Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100962
Name   oriT_tig00008015 in_silico
Organism   Escherichia coli strain AR_0162
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP021684 (53820..54369 [-], 550 nt)
oriT length   550 nt
IRs (inverted repeats)      243..255, 257..269  (TATTTAATAATTC..GAATTATTAAATA)
 311..318, 321..328  (GCAAAAAC..GTTTTTGC)
Location of nic site      337..338
Conserved sequence flanking the
  nic site    		  GTAGTGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 550 nt

>oriT_tig00008015
TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAATGAACTTTTCACTATAAATATGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTATAAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCATGAAAATTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTCTCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCAATCTGCCTGATGTTTATAAATGGGATCTGCGAAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTGAGAGCGATATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1032 GenBank   WP_087760850
Name   TraI_tig00008015 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191655.16 Da        Isoelectric Point: 5.6912

>WP_087760850.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREAMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 53432..84179

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AM408_RS26915 48604..48900 - 297 Protein_60 hypothetical protein -
AM408_RS26070 (AM408_25935) 49200..49496 + 297 WP_001272251 hypothetical protein -
AM408_RS26075 (AM408_25940) 49607..50428 + 822 WP_001234445 DUF932 domain-containing protein -
AM408_RS26085 (AM408_25950) 50506..52077 - 1572 WP_000381395 IS66-like element ISCro1 family transposase -
AM408_RS26090 (AM408_25955) 52097..52444 - 348 WP_000624622 IS66 family insertion sequence element accessory protein TnpB -
AM408_RS26095 (AM408_25960) 52444..53121 - 678 WP_001339397 IS66-like element accessory protein TnpA -
AM408_RS26100 (AM408_25965) 53432..54034 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
AM408_RS26105 (AM408_25970) 54357..54740 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
AM408_RS26110 (AM408_25975) 54934..55605 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
AM408_RS26115 (AM408_25980) 55742..55969 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
AM408_RS26120 (AM408_25985) 56002..56361 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
AM408_RS26125 (AM408_25990) 56376..56687 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
AM408_RS26130 (AM408_25995) 56709..57275 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
AM408_RS26135 (AM408_26000) 57262..57990 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
AM408_RS26140 (AM408_26005) 57990..59441 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
AM408_RS26145 (AM408_26010) 59431..59997 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
AM408_RS26150 (AM408_26015) 59984..60304 + 321 WP_001057307 conjugal transfer protein TrbD -
AM408_RS26155 (AM408_26020) 60301..60816 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
AM408_RS26160 (AM408_26025) 60951..61172 + 222 WP_001278683 conjugal transfer protein TraR -
AM408_RS26165 (AM408_26030) 61165..61641 + 477 WP_000549587 hypothetical protein -
AM408_RS26170 (AM408_26035) 61721..61939 + 219 WP_000556745 hypothetical protein -
AM408_RS26695 61967..62314 + 348 WP_000836682 hypothetical protein -
AM408_RS26180 (AM408_26045) 62440..65070 + 2631 WP_000069777 type IV secretion system protein TraC virb4
AM408_RS26185 (AM408_26050) 65067..65453 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
AM408_RS26190 (AM408_26055) 65450..66082 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
AM408_RS26195 (AM408_26060) 66079..67071 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
AM408_RS26200 (AM408_26065) 67101..67406 + 306 WP_000224416 hypothetical protein -
AM408_RS26205 (AM408_26070) 67415..68053 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
AM408_RS26210 (AM408_26075) 68050..69900 + 1851 WP_087760847 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AM408_RS26215 (AM408_26080) 69927..70184 + 258 WP_000864353 conjugal transfer protein TrbE -
AM408_RS26220 (AM408_26085) 70177..70920 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
AM408_RS26225 (AM408_26090) 70934..71278 + 345 WP_000556796 conjugal transfer protein TrbA -
AM408_RS26230 (AM408_26095) 71397..71681 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
AM408_RS26235 (AM408_26100) 71668..72213 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AM408_RS26240 (AM408_26105) 72143..72490 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
AM408_RS26245 (AM408_26110) 72471..72863 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
AM408_RS26250 (AM408_26115) 72850..74223 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
AM408_RS26255 (AM408_26120) 74220..77042 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
AM408_RS26260 (AM408_26125) 77064..77396 + 333 Protein_98 surface exclusion protein -
AM408_RS26265 (AM408_26130) 77589..79130 + 1542 WP_002431311 IS21-like element ISEc12 family transposase -
AM408_RS26270 (AM408_26135) 79145..79891 + 747 WP_001016257 IS21-like element ISEc12 family helper ATPase IstB -
AM408_RS27275 79977..80129 + 153 Protein_101 surface exclusion protein -
AM408_RS26275 (AM408_26140) 80178..80909 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
AM408_RS26280 (AM408_26145) 81112..81849 + 738 WP_000199905 hypothetical protein -
AM408_RS26285 (AM408_26150) 81900..84179 + 2280 WP_087760849 type IV conjugative transfer system coupling protein TraD prgC

Host bacterium

ID   1420 GenBank   NZ_CP021684
Plasmid name   tig00008015 Incompatibility group   IncFII
Plasmid size   84929 bp Coordinate of oriT [Strand]   53820..54369 [-]
Host baterium   Escherichia coli strain AR_0162

Cargo genes

Drug resistance gene   erm(B), mph(A), blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -