Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107812
Name   oriT_Effluent_3|unnamed1 in_silico
Organism   Enterobacter cloacae strain Effluent_3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039312 (117635..117683 [+], 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    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_Effluent_3|unnamed1
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5245 GenBank   WP_040118495
Name   traI_E7735_RS25300_Effluent_3|unnamed1 insolico UniProt ID   A0A7H9GIQ2
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190247.71 Da        Isoelectric Point: 6.0516

>WP_040118495.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLAGTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENLLANRIALGKIYQSALRADIES
MGYKTVDAGKHGMWEMKDVPVEAFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADAHAAELARAPAAPVKTDGPDIADVVTRAIAGLSDRKVQFTYADVLARTVGQLEA
KPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVMREKPF
SDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGRQATADIISEPDKSVRYSRLAQEFAVSVREGQESVAQISGTREQNVLNNVIRDTLKNEGALGNRDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPEARKHDRFVIDRVTASSNMLTLKDREGERLDLKVSVVD
SQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKVRSGEADLEAAIAQQKAGLHTPAEQAIHLSVPLLESNSLTFTRTQLLATALETGGGKVPMTDIDATIQ
AQIKAGSLLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAMTPLMDRVPGSLMTDLTAGQRAATRM
ILETPDRFTVVQGYAGVGKTTQFKSVMSAISLLPEEARSRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDISRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIQD
ALKEGKEIPPDTPASLHDAIVKDYTGRTPAAQASTLIITHLNADRRALNGLIHDARVQNGEVSKEEVTLP
VLVTSNIRDGELRKLSTWSEHQGAVALLDNTYQRIESVDKENQLITLKDNEGNIRLLSPREASAEGVTLY
RPEHITVSQGDRMRFSKSDPERGYVANSVWEVKAFSGDSVTLTDGKTTRTLNPKADEAQRHIDLAYAITA
HGAQGASEPFAIALEGVEGRRKALVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLEP
QNARAVRNAGQLYGRAQPLDETAAGRAALQQSGLARGRSPGKFISPGKKYPQPHVALPAFDKNGKEAGIW
LSPLTDRDGRLEAIGGEGRIMGDETARFVALQNSRNGESLLAGNMGEGVRAARNHPDSGVIVRLAGDDRP
WNPEAITGGRVWADPLPNTPLPDTGTDIPLPPDVLAQRAAEEVQRREMEKQAEQTAREVAGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTLLPDDPQTRRQEAAIQQVASESLQRERLQQMERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   2403 GenBank   WP_032426796
Name   WP_032426796_Effluent_3|unnamed1 insolico UniProt ID   _
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15036.10 Da        Isoelectric Point: 4.5326

>WP_032426796.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKEKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMRTFFPDEQEEADE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   5491 GenBank   WP_065806281
Name   traD_E7735_RS25305_Effluent_3|unnamed1 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 85820.59 Da        Isoelectric Point: 4.8107

>WP_065806281.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
EIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKDVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRCYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRTLDTRVDARLSALLEAREAEGNLVRVLFTPDAPEPEQRDADSRTSPGQPEPENAP
VSPAPVKSASTAETLAAPPSVKASEAPQATVTTVPLTRPAPATTPAASSATASSVAATAATTGGTEQELA
QQPADTGQEVMPAGMNEDGEIEDMQAYDTWLADEQTQREMQRREEVNINHSHRRDEQDDIEIGGNF

