Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105232
Name   oriT_pRHBSTW-00634_3 in_silico
Organism   Klebsiella grimontii strain RHBSTW-00634
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056684 (95178..95226 [-], 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_pRHBSTW-00634_3
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3594 GenBank   WP_075606914
Name   traI_HV252_RS29985_pRHBSTW-00634_3 insolico UniProt ID   A0A6M3HIK1
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190386.65 Da        Isoelectric Point: 5.5084

>WP_075606914.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTNNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADTRAKELASAPAAPVKTDVPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
KPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDTAVVRQSPF
SDAVSVLAQDRPTMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLSADARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKMSLKETLSMLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKSEGVLGEKDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLTVAEGERLAVLGKIPDTRLKGGESVTVLKAEEGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQGTARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIASQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
SQIQAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDNVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQVTPEQVPRKDGAWVPENSVVEFTPAQEEAIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKSTRTLNPKADQAQQHIDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESAYVGLSRMKQHVQVYTDNREGWIKAINNSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1432-1552)

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

(577-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1157)

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

(634-713)


  Protein structure



No available structure.




Auxiliary protein

ID   1609 GenBank   WP_020805752
Name   WP_020805752_pRHBSTW-00634_3 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   3554 GenBank   WP_075606915
Name   traD_HV252_RS29980_pRHBSTW-00634_3 insolico UniProt ID   _
Length   772 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 772 a.a.        Molecular weight: 86712.47 Da        Isoelectric Point: 5.0825

>WP_075606915.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLILMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGKSLEYNSEQILADKYTIWCGEQLWTSFVFAAIVSLTVCIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKHSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDIWRECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFSEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLKNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKSRPKIAEGFILRNLDTRTDARLDTLLEAREAESSHARTLFTPDAPAPELAEKDEKVGNPPEQSQPAE
SSGTPATVKVPSTAKTPEADESGQSPEVSNPAALLTKVVTVPLTRPRPAAATGTAAVASATDVRATPAGG
TEQALETQPAEQGQDMLPPGVNEYGEIDDMHAWDEWQSGEQTQRDMQRREEVNINHSHRRDEQDDIEIGG
NF

  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: 94611..123855

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV252_RS29775 (HV252_29785) 89801..90676 + 876 WP_060415463 DUF4942 domain-containing protein -
HV252_RS29780 (HV252_29790) 91456..91794 + 339 WP_020804855 hypothetical protein -
HV252_RS29785 (HV252_29795) 91851..92198 + 348 WP_064182675 hypothetical protein -
HV252_RS29790 (HV252_29800) 92287..92517 + 231 WP_060415465 hypothetical protein -
HV252_RS29795 (HV252_29805) 92564..93397 + 834 WP_060415466 N-6 DNA methylase -
HV252_RS29800 (HV252_29810) 93683..94051 - 369 WP_080848162 hypothetical protein -
HV252_RS29805 (HV252_29815) 94046..94588 + 543 WP_060415467 antirestriction protein -
HV252_RS29810 (HV252_29820) 94611..95033 - 423 WP_073972322 transglycosylase SLT domain-containing protein virB1
HV252_RS29815 (HV252_29825) 95537..95929 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
HV252_RS32640 96167..96868 + 702 WP_223174962 hypothetical protein -
HV252_RS29825 (HV252_29835) 96954..97154 + 201 WP_048289787 TraY domain-containing protein -
HV252_RS29830 (HV252_29840) 97223..97591 + 369 WP_064343525 type IV conjugative transfer system pilin TraA -
HV252_RS29835 (HV252_29845) 97605..97910 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
HV252_RS29840 (HV252_29850) 97926..98492 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
HV252_RS29845 (HV252_29855) 98479..99213 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
HV252_RS29850 (HV252_29860) 99213..100634 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
HV252_RS29855 (HV252_29865) 100627..101061 + 435 WP_020322358 conjugal transfer protein TraP -
HV252_RS29860 (HV252_29870) 101095..101679 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
HV252_RS29865 (HV252_29875) 102292..102480 + 189 WP_053390286 hypothetical protein -
HV252_RS32645 102564..102965 + 402 WP_064343532 hypothetical protein -
HV252_RS29875 (HV252_29885) 102962..103261 + 300 WP_053390308 hypothetical protein -
HV252_RS29880 (HV252_29890) 103349..103732 + 384 WP_042946290 hypothetical protein -
HV252_RS29885 (HV252_29895) 103825..106464 + 2640 WP_064343533 type IV secretion system protein TraC virb4
HV252_RS29890 (HV252_29900) 106464..106856 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
HV252_RS29895 (HV252_29905) 106853..107479 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
HV252_RS29900 (HV252_29910) 107523..108482 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
HV252_RS29905 (HV252_29915) 108495..109142 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV252_RS29910 (HV252_29920) 109139..109522 + 384 WP_053390297 hypothetical protein -
HV252_RS29915 (HV252_29925) 109519..111474 + 1956 WP_064359956 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV252_RS29920 (HV252_29930) 111506..111766 + 261 WP_053390216 hypothetical protein -
HV252_RS29925 (HV252_29935) 111759..112370 + 612 WP_053390217 hypothetical protein -
HV252_RS29930 (HV252_29940) 112360..112602 + 243 WP_053390218 conjugal transfer protein TrbE -
HV252_RS29935 (HV252_29945) 112648..112974 + 327 WP_053390219 hypothetical protein -
HV252_RS29940 (HV252_29950) 112995..113747 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
HV252_RS29945 (HV252_29955) 113758..113994 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
HV252_RS29950 (HV252_29960) 113969..114529 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV252_RS29955 (HV252_29965) 114516..115886 + 1371 WP_075606918 conjugal transfer pilus assembly protein TraH traH
HV252_RS29960 (HV252_29970) 115886..118765 + 2880 WP_064386194 conjugal transfer mating-pair stabilization protein TraG traG
HV252_RS29965 (HV252_29975) 118782..119450 + 669 WP_128317877 hypothetical protein -
HV252_RS29970 (HV252_29980) 119803..120534 + 732 WP_064386198 conjugal transfer complement resistance protein TraT -
HV252_RS32650 120726..121418 + 693 WP_202395549 hypothetical protein -
HV252_RS29980 (HV252_29990) 121537..123855 + 2319 WP_075606915 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5670 GenBank   NZ_CP056684
Plasmid name   pRHBSTW-00634_3 Incompatibility group   IncFII
Plasmid size   134986 bp Coordinate of oriT [Strand]   95178..95226 [-]
Host baterium   Klebsiella grimontii strain RHBSTW-00634

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merR, merT, merP, merC, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -