Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118278
Name   oriT_p3024-KPC in_silico
Organism   Serratia marcescens strain 3024
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP047683 (76545..76593 [+], 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_p3024-KPC
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11615 GenBank   WP_064291677
Name   traI_GV218_RS26075_p3024-KPC 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   13600 GenBank   WP_072101984
Name   traD_GV218_RS26080_p3024-KPC 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: 48678..77151

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GV218_RS26080 (GV218_26080) 48678..50990 - 2313 WP_072101984 type IV conjugative transfer system coupling protein TraD virb4
GV218_RS26590 51119..51808 - 690 WP_072101983 hypothetical protein -
GV218_RS26090 (GV218_26090) 52001..52732 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
GV218_RS26095 (GV218_26095) 52918..53451 - 534 WP_014343486 conjugal transfer protein TraS -
GV218_RS26100 (GV218_26100) 53454..56303 - 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
GV218_RS26105 (GV218_26105) 56303..57682 - 1380 WP_014343487 conjugal transfer pilus assembly protein TraH traH
GV218_RS26110 (GV218_26110) 57660..58103 - 444 WP_004194305 F-type conjugal transfer protein TrbF -
GV218_RS26115 (GV218_26115) 58149..58706 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
GV218_RS26120 (GV218_26120) 58678..58917 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
GV218_RS26125 (GV218_26125) 58928..59680 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
GV218_RS26130 (GV218_26130) 59701..60027 - 327 WP_004152676 hypothetical protein -
GV218_RS26135 (GV218_26135) 60040..60288 - 249 WP_004152675 hypothetical protein -
GV218_RS26140 (GV218_26140) 60266..60520 - 255 WP_004152674 conjugal transfer protein TrbE -
GV218_RS26145 (GV218_26145) 60552..62507 - 1956 WP_030003482 type-F conjugative transfer system mating-pair stabilization protein TraN traN
GV218_RS26150 (GV218_26150) 62566..63204 - 639 WP_069985712 type-F conjugative transfer system pilin assembly protein TrbC trbC
GV218_RS26155 (GV218_26155) 63217..64206 - 990 WP_160208050 conjugal transfer pilus assembly protein TraU traU
GV218_RS26160 (GV218_26160) 64203..64604 - 402 WP_004194979 hypothetical protein -
GV218_RS26165 (GV218_26165) 64639..65274 - 636 WP_029497419 type-F conjugative transfer system protein TraW traW
GV218_RS26170 (GV218_26170) 65274..65663 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
GV218_RS26175 (GV218_26175) 65663..68302 - 2640 WP_013214024 type IV secretion system protein TraC virb4
GV218_RS26180 (GV218_26180) 68374..68772 - 399 WP_023179972 hypothetical protein -
GV218_RS26185 (GV218_26185) 69151..69555 - 405 WP_004197817 hypothetical protein -
GV218_RS26190 (GV218_26190) 69622..69933 - 312 WP_029497417 hypothetical protein -
GV218_RS26595 69934..70152 - 219 WP_004195468 hypothetical protein -
GV218_RS26195 (GV218_26195) 70475..71059 - 585 WP_032440547 type IV conjugative transfer system lipoprotein TraV traV
GV218_RS26200 (GV218_26200) 71132..72556 - 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
GV218_RS26205 (GV218_26205) 72556..73296 - 741 WP_013023821 type-F conjugative transfer system secretin TraK traK
GV218_RS26210 (GV218_26210) 73283..73849 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
GV218_RS26215 (GV218_26215) 73869..74174 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
GV218_RS26220 (GV218_26220) 74188..74556 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
GV218_RS26880 (GV218_26225) 74625..74825 - 201 WP_004194116 TraY domain-containing protein -
GV218_RS26230 (GV218_26230) 74911..75612 - 702 WP_004194113 hypothetical protein -
GV218_RS26235 (GV218_26235) 75842..76234 - 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
GV218_RS26240 (GV218_26240) 76666..77151 + 486 WP_032440470 transglycosylase SLT domain-containing protein virB1
GV218_RS26245 (GV218_26245) 77184..77513 - 330 WP_071994324 DUF5983 family protein -
GV218_RS26250 (GV218_26250) 77546..78367 - 822 WP_023287138 DUF932 domain-containing protein -
GV218_RS26255 (GV218_26255) 79197..79610 - 414 WP_069985713 type II toxin-antitoxin system HigA family antitoxin -
GV218_RS26260 (GV218_26260) 79611..79889 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
GV218_RS26265 (GV218_26265) 79879..80199 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
GV218_RS26270 (GV218_26270) 80280..80504 - 225 WP_014343499 hypothetical protein -
GV218_RS26275 (GV218_26275) 80515..80727 - 213 WP_019706020 hypothetical protein -
GV218_RS26280 (GV218_26280) 80788..81144 - 357 WP_019706019 hypothetical protein -
GV218_RS26285 (GV218_26285) 81776..82126 - 351 WP_023287104 hypothetical protein -

Host bacterium

ID   18711 GenBank   NZ_CP047683
Plasmid name   p3024-KPC Incompatibility group   -
Plasmid size   103175 bp Coordinate of oriT [Strand]   76545..76593 [+]
Host baterium   Serratia marcescens strain 3024

Cargo genes

Drug resistance gene   blaKPC-2, qnrS1
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9