  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: 92197..118241

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
E7735_RS25305 (E7735_25345) 92197..94497 - 2301 WP_065806281 type IV conjugative transfer system coupling protein TraD virb4
E7735_RS25310 (E7735_25350) 94741..95274 - 534 WP_136404567 hypothetical protein -
E7735_RS25315 (E7735_25355) 95285..98158 - 2874 WP_065806280 conjugal transfer mating-pair stabilization protein TraG traG
E7735_RS25320 (E7735_25360) 98158..99528 - 1371 WP_040118491 conjugal transfer pilus assembly protein TraH traH
E7735_RS25325 (E7735_25365) 99515..100090 - 576 WP_040118490 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
E7735_RS25330 (E7735_25370) 100062..100301 - 240 WP_040118489 type-F conjugative transfer system pilin chaperone TraQ -
E7735_RS25335 (E7735_25375) 100312..101064 - 753 WP_136404568 type-F conjugative transfer system pilin assembly protein TraF traF
E7735_RS25340 (E7735_25380) 101083..101409 - 327 WP_040118487 hypothetical protein -
E7735_RS25345 (E7735_25385) 101420..101647 - 228 WP_065806278 conjugal transfer protein TrbE -
E7735_RS25350 (E7735_25390) 101637..101918 - 282 WP_040118485 hypothetical protein -
E7735_RS25355 (E7735_25395) 101956..103836 - 1881 WP_136404569 type-F conjugative transfer system mating-pair stabilization protein TraN traN
E7735_RS25360 (E7735_25400) 103833..104450 - 618 WP_040118483 type-F conjugative transfer system pilin assembly protein TrbC trbC
E7735_RS25365 (E7735_25405) 104463..105446 - 984 WP_074423225 conjugal transfer pilus assembly protein TraU traU
E7735_RS25370 (E7735_25410) 105466..106092 - 627 WP_040118481 type-F conjugative transfer system protein TraW traW
E7735_RS25375 (E7735_25415) 106089..106490 - 402 WP_136404573 type-F conjugative transfer system protein TrbI -
E7735_RS25380 (E7735_25420) 106523..109162 - 2640 WP_136404570 type IV secretion system protein TraC virb4
E7735_RS25385 (E7735_25425) 109293..109697 - 405 WP_064174410 hypothetical protein -
E7735_RS25390 (E7735_25430) 109694..109918 - 225 WP_064381372 hypothetical protein -
E7735_RS25395 (E7735_25435) 109942..110235 - 294 WP_049071697 hypothetical protein -
E7735_RS27025 110264..110668 - 405 WP_064381370 hypothetical protein -
E7735_RS25405 (E7735_25445) 110785..111366 - 582 WP_064381368 type IV conjugative transfer system lipoprotein TraV traV
E7735_RS27175 (E7735_25450) 111389..111526 - 138 Protein_104 conjugal transfer protein TraP -
E7735_RS25415 (E7735_25455) 111594..112190 - 597 WP_136404571 conjugal transfer protein TraP -
E7735_RS25420 (E7735_25460) 112183..113598 - 1416 WP_064381364 F-type conjugal transfer pilus assembly protein TraB traB
E7735_RS25425 (E7735_25465) 113598..114338 - 741 WP_064381362 type-F conjugative transfer system secretin TraK traK
E7735_RS25430 (E7735_25470) 114325..114891 - 567 WP_020323527 type IV conjugative transfer system protein TraE traE
E7735_RS25435 (E7735_25475) 114911..115216 - 306 WP_020323523 type IV conjugative transfer system protein TraL traL
E7735_RS25440 (E7735_25480) 115230..115595 - 366 WP_064381359 type IV conjugative transfer system pilin TraA -
E7735_RS25445 (E7735_25485) 115659..115823 - 165 WP_032426810 TraY domain-containing protein -
E7735_RS27035 116347..116691 - 345 WP_228725893 hypothetical protein -
E7735_RS25455 (E7735_25495) 116929..117321 - 393 WP_032426796 conjugal transfer relaxosome DNA-binding protein TraM -
E7735_RS25460 (E7735_25500) 117756..118241 + 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
E7735_RS25465 (E7735_25505) 118274..118603 - 330 WP_069335041 DUF5983 family protein -
E7735_RS25470 (E7735_25510) 118636..119457 - 822 WP_004152492 DUF932 domain-containing protein -
E7735_RS25480 (E7735_25520) 120286..120687 - 402 WP_015065522 helix-turn-helix domain-containing protein -
E7735_RS25485 (E7735_25525) 120688..120966 - 279 WP_020801586 helix-turn-helix transcriptional regulator -
E7735_RS25490 (E7735_25530) 120956..121276 - 321 WP_015065521 type II toxin-antitoxin system RelE/ParE family toxin -
E7735_RS25495 (E7735_25535) 121357..121572 - 216 WP_142381705 hypothetical protein -
E7735_RS25500 (E7735_25540) 121592..121804 - 213 WP_019706020 hypothetical protein -
E7735_RS25505 (E7735_25545) 121865..122221 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   8247 GenBank   NZ_CP039312
Plasmid name   Effluent_3|unnamed1 Incompatibility group   IncFII
Plasmid size   145588 bp Coordinate of oriT [Strand]   117635..117683 [+]
Host baterium   Enterobacter cloacae strain Effluent_3

Cargo genes

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