - 405 WP_016831042 hypothetical protein -
LGM24_RS27640 (LGM24_27640) 158681..158992 - 312 WP_016831041 hypothetical protein -
LGM24_RS27645 (LGM24_27645) 158993..159211 - 219 WP_014386199 hypothetical protein -
LGM24_RS27650 (LGM24_27650) 159235..159524 - 290 Protein_174 hypothetical protein -
LGM24_RS27655 (LGM24_27655) 159529..159939 - 411 WP_016831039 hypothetical protein -
LGM24_RS27660 (LGM24_27660) 160071..160655 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
LGM24_RS27665 (LGM24_27665) 160678..161274 - 597 WP_029498374 conjugal transfer pilus-stabilizing protein TraP -
LGM24_RS27670 (LGM24_27670) 161267..162691 - 1425 WP_136071134 F-type conjugal transfer pilus assembly protein TraB traB
LGM24_RS27675 (LGM24_27675) 162691..163431 - 741 WP_029498376 type-F conjugative transfer system secretin TraK traK
LGM24_RS27680 (LGM24_27680) 163418..163984 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
LGM24_RS27685 (LGM24_27685) 164004..164309 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LGM24_RS27690 (LGM24_27690) 164323..164691 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LGM24_RS27695 (LGM24_27695) 164753..164959 - 207 WP_171773970 TraY domain-containing protein -
LGM24_RS27700 (LGM24_27700) 165092..165811 - 720 WP_014386192 conjugal transfer protein -
LGM24_RS27705 (LGM24_27705) 166011..166427 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
LGM24_RS27710 (LGM24_27710) 166818..167303 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
LGM24_RS27715 (LGM24_27715) 167336..167665 - 330 WP_011977736 DUF5983 family protein -
LGM24_RS27720 (LGM24_27720) 167698..168519 - 822 WP_023316395 DUF932 domain-containing protein -
LGM24_RS27725 (LGM24_27725) 169441..170730 - 1290 WP_136070812 ISL3-like element ISPpu12 family transposase -
LGM24_RS27730 (LGM24_27730) 170752..171264 - 513 WP_004863699 signal peptidase II -
LGM24_RS27735 (LGM24_27735) 171268..172164 - 897 WP_004574643 cation transporter -

Host bacterium

ID   21157 GenBank   NZ_CP084790
Plasmid name   pKqq_U41_1 Incompatibility group   IncFIB
Plasmid size   205084 bp Coordinate of oriT [Strand]   166696..166745 [+]
Host baterium   Klebsiella quasipneumoniae subsp. quasipneumoniae strain U41

Cargo genes

Drug resistance gene   sul1, qacE, aadA2
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, merR, merT, merP, merC, merA, merD, merE, merR2, merF
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9