Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107831
Name   oriT_pEF45-3 in_silico
Organism   Escherichia fergusonii strain EF20JDJ4045
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP086607 (65923..66010 [-], 88 nt)
oriT length   88 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 88 nt

>oriT_pEF45-3
GGGGTGTCGGGGCGAAGCCATGACCAGATGGTAATTGTAATAGTGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCTGTTTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5256 GenBank   WP_104920583
Name   traI_LNN29_RS24550_pEF45-3 insolico UniProt ID   _
Length   1537 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1537 a.a.        Molecular weight: 168867.13 Da        Isoelectric Point: 5.8421

>WP_104920583.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT
LKETGFDIRAYRDAAEQRAYTRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
AGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMLVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENCWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPARERAEQHIDLAYAI
TGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLPDGKTEQAVR
EIAGQERERAVTSERETALPESVLRELQREREAVREIARENLLQERLQQMERDMVRDLQKEKTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

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

(633-711)


  Protein structure



No available structure.




T4CP

ID   5500 GenBank   WP_001289276
Name   trbC_LNN29_RS24425_pEF45-3 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86941.11 Da        Isoelectric Point: 6.7713

>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.



ID   5501 GenBank   WP_104920584
Name   traD_LNN29_RS24545_pEF45-3 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81382.87 Da        Isoelectric Point: 4.9496

>WP_104920584.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENSNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENCLSAVLAAREAEGRQMVSLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKSEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  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



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 71387..95213

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LNN29_RS24425 (LNN29_24375) 69103..71394 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
LNN29_RS24430 (LNN29_24380) 71387..72457 - 1071 WP_000151576 IncI1-type conjugal transfer protein TrbB trbB
LNN29_RS24435 (LNN29_24385) 72476..73684 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
LNN29_RS24440 (LNN29_24390) 73976..74128 + 153 WP_001303307 Hok/Gef family protein -
LNN29_RS24445 (LNN29_24395) 74200..74451 - 252 WP_001291965 hypothetical protein -
LNN29_RS25270 74951..75046 + 96 WP_001303310 DinQ-like type I toxin DqlB -
LNN29_RS24455 (LNN29_24405) 75111..75248 - 138 WP_047088497 hypothetical protein -
LNN29_RS24460 (LNN29_24410) 75293..76519 - 1227 WP_024186316 RNA-guided endonuclease TnpB family protein -
LNN29_RS24465 (LNN29_24415) 76578..76982 + 405 WP_001175009 IS200/IS605 family transposase -
LNN29_RS24470 (LNN29_24420) 77314..77523 - 210 WP_032178830 hemolysin expression modulator Hha -
LNN29_RS24475 (LNN29_24425) 77621..78283 - 663 WP_000644794 plasmid IncI1-type surface exclusion protein ExcA -
LNN29_RS24480 (LNN29_24430) 78354..80522 - 2169 WP_000698368 DotA/TraY family protein traY
LNN29_RS24485 (LNN29_24435) 80619..81203 - 585 WP_001037985 IncI1-type conjugal transfer protein TraX -
LNN29_RS24490 (LNN29_24440) 81232..82434 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
LNN29_RS24495 (LNN29_24445) 82401..83015 - 615 WP_000337400 IncI1-type conjugal transfer protein TraV traV
LNN29_RS24500 (LNN29_24450) 83015..86059 - 3045 WP_229321789 IncI1-type conjugal transfer protein TraU traU
LNN29_RS24505 (LNN29_24455) 86116..87654 - 1539 WP_001547431 IS66-like element ISEc8 family transposase -
LNN29_RS24510 (LNN29_24460) 87704..88051 - 348 WP_000612591 IS66 family insertion sequence element accessory protein TnpB -
LNN29_RS24515 (LNN29_24465) 88048..88428 - 381 WP_072157534 transposase -
LNN29_RS24520 (LNN29_24470) 88521..89336 - 816 Protein_101 IS4 family transposase -
LNN29_RS24525 (LNN29_24475) 89375..90100 + 726 WP_104920585 conjugal transfer complement resistance protein TraT -
LNN29_RS24530 (LNN29_24480) 90282..90959 + 678 WP_001682408 IS66-like element accessory protein TnpA -
LNN29_RS24535 (LNN29_24485) 90959..91306 + 348 WP_000624622 IS66 family insertion sequence element accessory protein TnpB -
LNN29_RS24540 (LNN29_24490) 91326..92897 + 1572 WP_000381395 IS66-like element ISCro1 family transposase -
LNN29_RS24545 (LNN29_24495) 93060..95213 + 2154 WP_104920584 type IV conjugative transfer system coupling protein TraD virb4
LNN29_RS24550 (LNN29_24500) 95213..99826 + 4614 WP_104920583 conjugative transfer relaxase/helicase TraI -
LNN29_RS24555 (LNN29_24505) 99860..100105 + 246 Protein_108 thermonuclease family protein -

Host bacterium

ID   8266 GenBank   NZ_CP086607
Plasmid name   pEF45-3 Incompatibility group   -
Plasmid size   101785 bp Coordinate of oriT [Strand]   65923..66010 [-]
Host baterium   Escherichia fergusonii strain EF20JDJ4045

Cargo genes

Drug resistance gene   -
Virulence gene   iutA, iucD, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -