Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105256
Name   oriT_pRHBSTW-00167_4 in_silico
Organism   Klebsiella michiganensis strain RHBSTW-00167
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058121 (28844..28892 [-], 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-00167_4
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3606 GenBank   WP_181250934
Name   traI_HV105_RS31545_pRHBSTW-00167_4 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: 190657.39 Da        Isoelectric Point: 6.1568

>WP_181250934.1 conjugative transfer relaxase/helicase TraI [Klebsiella michiganensis]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQIFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIAFGKIYQNTLRADVES
LGYRTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTSDASVVRQAPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRNEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGNHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPDSLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)

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

(576-628)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   1615 GenBank   WP_087829209
Name   WP_087829209_pRHBSTW-00167_4 insolico UniProt ID   _
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14907.97 Da        Isoelectric Point: 4.5248

>WP_087829209.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure



No available structure.




T4CP

ID   3569 GenBank   WP_228761939
Name   traD_HV105_RS31540_pRHBSTW-00167_4 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85659.79 Da        Isoelectric Point: 5.2446

>WP_228761939.1 type IV conjugative transfer system coupling protein TraD [Klebsiella michiganensis]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFIFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPDDAGSHAGEQPEPVSQPA
PAVMTVTPAPVKSPPTTKRPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAGTAATASSAGTPAAAAGGTE
QVLAQQSAEQGQAMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDLEIGGNF

  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: 31306..57080

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV105_RS31340 (HV105_31340) 26492..26839 + 348 WP_022644944 hypothetical protein -
HV105_RS31345 (HV105_31345) 26932..27078 + 147 WP_022644943 hypothetical protein -
HV105_RS32195 27126..27362 + 237 Protein_39 SAM-dependent DNA methyltransferase -
HV105_RS31350 (HV105_31350) 27336..27518 - 183 WP_071562612 hypothetical protein -
HV105_RS31355 (HV105_31355) 27711..28253 + 543 WP_022644941 antirestriction protein -
HV105_RS31360 (HV105_31360) 28277..28759 - 483 WP_022644940 transglycosylase SLT domain-containing protein -
HV105_RS31365 (HV105_31365) 29204..29593 + 390 WP_087829209 conjugal transfer relaxosome DNA-binding protein TraM -
HV105_RS31370 (HV105_31370) 29832..30506 + 675 WP_095033684 hypothetical protein -
HV105_RS31375 (HV105_31375) 30698..30862 + 165 WP_032444506 TraY domain-containing protein -
HV105_RS31380 (HV105_31380) 30924..31292 + 369 WP_087829211 type IV conjugative transfer system pilin TraA -
HV105_RS31385 (HV105_31385) 31306..31611 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HV105_RS31390 (HV105_31390) 31631..32197 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
HV105_RS31395 (HV105_31395) 32184..32924 + 741 WP_020804840 type-F conjugative transfer system secretin TraK traK
HV105_RS31400 (HV105_31400) 32924..34348 + 1425 WP_023316397 F-type conjugal transfer pilus assembly protein TraB traB
HV105_RS31405 (HV105_31405) 34341..34937 + 597 WP_023316398 conjugal transfer pilus-stabilizing protein TraP -
HV105_RS31410 (HV105_31410) 34960..35529 + 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
HV105_RS31415 (HV105_31415) 35661..36071 + 411 WP_023316400 hypothetical protein -
HV105_RS31420 (HV105_31420) 36076..36360 + 285 WP_023316401 hypothetical protein -
HV105_RS31425 (HV105_31425) 36384..36602 + 219 WP_023316402 hypothetical protein -
HV105_RS31430 (HV105_31430) 36603..36914 + 312 WP_023316403 hypothetical protein -
HV105_RS31435 (HV105_31435) 36981..37385 + 405 WP_023316404 hypothetical protein -
HV105_RS31440 (HV105_31440) 37382..37672 + 291 WP_181250933 hypothetical protein -
HV105_RS31445 (HV105_31445) 37680..38078 + 399 WP_072156904 hypothetical protein -
HV105_RS31450 (HV105_31450) 38150..40789 + 2640 WP_020323518 type IV secretion system protein TraC virb4
HV105_RS31455 (HV105_31455) 40789..41178 + 390 WP_020314627 type-F conjugative transfer system protein TrbI -
HV105_RS31460 (HV105_31460) 41178..41804 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
HV105_RS31465 (HV105_31465) 41848..42807 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
HV105_RS31470 (HV105_31470) 42820..43458 + 639 WP_020321224 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV105_RS31475 (HV105_31475) 43517..45472 + 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV105_RS31480 (HV105_31480) 45505..45786 + 282 WP_022644736 hypothetical protein -
HV105_RS31485 (HV105_31485) 45776..46003 + 228 WP_012540032 conjugal transfer protein TrbE -
HV105_RS31490 (HV105_31490) 46014..46340 + 327 WP_020323521 hypothetical protein -
HV105_RS31495 (HV105_31495) 46361..47113 + 753 WP_023316406 type-F conjugative transfer system pilin assembly protein TraF traF
HV105_RS31500 (HV105_31500) 47568..47807 + 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
HV105_RS31505 (HV105_31505) 47779..48336 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV105_RS31510 (HV105_31510) 48382..48825 + 444 WP_020804675 F-type conjugal transfer protein TrbF -
HV105_RS31515 (HV105_31515) 48803..50182 + 1380 WP_162495503 conjugal transfer pilus assembly protein TraH traH
HV105_RS31520 (HV105_31520) 50182..53031 + 2850 WP_032744228 conjugal transfer mating-pair stabilization protein TraG traG
HV105_RS31525 (HV105_31525) 53037..53564 + 528 WP_020803849 hypothetical protein -
HV105_RS32200 53747..54415 + 669 WP_020803846 hypothetical protein -
HV105_RS31535 (HV105_31535) 54439..54699 + 261 WP_020803850 hypothetical protein -
HV105_RS31540 (HV105_31540) 54771..57080 + 2310 WP_228761939 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5694 GenBank   NZ_CP058121
Plasmid name   pRHBSTW-00167_4 Incompatibility group   -
Plasmid size   67562 bp Coordinate of oriT [Strand]   28844..28892 [-]
Host baterium   Klebsiella michiganensis strain RHBSTW-00167

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -