Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118919
Name   oriT_pSDM004 in_silico
Organism   Proteus mirabilis strain SDM004
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_ON843497 (49856..49904 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pSDM004
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11989 GenBank   WP_047665818
Name   traI_OTE98_RS00540_pSDM004 insolico UniProt ID   A0A0S1TL23
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190754.90 Da        Isoelectric Point: 6.3385

>WP_047665818.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKDAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDAFVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTGSSNMLTLKDREGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAMGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQLRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLTQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

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

(577-629)

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   14039 GenBank   WP_013023832
Name   traD_OTE98_RS00535_pSDM004 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 85974.10 Da        Isoelectric Point: 5.1149

>WP_013023832.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDYVEIGGNF

  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: 49298..78118

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OTE98_RS00325 44400..44612 + 213 WP_013023815 hypothetical protein -
OTE98_RS00330 44623..44847 + 225 WP_004152719 hypothetical protein -
OTE98_RS00335 44928..45248 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
OTE98_RS00340 45238..45516 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
OTE98_RS00345 45517..45930 + 414 WP_013023817 type II toxin-antitoxin system HigA family antitoxin -
OTE98_RS00350 46066..47274 - 1209 WP_015344990 IS256 family transposase -
OTE98_RS00355 48082..48903 + 822 WP_004152492 DUF932 domain-containing protein -
OTE98_RS00360 48936..49265 + 330 WP_011977736 DUF5983 family protein -
OTE98_RS00365 49298..49783 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
OTE98_RS00370 50215..50607 + 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
OTE98_RS00375 50837..51538 + 702 WP_004194113 hypothetical protein -
OTE98_RS00380 51624..51824 + 201 WP_004194116 TraY domain-containing protein -
OTE98_RS00385 51893..52261 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
OTE98_RS00390 52275..52580 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
OTE98_RS00395 52600..53166 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
OTE98_RS00400 53153..53893 + 741 WP_013023821 type-F conjugative transfer system secretin TraK traK
OTE98_RS00405 53893..55317 + 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
OTE98_RS00410 55431..56015 + 585 WP_013023822 type IV conjugative transfer system lipoprotein TraV traV
OTE98_RS00415 56147..56557 + 411 WP_009309869 hypothetical protein -
OTE98_RS00420 56663..56881 + 219 WP_015344987 hypothetical protein -
OTE98_RS00425 56882..57193 + 312 WP_015344986 hypothetical protein -
OTE98_RS00430 57260..57664 + 405 WP_004197817 hypothetical protein -
OTE98_RS00435 58040..58438 + 399 WP_013609531 hypothetical protein -
OTE98_RS00440 58510..61149 + 2640 WP_013023824 type IV secretion system protein TraC virb4
OTE98_RS00445 61149..61538 + 390 WP_004197815 type-F conjugative transfer system protein TrbI -
OTE98_RS00450 61538..62164 + 627 WP_009309871 type-F conjugative transfer system protein TraW traW
OTE98_RS00455 62206..62595 + 390 WP_004194992 hypothetical protein -
OTE98_RS00460 62592..63581 + 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
OTE98_RS00465 63594..64232 + 639 WP_011977786 type-F conjugative transfer system pilin assembly protein TrbC trbC
OTE98_RS00470 64291..66246 + 1956 WP_013023827 type-F conjugative transfer system mating-pair stabilization protein TraN traN
OTE98_RS00475 66278..66532 + 255 WP_004152674 conjugal transfer protein TrbE -
OTE98_RS00480 66510..66758 + 249 WP_004152675 hypothetical protein -
OTE98_RS00485 66771..67097 + 327 WP_004152676 hypothetical protein -
OTE98_RS00490 67118..67870 + 753 WP_048337413 type-F conjugative transfer system pilin assembly protein TraF traF
OTE98_RS00495 67881..68120 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
OTE98_RS00500 68092..68649 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
OTE98_RS00505 68695..69138 + 444 WP_013023828 F-type conjugal transfer protein TrbF -
OTE98_RS00510 69116..70495 + 1380 WP_014343487 conjugal transfer pilus assembly protein TraH traH
OTE98_RS00515 70495..73344 + 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
OTE98_RS00520 73347..73880 + 534 WP_014343486 conjugal transfer protein TraS -
OTE98_RS00525 74066..74797 + 732 WP_013023830 conjugal transfer complement resistance protein TraT -
OTE98_RS00530 74990..75679 + 690 WP_013023831 hypothetical protein -
OTE98_RS00535 75806..78118 + 2313 WP_013023832 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   19351 GenBank   NZ_ON843497
Plasmid name   pSDM004 Incompatibility group   IncFII
Plasmid size   135720 bp Coordinate of oriT [Strand]   49856..49904 [-]
Host baterium   Proteus mirabilis strain SDM004

Cargo genes

Drug resistance gene   aac(3)-IId, floR, tet(A), aac(6')-Ib-cr, ARR-3, dfrA27, aadA16, qacE, sul1, qnrB91, mph(A), aph(3')-Ia
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9