Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101776
Name   oriT_pA6sk3_5 in_silico
Organism   Klebsiella michiganensis strain CPE6
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JACYGP010000009 (55102..55151 [+], 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_pA6sk3_5
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1492 GenBank   WP_075606914
Name   traI_IY146_RS28985_pA6sk3_5 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   596 GenBank   WP_053390193
Name   WP_053390193_pA6sk3_5 insolico UniProt ID   A0A8G2A327
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14883.89 Da        Isoelectric Point: 4.3779

>WP_053390193.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEVADKINAIVEKRRVEGAKDKDISFSSISTMLLELGLRVYEAQMERKESGFNQMAFNKAL
LESVIKTQFTVNKVLGIECLSPHVSGNPRWEWPGLIENIRDDVQEVMLRFFPDEESEDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   1169 GenBank   WP_075606915
Name   traD_IY146_RS28990_pA6sk3_5 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: 26434..52690

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IY146_RS28990 26434..28752 - 2319 WP_075606915 type IV conjugative transfer system coupling protein TraD virb4
IY146_RS29740 28871..29563 - 693 WP_202395549 hypothetical protein -
IY146_RS29000 29755..30486 - 732 WP_064386198 conjugal transfer complement resistance protein TraT -
IY146_RS29005 30845..31513 - 669 WP_128317877 hypothetical protein -
IY146_RS29010 31530..34409 - 2880 WP_064386194 conjugal transfer mating-pair stabilization protein TraG traG
IY146_RS29015 34409..35779 - 1371 WP_075606918 conjugal transfer pilus assembly protein TraH traH
IY146_RS29020 35766..36326 - 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IY146_RS29025 36301..36537 - 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
IY146_RS29030 36548..37300 - 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
IY146_RS29035 37321..37647 - 327 WP_053390219 hypothetical protein -
IY146_RS29040 37693..37935 - 243 WP_053390218 conjugal transfer protein TrbE -
IY146_RS29045 37925..38536 - 612 WP_053390217 hypothetical protein -
IY146_RS29050 38529..38789 - 261 WP_053390216 hypothetical protein -
IY146_RS29055 38821..40776 - 1956 WP_064343537 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IY146_RS29060 40773..41156 - 384 WP_053390297 hypothetical protein -
IY146_RS29065 41153..41800 - 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
IY146_RS29070 41813..42772 - 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
IY146_RS29075 42816..43442 - 627 WP_064343535 type-F conjugative transfer system protein TraW traW
IY146_RS29080 43439..43831 - 393 WP_064343534 type-F conjugative transfer system protein TrbI -
IY146_RS29085 43831..46470 - 2640 WP_064343533 type IV secretion system protein TraC virb4
IY146_RS29090 46563..46946 - 384 WP_042946290 hypothetical protein -
IY146_RS29095 47034..47333 - 300 WP_053390308 hypothetical protein -
IY146_RS29745 47330..47731 - 402 WP_064343532 hypothetical protein -
IY146_RS29105 47815..48003 - 189 WP_053390286 hypothetical protein -
IY146_RS29110 48616..49200 - 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
IY146_RS29115 49234..49668 - 435 WP_020322358 conjugal transfer protein TraP -
IY146_RS29120 49661..51082 - 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
IY146_RS29125 51082..51816 - 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
IY146_RS29130 51803..52369 - 567 WP_064359954 type IV conjugative transfer system protein TraE traE
IY146_RS29135 52385..52690 - 306 WP_064343526 type IV conjugative transfer system protein TraL traL
IY146_RS29140 52704..53072 - 369 WP_064386081 type IV conjugative transfer system pilin TraA -
IY146_RS29145 53137..53298 - 162 WP_172686697 TraY domain-containing protein -
IY146_RS29150 53459..54160 - 702 WP_094898581 hypothetical protein -
IY146_RS29155 54398..54790 - 393 WP_053390193 conjugal transfer relaxosome DNA-binding protein TraM -
IY146_RS29160 55296..55718 + 423 WP_077268549 transglycosylase SLT domain-containing protein -
IY146_RS29165 55741..56283 - 543 WP_053390246 antirestriction protein -

Host bacterium

ID   2220 GenBank   NZ_JACYGP010000009
Plasmid name   pA6sk3_5 Incompatibility group   IncFII
Plasmid size   102823 bp Coordinate of oriT [Strand]   55102..55151 [+]
Host baterium   Klebsiella michiganensis strain CPE6

Cargo genes

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