Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116905
Name   oriT_pE28_001 in_silico
Organism   Serratia marcescens strain E28
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP042513 (132969..133018 [+], 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_pE28_001
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10786 GenBank   WP_151523151
Name   traI_FR888_RS26870_pE28_001 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190322.77 Da        Isoelectric Point: 5.8571

>WP_151523151.1 conjugative transfer relaxase/helicase TraI [Serratia marcescens]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINTTQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARAGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMNVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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

(576-628)

TrwC relaxase (TrwC)

(10-283)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   12607 GenBank   WP_151523152
Name   traD_FR888_RS26875_pE28_001 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85636.75 Da        Isoelectric Point: 5.2499

>WP_151523152.1 type IV conjugative transfer system coupling protein TraD [Serratia marcescens]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWASFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGTADTNSHAGEQPEPVSQPA
PAEVTVSPAPVKAPATTKMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 104661..133576

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FR888_RS26875 (FR888_26870) 104661..106970 - 2310 WP_151523152 type IV conjugative transfer system coupling protein TraD virb4
FR888_RS28690 107097..107786 - 690 WP_013023831 hypothetical protein -
FR888_RS26885 (FR888_26880) 107979..108708 - 730 Protein_118 conjugal transfer complement resistance protein TraT -
FR888_RS26895 (FR888_26890) 108897..109427 - 531 WP_074187241 conjugal transfer protein TraS -
FR888_RS26900 (FR888_26895) 109430..112279 - 2850 WP_042922342 conjugal transfer mating-pair stabilization protein TraG traG
FR888_RS26905 (FR888_26900) 112279..113658 - 1380 WP_074187239 conjugal transfer pilus assembly protein TraH traH
FR888_RS26910 (FR888_26905) 113636..114079 - 444 WP_015065638 F-type conjugal transfer protein TrbF -
FR888_RS26915 (FR888_26910) 114124..114681 - 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
FR888_RS26920 (FR888_26915) 114653..114892 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
FR888_RS26925 (FR888_26920) 114903..115655 - 753 WP_042922347 type-F conjugative transfer system pilin assembly protein TraF traF
FR888_RS26930 (FR888_26925) 115676..116002 - 327 WP_016529362 hypothetical protein -
FR888_RS29180 (FR888_26930) 116048..116233 - 186 WP_042922350 hypothetical protein -
FR888_RS26940 (FR888_26935) 116230..116466 - 237 WP_042922352 conjugal transfer protein TrbE -
FR888_RS26945 (FR888_26940) 116498..118453 - 1956 WP_015065636 type-F conjugative transfer system mating-pair stabilization protein TraN traN
FR888_RS26950 (FR888_26945) 118512..119150 - 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
FR888_RS26955 (FR888_26950) 119163..120152 - 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
FR888_RS26960 (FR888_26955) 120149..120538 - 390 WP_042922355 hypothetical protein -
FR888_RS26965 (FR888_26960) 120580..121206 - 627 WP_009309871 type-F conjugative transfer system protein TraW traW
FR888_RS26970 (FR888_26965) 121206..121595 - 390 WP_004152591 type-F conjugative transfer system protein TrbI -
FR888_RS26975 (FR888_26970) 121595..124234 - 2640 WP_042922359 type IV secretion system protein TraC virb4
FR888_RS26980 (FR888_26975) 124306..124704 - 399 WP_023179972 hypothetical protein -
FR888_RS26995 (FR888_26990) 125082..125486 - 405 WP_004197817 hypothetical protein -
FR888_RS27000 (FR888_26995) 125553..125864 - 312 WP_004195240 hypothetical protein -
FR888_RS27005 (FR888_27000) 125865..126083 - 219 WP_004195235 hypothetical protein -
FR888_RS27010 (FR888_27005) 126189..126599 - 411 WP_004152499 hypothetical protein -
FR888_RS27015 (FR888_27010) 126731..127315 - 585 WP_032441881 type IV conjugative transfer system lipoprotein TraV traV
FR888_RS27020 (FR888_27015) 127429..128853 - 1425 WP_042922367 F-type conjugal transfer pilus assembly protein TraB traB
FR888_RS27025 (FR888_27020) 128853..129593 - 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
FR888_RS27030 (FR888_27025) 129580..130146 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
FR888_RS27035 (FR888_27030) 130166..130471 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
FR888_RS27040 (FR888_27035) 130485..130853 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
FR888_RS27045 (FR888_27040) 130907..131278 - 372 WP_004208838 TraY domain-containing protein -
FR888_RS27050 (FR888_27045) 131362..132048 - 687 WP_071561590 transcriptional regulator TraJ family protein -
FR888_RS27055 (FR888_27050) 132264..132656 - 393 WP_032441878 conjugal transfer relaxosome DNA-binding protein TraM -
FR888_RS27060 (FR888_27055) 133091..133576 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
FR888_RS27065 (FR888_27060) 133609..133938 - 330 WP_192802326 DUF5983 family protein -
FR888_RS27070 (FR888_27065) 133971..134792 - 822 WP_023316395 DUF932 domain-containing protein -
FR888_RS27080 (FR888_27075) 135620..136033 - 414 WP_021312979 type II toxin-antitoxin system HigA family antitoxin -
FR888_RS27085 (FR888_27080) 136034..136312 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
FR888_RS27090 (FR888_27085) 136302..136622 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
FR888_RS27095 (FR888_27090) 136703..136927 - 225 WP_014343499 hypothetical protein -
FR888_RS27100 (FR888_27095) 136938..137150 - 213 WP_019706020 hypothetical protein -
FR888_RS27105 (FR888_27100) 137211..137567 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   17338 GenBank   NZ_CP042513
Plasmid name   pE28_001 Incompatibility group   IncFIB
Plasmid size   186249 bp Coordinate of oriT [Strand]   132969..133018 [+]
Host baterium   Serratia marcescens strain E28

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, merR2, merT, merP, merF, merA, merD, merE, ncrA, ncrB, ncrC, ncrY
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9