Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101712
Name   oriT_pRHBSTW-00265_4 in_silico
Organism   Escherichia marmotae strain RHBSTW-00265
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXQN010000004 (30290..30412 [+], 123 nt)
oriT length   123 nt
IRs (inverted repeats)      100..105, 118..123  (TTTAAT..ATTAAA)
 90..98, 112..120  (AATAATGTA..TACATTATT)
 89..94, 106..111  (AAATAA..TTATTT)
 87..92, 104..109  (ATAAAT..ATTTAT)
 38..45, 48..55  (GCAAAAAC..GTTTTTGC)
 2..9, 14..21  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 123 nt

>oriT_pRHBSTW-00265_4
GTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTGGTTTATGTTATAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1459 GenBank   WP_182140475
Name   traI_HV138_RS23340_pRHBSTW-00265_4 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191901.45 Da        Isoelectric Point: 5.8177

>WP_182140475.1 conjugative transfer relaxase/helicase TraI [Escherichia marmotae]
MLSISVVKSAGSAGNYYTDKDNYYVLGSMEERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTLAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQILITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAEDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRQEKMPVADGERLRVTGKIPGLRVSGGDRLQVASTSEGSMTVVVPGRAEPATLPVGDSPFTALKL
ESGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLTRHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFATEGTSFADLGQEIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQIM
VPVLSTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKGDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGLQTRVIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWTDAINNAVQKGTAHDVL
EPKADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDISDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERERAAITEREAALPESVLRESQREREAIREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   582 GenBank   WP_059222172
Name   WP_059222172_pRHBSTW-00265_4 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14581.61 Da        Isoelectric Point: 5.0359

>WP_059222172.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Escherichia]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQVERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYTNMVDDIREKVSVEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   583 GenBank   WP_071645896
Name   WP_071645896_pRHBSTW-00265_4 insolico UniProt ID   _
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.06 Da        Isoelectric Point: 9.7727

>WP_071645896.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MRRRNARGGISRTVSVYLDEDTNNRLIQAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure



No available structure.




T4CP

ID   1136 GenBank   WP_182140459
Name   traC_HV138_RS23240_pRHBSTW-00265_4 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99148.88 Da        Isoelectric Point: 6.0798

>WP_182140459.1 type IV secretion system protein TraC [Escherichia marmotae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVKASWLAKKNQARIDDVVNFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVV

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-763)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   1137 GenBank   WP_182140473
Name   traD_HV138_RS23335_pRHBSTW-00265_4 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82916.64 Da        Isoelectric Point: 5.1730

>WP_182140473.1 type IV conjugative transfer system coupling protein TraD [Escherichia marmotae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDKKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGISTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPREINPEMENRLSAVLAAREAEGRQVASLFEPDVPEVVSGEDVVQAEQPQQPQQPQQ
PQQPQQPVSSVINDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
TQQQMQRREEVNINVHRERGEDVEPGDDF

  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)

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 32665..52983

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV138_RS24200 27962..28168 + 207 WP_249423634 single-stranded DNA-binding protein -
HV138_RS23165 (HV138_23165) 28192..28488 + 297 WP_182140510 hypothetical protein -
HV138_RS23170 (HV138_23170) 28598..29419 + 822 WP_182140512 DUF932 domain-containing protein -
HV138_RS23175 (HV138_23175) 29717..30286 - 570 Protein_48 transglycosylase SLT domain-containing protein -
HV138_RS23180 (HV138_23180) 30642..31025 + 384 WP_059222172 conjugal transfer relaxosome DNA-binding protein TraM -
HV138_RS23185 (HV138_23185) 31217..31903 + 687 WP_182140514 PAS domain-containing protein -
HV138_RS23190 (HV138_23190) 31997..32224 + 228 WP_071645896 conjugal transfer relaxosome protein TraY -
HV138_RS23195 (HV138_23195) 32258..32650 + 393 WP_170898794 type IV conjugative transfer system pilin TraA -
HV138_RS23200 (HV138_23200) 32665..32976 + 312 WP_000012118 type IV conjugative transfer system protein TraL traL
HV138_RS23205 (HV138_23205) 32998..33564 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HV138_RS23210 (HV138_23210) 33551..34279 + 729 WP_016233172 type-F conjugative transfer system secretin TraK traK
HV138_RS23215 (HV138_23215) 34279..35727 + 1449 WP_182140516 F-type conjugal transfer pilus assembly protein TraB traB
HV138_RS23220 (HV138_23220) 35717..36304 + 588 WP_182140455 conjugal transfer pilus-stabilizing protein TraP -
HV138_RS23225 (HV138_23225) 36291..36611 + 321 WP_045896528 conjugal transfer protein TrbD -
HV138_RS23230 (HV138_23230) 36608..37123 + 516 WP_045896530 type IV conjugative transfer system lipoprotein TraV traV
HV138_RS23235 (HV138_23235) 37258..37479 + 222 WP_182140457 conjugal transfer protein TraR -
HV138_RS23240 (HV138_23240) 37639..40266 + 2628 WP_182140459 type IV secretion system protein TraC virb4
HV138_RS23245 (HV138_23245) 40263..40649 + 387 WP_000214093 type-F conjugative transfer system protein TrbI -
HV138_RS23250 (HV138_23250) 40646..41278 + 633 WP_045896538 type-F conjugative transfer system protein TraW traW
HV138_RS23255 (HV138_23255) 41275..42267 + 993 WP_045896540 conjugal transfer pilus assembly protein TraU traU
HV138_RS23260 (HV138_23260) 42421..42789 + 369 WP_045896542 hypothetical protein -
HV138_RS23265 (HV138_23265) 42951..43286 + 336 WP_182140461 hypothetical protein -
HV138_RS23270 (HV138_23270) 43279..43731 + 453 WP_170898601 hypothetical protein -
HV138_RS23275 (HV138_23275) 43759..44397 + 639 WP_170898603 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV138_RS23280 (HV138_23280) 44394..46202 + 1809 WP_182140463 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV138_RS23285 (HV138_23285) 46229..46486 + 258 WP_157940592 conjugal transfer protein TrbE -
HV138_RS23290 (HV138_23290) 46479..47222 + 744 WP_170898607 type-F conjugative transfer system pilin assembly protein TraF traF
HV138_RS23295 (HV138_23295) 47383..47619 + 237 WP_212768171 type-F conjugative transfer system pilin chaperone TraQ -
HV138_RS23300 (HV138_23300) 47606..48151 + 546 WP_182140465 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV138_RS23305 (HV138_23305) 48081..48422 + 342 WP_182140467 P-type conjugative transfer protein TrbJ -
HV138_RS23310 (HV138_23310) 48409..48801 + 393 WP_249423636 F-type conjugal transfer protein TrbF -
HV138_RS23315 (HV138_23315) 48788..50161 + 1374 WP_105266958 conjugal transfer pilus assembly protein TraH traH
HV138_RS23320 (HV138_23320) 50158..52983 + 2826 WP_182140471 conjugal transfer mating-pair stabilization protein TraG traG
HV138_RS23325 (HV138_23325) 52980..53489 + 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
HV138_RS23330 (HV138_23330) 53503..54234 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
HV138_RS23335 (HV138_23335) 54487..56676 + 2190 WP_182140473 type IV conjugative transfer system coupling protein TraD -

Host bacterium

ID   2156 GenBank   NZ_JABXQN010000004
Plasmid name   pRHBSTW-00265_4 Incompatibility group   -
Plasmid size   70794 bp Coordinate of oriT [Strand]   30290..30412 [+]
Host baterium   Escherichia marmotae strain RHBSTW-00265

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11