Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119838
Name   oriT_pKLVA-1 in_silico
Organism   Klebsiella variicola strain JCM 12419
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP024593 (134041..134089 [+], 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    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pKLVA-1
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12532 GenBank   WP_119867256
Name   traI_KI238_RS27300_pKLVA-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: 190170.76 Da        Isoelectric Point: 6.1710

>WP_119867256.1 conjugative transfer relaxase/helicase TraI [Klebsiella variicola]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTWIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGNIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKARSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIETTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMGRVPDSLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKNLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSDGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAITA
HGAQGASERYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMSRDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVAPVPQAGADILLPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)

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

(634-713)


  Protein structure



No available structure.




Auxiliary protein

ID   7096 GenBank   WP_020805752
Name   WP_020805752_pKLVA-1 insolico 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

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   14724 GenBank   WP_119867257
Name   traD_KI238_RS27305_pKLVA-1 insolico UniProt ID   _
Length   775 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 775 a.a.        Molecular weight: 86435.56 Da        Isoelectric Point: 5.0101

>WP_119867257.1 type IV conjugative transfer system coupling protein TraD [Klebsiella variicola]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSDQILADKYTVWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEAREAEGSLARVLFTPDAPASGPADTNSHAGEQPEPISQPA
PAEVTVSPAPVKAPPPTKMPAEEPSARAPASPPPEAPVLRVTTVPLIKPKAAAAAAAASTASSAVTPAAA
AGGTEQELAQQSAEQGPDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVE
IGGNF

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 106091..131661

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KI238_RS27305 (KLVA_52950) 106091..108418 - 2328 WP_119867257 type IV conjugative transfer system coupling protein TraD virb4
KI238_RS27310 (KLVA_52960) 108780..109511 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
KI238_RS27315 (KLVA_52980) 109924..110457 - 534 WP_114501468 hypothetical protein -
KI238_RS27320 (KLVA_52990) 110468..113311 - 2844 WP_119867258 conjugal transfer mating-pair stabilization protein TraG traG
KI238_RS27325 (KLVA_53000) 113311..114690 - 1380 WP_072198238 conjugal transfer pilus assembly protein TraH traH
KI238_RS27330 (KLVA_53010) 114668..115111 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
KI238_RS27335 (KLVA_53020) 115157..115714 - 558 WP_032441889 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KI238_RS27340 (KLVA_53030) 115686..115925 - 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
KI238_RS27345 (KLVA_53040) 115936..116688 - 753 WP_042934721 type-F conjugative transfer system pilin assembly protein TraF traF
KI238_RS27350 (KLVA_53050) 116709..117035 - 327 WP_064144773 hypothetical protein -
KI238_RS27355 (KLVA_53060) 117046..117273 - 228 WP_065808180 conjugal transfer protein TrbE -
KI238_RS27360 (KLVA_53070) 117263..117544 - 282 WP_064144771 hypothetical protein -
KI238_RS27365 (KLVA_53080) 117577..119532 - 1956 WP_119867267 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KI238_RS27370 (KLVA_53090) 119529..119912 - 384 WP_065808179 hypothetical protein -
KI238_RS27375 (KLVA_53100) 119909..120547 - 639 WP_065901066 type-F conjugative transfer system pilin assembly protein TrbC trbC
KI238_RS27380 (KLVA_53110) 120560..121519 - 960 WP_168712236 conjugal transfer pilus assembly protein TraU traU
KI238_RS27385 (KLVA_53120) 121563..122189 - 627 WP_065808176 type-F conjugative transfer system protein TraW traW
KI238_RS27390 (KLVA_53130) 122189..122578 - 390 WP_020326931 type-F conjugative transfer system protein TrbI -
KI238_RS27395 (KLVA_53140) 122578..125217 - 2640 WP_119867259 type IV secretion system protein TraC virb4
KI238_RS27400 125288..125686 - 399 WP_164078962 hypothetical protein -
KI238_RS27405 (KLVA_53150) 125694..125984 - 291 WP_119867261 hypothetical protein -
KI238_RS27410 (KLVA_53160) 125981..126385 - 405 WP_119867262 hypothetical protein -
KI238_RS27415 (KLVA_53170) 126452..126769 - 318 WP_023307544 hypothetical protein -
KI238_RS27420 (KLVA_53180) 126770..126988 - 219 WP_004171484 hypothetical protein -
KI238_RS27425 (KLVA_53190) 127012..127302 - 291 WP_032429299 hypothetical protein -
KI238_RS27430 127307..127717 - 411 WP_023292154 hypothetical protein -
KI238_RS27435 127849..128418 - 570 WP_032429300 type IV conjugative transfer system lipoprotein TraV traV
KI238_RS27440 (KLVA_53210) 128437..128622 - 186 WP_038990989 hypothetical protein -
KI238_RS27445 (KLVA_53220) 128619..130043 - 1425 WP_071080849 F-type conjugal transfer pilus assembly protein TraB traB
KI238_RS27450 (KLVA_53230) 130043..130783 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
KI238_RS27455 (KLVA_53240) 130770..131336 - 567 WP_020316627 type IV conjugative transfer system protein TraE traE
KI238_RS27460 (KLVA_53250) 131356..131661 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
KI238_RS27465 (KLVA_53260) 131675..132043 - 369 WP_049155512 type IV conjugative transfer system pilin TraA -
KI238_RS27470 132112..132312 - 201 WP_071080869 TraY domain-containing protein -
KI238_RS27475 (KLVA_53270) 132396..133100 - 705 WP_071080847 hypothetical protein -
KI238_RS27480 (KLVA_53280) 133338..133730 - 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
KI238_RS27485 (KLVA_53290) 134234..134641 + 408 WP_223170089 transglycosylase SLT domain-containing protein -
KI238_RS27490 (KLVA_53300) 134679..135209 - 531 WP_023292160 antirestriction protein -

Host bacterium

ID   20268 GenBank   NZ_AP024593
Plasmid name   pKLVA-1 Incompatibility group   IncFIB
Plasmid size   163252 bp Coordinate of oriT [Strand]   134041..134089 [+]
Host baterium   Klebsiella variicola strain JCM 12419

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsC, arsB, arsR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -