Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115077
Name   oriT_pSMBC50-107K in_silico
Organism   Serratia marcescens strain SMBC50
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP109830 (55571..55619 [-], 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_pSMBC50-107K
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9648 GenBank   WP_064291677
Name   traI_OHZ00_RS26445_pSMBC50-107K insolico UniProt ID   A0A6I4Y321
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190676.77 Da        Isoelectric Point: 6.3386

>WP_064291677.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKDAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTGSSNMLTLKDREGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
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   11256 GenBank   WP_072101984
Name   traD_OHZ00_RS26440_pSMBC50-107K 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: 85967.95 Da        Isoelectric Point: 5.0577

>WP_072101984.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIS
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPASGPADTDSHASEQPEPVSPPA
PAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLTDEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 55013..83485

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OHZ00_RS26230 (OHZ00_26260) 50038..50388 + 351 WP_023287104 hypothetical protein -
OHZ00_RS26235 (OHZ00_26265) 51020..51376 + 357 WP_019706019 hypothetical protein -
OHZ00_RS26240 (OHZ00_26270) 51437..51649 + 213 WP_019706020 hypothetical protein -
OHZ00_RS26245 (OHZ00_26275) 51660..51884 + 225 WP_014343499 hypothetical protein -
OHZ00_RS26250 (OHZ00_26280) 51965..52285 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
OHZ00_RS26255 (OHZ00_26285) 52275..52553 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
OHZ00_RS26260 (OHZ00_26290) 52554..52967 + 414 WP_069985713 type II toxin-antitoxin system HigA family antitoxin -
OHZ00_RS26265 (OHZ00_26295) 53797..54618 + 822 WP_023287138 DUF932 domain-containing protein -
OHZ00_RS26270 (OHZ00_26300) 54651..54980 + 330 WP_071994324 DUF5983 family protein -
OHZ00_RS26275 (OHZ00_26305) 55013..55498 - 486 WP_032440470 transglycosylase SLT domain-containing protein virB1
OHZ00_RS26280 (OHZ00_26310) 55930..56322 + 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
OHZ00_RS26285 (OHZ00_26315) 56552..57253 + 702 WP_004194113 hypothetical protein -
OHZ00_RS26290 (OHZ00_26320) 57338..57538 + 201 WP_004194116 TraY domain-containing protein -
OHZ00_RS26295 (OHZ00_26325) 57607..57975 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
OHZ00_RS26300 (OHZ00_26330) 57989..58294 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
OHZ00_RS26305 (OHZ00_26335) 58314..58880 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
OHZ00_RS26310 (OHZ00_26340) 58867..59607 + 741 WP_013023821 type-F conjugative transfer system secretin TraK traK
OHZ00_RS26315 (OHZ00_26345) 59607..61031 + 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
OHZ00_RS26320 (OHZ00_26350) 61104..61688 + 585 WP_032440547 type IV conjugative transfer system lipoprotein TraV traV
OHZ00_RS26325 (OHZ00_26355) 62011..62229 + 219 WP_004195468 hypothetical protein -
OHZ00_RS26330 (OHZ00_26360) 62230..62541 + 312 WP_029497417 hypothetical protein -
OHZ00_RS26335 (OHZ00_26365) 62608..63012 + 405 WP_004197817 hypothetical protein -
OHZ00_RS26340 (OHZ00_26370) 63391..63789 + 399 WP_023179972 hypothetical protein -
OHZ00_RS26345 (OHZ00_26375) 63861..66500 + 2640 WP_013214024 type IV secretion system protein TraC virb4
OHZ00_RS26350 (OHZ00_26380) 66500..66889 + 390 WP_004167468 type-F conjugative transfer system protein TrbI -
OHZ00_RS26355 (OHZ00_26385) 66889..67524 + 636 WP_029497419 type-F conjugative transfer system protein TraW traW
OHZ00_RS26360 (OHZ00_26390) 67559..67960 + 402 WP_004194979 hypothetical protein -
OHZ00_RS26365 (OHZ00_26395) 67957..68946 + 990 WP_029497420 conjugal transfer pilus assembly protein TraU traU
OHZ00_RS26370 (OHZ00_26400) 68959..69597 + 639 WP_069985712 type-F conjugative transfer system pilin assembly protein TrbC trbC
OHZ00_RS26375 (OHZ00_26405) 69656..71611 + 1956 WP_030003482 type-F conjugative transfer system mating-pair stabilization protein TraN traN
OHZ00_RS26380 (OHZ00_26410) 71643..71897 + 255 WP_004152674 conjugal transfer protein TrbE -
OHZ00_RS26385 (OHZ00_26415) 71875..72123 + 249 WP_004152675 hypothetical protein -
OHZ00_RS26390 (OHZ00_26420) 72136..72462 + 327 WP_004152676 hypothetical protein -
OHZ00_RS26395 (OHZ00_26425) 72483..73235 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
OHZ00_RS26400 (OHZ00_26430) 73246..73485 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
OHZ00_RS26405 (OHZ00_26435) 73457..74014 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
OHZ00_RS26410 (OHZ00_26440) 74060..74503 + 444 WP_004194305 F-type conjugal transfer protein TrbF -
OHZ00_RS26415 (OHZ00_26445) 74481..75860 + 1380 WP_014343487 conjugal transfer pilus assembly protein TraH traH
OHZ00_RS26420 (OHZ00_26450) 75860..78709 + 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
OHZ00_RS26425 (OHZ00_26455) 78712..79245 + 534 WP_014343486 conjugal transfer protein TraS -
OHZ00_RS26430 (OHZ00_26460) 79431..80162 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
OHZ00_RS26435 (OHZ00_26465) 80355..81044 + 690 WP_072101983 hypothetical protein -
OHZ00_RS26440 (OHZ00_26470) 81173..83485 + 2313 WP_072101984 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   15512 GenBank   NZ_CP109830
Plasmid name   pSMBC50-107K Incompatibility group   IncR
Plasmid size   107807 bp Coordinate of oriT [Strand]   55571..55619 [-]
Host baterium   Serratia marcescens strain SMBC50

Cargo genes

Drug resistance gene   blaKPC-2
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9