Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100096
Name   oriT_pEC958 in_silico
Organism   Escherichia coli ST131 strain EC958
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   HG941719 (26048..26497 [-], 450 nt)
oriT length   450 nt
IRs (inverted repeats)      IR1: 201..215, 222..236  (ATTCATTGGTGAATC..GATTCACCAATGAAT)
 IR2: 308..315, 318..325  (GCAAAAAC..GTTTTTGC)
Location of nic site      334..335
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   

  oriT sequence  


Download         Length: 450 nt

>oriT_pEC958
ATATGTATACCTCTTTATTTTCTTATCGCATCAAATTTATTTCACATATAAAAAAATGACAATTCATCGATGAATCGAATCGTGACGCAAGTTACGAAAATTACGATTCATGCAGCAAATCACATCACGAATTGAATCTAGAGTCAATTCGCTTTAACTCGTTGTTTTATTATTACTGATTCATCTATGAGTTGCGTTAAATTCATTGGTGAATCATATGCGATTCACCAATGAATCCTTTTTATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGTTAATGATTCAAATAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Forde BM et al. (2014) The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One. 9(8):e104400. [PMID:25126841]


Relaxase

ID   91 GenBank   CDN85420
Name   TraI_pEC958 insolico UniProt ID   W8ZTK0
Length   1756 a.a. PDB ID   
Note   conjugal transfer nickase/helicase TraI

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>CDN85420.1 TraI (plasmid) [Escherichia coli O25b:H4-ST131]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.



  Reference


[1] Forde BM et al. (2014) The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One. 9(8):e104400. [PMID:25126841]


Auxiliary protein

ID   131 GenBank   CDN85382
Name   TraM_pEC958 insolico UniProt ID   W9APS2
Length   127 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14446.39 Da        Isoelectric Point: 4.7197

>CDN85382.1 TraM (plasmid) [Escherichia coli O25b:H4-ST131]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB W9APS2

ID   132 GenBank   CDN85384
Name   TraY_pEC958 insolico UniProt ID   W9A0Z2
Length   75 a.a. PDB ID   _
Note   conjugal transfer protein TraY

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>CDN85384.1 conjugal transfer protein TraY (plasmid) [Escherichia coli O25b:H4-ST131]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB W9A0Z2


T4CP

ID   91 GenBank   CDN85419
Name   TraD_pEC958 insolico UniProt ID   W9A124
Length   732 a.a. PDB ID   _
Note   type IV conjugative transfer system coupling protein TraD

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 83193.81 Da        Isoelectric Point: 5.1644

>CDN85419.1 TraD (plasmid) [Escherichia coli O25b:H4-ST131]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure


Source ID Structure
AlphaFold DB W9A124


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 25563..58718

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EC958_A0025 21528..21962 + 435 CDN85375 PsiB -
EC958_A0026 21959..22678 + 720 CDN85376 PsiA -
EC958_A0027 22690..22914 - 225 CDN85377 modulator of Hok protein -
EC958_A0029 22900..23112 + 213 CDN85378 post-segregational killing protein -
EC958_A0030 24035..24322 + 288 CDN85379 hypothetical protein -
EC958_A0031 24443..25264 + 822 CDN85380 YubP -
EC958_A0032 25563..26240 - 678 CDN85381 X polypeptide virB1
EC958_A0033 26496..26879 + 384 CDN85382 TraM -
EC958_A0036 27073..27759 + 687 CDN85383 TraJ -
EC958_A0037 27853..28080 + 228 CDN85384 conjugal transfer protein TraY -
EC958_A0038 28114..28476 + 363 CDN85385 TraA -
EC958_A0039 28478..28792 + 315 CDN85386 TraL traL
EC958_A0040 28814..29380 + 567 CDN85387 TraE traE
EC958_A0041 29367..30095 + 729 CDN85388 TraK traK
EC958_A0042 30095..31522 + 1428 CDN85389 TraB traB
EC958_A0043 31512..32096 + 585 CDN85390 TraP -
EC958_A0044 32083..32403 + 321 CDN85391 TrbD virb4
EC958_A0045 32396..32647 + 252 CDN85392 TrbG -
EC958_A0046 32644..33159 + 516 CDN85393 TraV traV
EC958_A0047 33294..33515 + 222 CDN85394 TraR -
EC958_A0048 33675..36305 + 2631 CDN85395 TraC virb4
EC958_A0049 36352..37056 + 705 CDN85396 TnpA -
EC958_A0050 37300..38562 - 1263 CDN85397 TnpA -
EC958_A0051 38744..39121 - 378 Protein_46 Tn3 transposase -
EC958_A0052 39090..39683 + 594 CDN85399 transposon Tn3 resolvase -
EC958_A0053 39866..40726 + 861 CDN85400 TEM-1 -
EC958_A0054 40837..43344 - 2508 CDN85401 transposase TnpA, Tn21 -
EC958_A0056 43347..43439 - 93 Protein_50 resolvase of Tn21 -
EC958_A0057 43487..44191 - 705 CDN85403 TnpA -
EC958_A0058 44307..44612 + 306 CDN85404 hypothetical protein -
EC958_A0059 44621..45259 + 639 CDN85405 TrbC trbC
EC958_A0060 45256..47106 + 1851 CDN85406 TraN traN
EC958_A0061 47133..47390 + 258 CDN85407 TrbE -
EC958_A0062 47383..48126 + 744 CDN85408 TraF traF
EC958_A0063 48140..48484 + 345 CDN85409 TrbA -
EC958_A0064 48603..48887 + 285 CDN85410 TraQ -
EC958_A0065 48874..49419 + 546 CDN85411 TrbB traF
EC958_A0066 49424..49696 + 273 CDN85412 TrbJ -
EC958_A0067 49677..50069 + 393 CDN85413 TrbF -
EC958_A0068 50056..51429 + 1374 CDN85414 TraH traH
EC958_A0069 51495..54248 + 2754 CDN85415 TraG traG
EC958_A0070 54270..54749 + 480 CDN85416 TraS -
EC958_A0071 54798..55529 + 732 CDN85417 TraT -
EC958_A0072 55732..56469 + 738 CDN85418 YhfA -
EC958_A0073 56520..58718 + 2199 CDN85419 TraD virb4

Host bacterium

ID   91 GenBank   HG941719
Plasmid name   pEC958 Incompatibility group   IncFIA
Plasmid size   135602 bp Coordinate of oriT [Strand]   26048..26497 [-]
Host baterium   Escherichia coli ST131 strain EC958

Cargo genes

Drug resistance gene   blaTEM-1; blaCTX-M-15; blaOXA-1; tet gene cluster (resistance to tetracycline)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -