Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117836
Name   oriT_95|unnamed1 in_silico
Organism   Serratia marcescens strain 95
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP020506 (114014..114062 [-], 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_95|unnamed1
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11331 GenBank   WP_048235021
Name   traI_AM681_RS27035_95|unnamed1 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190795.84 Da        Isoelectric Point: 6.1046

>WP_048235021.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRLVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGSWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRLALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQFVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)

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

(577-629)

AAA domain (AAA_30)

(971-1157)


  Protein structure



No available structure.




T4CP

ID   13242 GenBank   WP_048235023
Name   traD_AM681_RS27030_95|unnamed1 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: 85941.02 Da        Isoelectric Point: 5.1149

>WP_048235023.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRSTEPSALRLTTVPLIKPKAAAAAAAAATVSSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDNVEIGGNF

  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: 113456..141920

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AM681_RS26810 (AM681_26685) 108851..109078 + 228 WP_001568050 hypothetical protein -
AM681_RS26815 (AM681_26690) 109170..109400 + 231 WP_009310031 hypothetical protein -
AM681_RS26820 (AM681_26695) 109452..110807 + 1356 WP_048235045 DUF3560 domain-containing protein -
AM681_RS26825 (AM681_26700) 110855..111418 + 564 WP_004152756 methyltransferase -
AM681_RS26840 (AM681_26720) 112240..113061 + 822 WP_023316395 DUF932 domain-containing protein -
AM681_RS26845 113094..113423 + 330 WP_011977736 DUF5983 family protein -
AM681_RS26850 (AM681_26725) 113456..113941 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
AM681_RS26855 (AM681_26730) 114373..114765 + 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
AM681_RS26860 (AM681_26735) 114995..115696 + 702 WP_025712700 hypothetical protein -
AM681_RS26865 (AM681_26740) 115782..115982 + 201 WP_046664192 TraY domain-containing protein -
AM681_RS26870 (AM681_26745) 116050..116418 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
AM681_RS26875 (AM681_26750) 116432..116737 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
AM681_RS26880 (AM681_26755) 116757..117323 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
AM681_RS26885 (AM681_26760) 117310..118050 + 741 WP_048235042 type-F conjugative transfer system secretin TraK traK
AM681_RS26890 (AM681_26765) 118050..119474 + 1425 WP_015065626 F-type conjugal transfer pilus assembly protein TraB traB
AM681_RS26895 (AM681_26770) 119548..120132 + 585 WP_020277945 type IV conjugative transfer system lipoprotein TraV traV
AM681_RS28150 120287..120685 + 399 WP_020277946 hypothetical protein -
AM681_RS28155 (AM681_26780) 120756..121004 + 249 WP_223175793 hypothetical protein -
AM681_RS26910 (AM681_26785) 121028..121246 + 219 WP_004195468 hypothetical protein -
AM681_RS26915 (AM681_26790) 121247..121558 + 312 WP_025712701 hypothetical protein -
AM681_RS26920 (AM681_26795) 121625..122029 + 405 WP_004197817 hypothetical protein -
AM681_RS26935 (AM681_26810) 122407..122805 + 399 WP_074194504 hypothetical protein -
AM681_RS26940 (AM681_26815) 122877..125516 + 2640 WP_004197813 type IV secretion system protein TraC virb4
AM681_RS26945 (AM681_26820) 125516..125905 + 390 WP_048235039 type-F conjugative transfer system protein TrbI -
AM681_RS26950 (AM681_26825) 125905..126540 + 636 WP_048235038 type-F conjugative transfer system protein TraW traW
AM681_RS26955 (AM681_26830) 126575..126976 + 402 WP_004194979 hypothetical protein -
AM681_RS26960 (AM681_26835) 126973..127962 + 990 WP_013214027 conjugal transfer pilus assembly protein TraU traU
AM681_RS26965 (AM681_26840) 127975..128613 + 639 WP_048235035 type-F conjugative transfer system pilin assembly protein TrbC trbC
AM681_RS26970 (AM681_26845) 128672..130627 + 1956 WP_048235034 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AM681_RS26975 (AM681_26850) 130659..130913 + 255 WP_020804203 conjugal transfer protein TrbE -
AM681_RS26980 (AM681_26855) 130891..131139 + 249 WP_004152675 hypothetical protein -
AM681_RS26985 (AM681_26860) 131152..131478 + 327 WP_048235032 hypothetical protein -
AM681_RS26990 (AM681_26865) 131499..132251 + 753 WP_048235030 type-F conjugative transfer system pilin assembly protein TraF traF
AM681_RS26995 (AM681_26870) 132262..132501 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
AM681_RS27000 (AM681_26875) 132473..133045 + 573 WP_048235029 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AM681_RS27005 (AM681_26880) 133038..133460 + 423 WP_049010971 hypothetical protein -
AM681_RS27010 (AM681_26885) 133447..134817 + 1371 WP_048235027 conjugal transfer pilus assembly protein TraH traH
AM681_RS27015 (AM681_26890) 134817..137639 + 2823 WP_048235025 conjugal transfer mating-pair stabilization protein TraG traG
AM681_RS27020 137663..138265 + 603 WP_023280878 hypothetical protein -
AM681_RS27025 (AM681_26895) 138517..139248 + 732 WP_032415736 conjugal transfer complement resistance protein TraT -
AM681_RS28160 139439..139552 + 114 Protein_154 hypothetical protein -
AM681_RS27030 (AM681_26900) 139608..141920 + 2313 WP_048235023 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   18269 GenBank   NZ_CP020506
Plasmid name   95|unnamed1 Incompatibility group   IncFIB
Plasmid size   219979 bp Coordinate of oriT [Strand]   114014..114062 [-]
Host baterium   Serratia marcescens strain 95

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE, pcoE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -