Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113209
Name   oriT_pRM055_1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Muenster strain RM055
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP117333 (25613..25734 [+], 122 nt)
oriT length   122 nt
IRs (inverted repeats)      91..98, 112..119  (ATAATGTA..TACATTAT)
 89..94, 106..111  (AAATAA..TTATTT)
 63..71, 85..93  (TATTTAAAA..TTTTAAATA)
 56..61, 69..74  (TGATTT..AAATCA)
 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: 122 nt

>oriT_pRM055_1
GTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGTATTTAAAATCATCATATTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8476 GenBank   WP_097178389
Name   traI_PQP79_RS23170_pRM055_1 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: 191530.26 Da        Isoelectric Point: 6.0001

>WP_097178389.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTVGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGRIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDAPRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQEAILKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSGGQQTRVIRPAQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGSRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAISKAVQKGTAHDVL
EPGADREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DDKTEQAVREIAGQERERAVTSEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
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)

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

(575-626)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   4877 GenBank   WP_000124826
Name   WP_000124826_pRM055_1 insolico UniProt ID   _
Length   128 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 128 a.a.        Molecular weight: 14661.78 Da        Isoelectric Point: 4.8581

>WP_000124826.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MARVILYISNDVYDKVNAIVEKRRQEGARDKEISISGTASMLLELGLRVYEAQMERKESSFNQTEFNKVL
LECVVKTQSSVAKILGIESLSPHIAGNPKFEYANMVEDIREKVSIEMDRFFPKIDNEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-123)


  Protein structure



No available structure.



ID   4878 GenBank   WP_096936277
Name   WP_096936277_pRM055_1 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: 9044.19 Da        Isoelectric Point: 10.1422

>WP_096936277.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure



No available structure.




T4CP

ID   9777 GenBank   WP_097178394
Name   traC_PQP79_RS23065_pRM055_1 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99387.28 Da        Isoelectric Point: 6.7391

>WP_097178394.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEILGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVKASWLAKKNQARIDDVVNFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraG P-loop domain (P-loop_TraG)

(468-772)

  Protein structure



No available structure.



ID   9778 GenBank   WP_274881681
Name   traD_PQP79_RS23165_pRM055_1 insolico UniProt ID   _
Length   753 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 753 a.a.        Molecular weight: 85751.68 Da        Isoelectric Point: 5.1755

>WP_274881681.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFSAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGRTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVAWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGSGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSRKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLSGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSPAINYKKSDAGVGVPAGGIEQELKMKPEEEMEQQLPP
GISESGEVVDMAVYEAWQREQNPDTQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 25040..54413

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PQP79_RS22925 (PQP79_22925) 20863..21012 + 150 Protein_30 plasmid maintenance protein Mok -
PQP79_RS22930 (PQP79_22930) 20954..21079 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
PQP79_RS22935 (PQP79_22935) 21314..21673 - 360 WP_024223173 hypothetical protein -
PQP79_RS22940 (PQP79_22940) 21743..22015 + 273 WP_223724002 single-stranded DNA-binding protein -
PQP79_RS22945 (PQP79_22945) 21969..22292 + 324 WP_000533253 hypothetical protein -
PQP79_RS22950 (PQP79_22950) 22351..22593 + 243 WP_000540591 hypothetical protein -
PQP79_RS22955 (PQP79_22955) 22793..23216 - 424 Protein_36 hypothetical protein -
PQP79_RS22960 (PQP79_22960) 23286..23492 + 207 WP_000547974 hypothetical protein -
PQP79_RS22965 (PQP79_22965) 23516..23812 + 297 WP_021553188 hypothetical protein -
PQP79_RS22970 (PQP79_22970) 23923..24744 + 822 WP_021553189 DUF932 domain-containing protein -
PQP79_RS22975 (PQP79_22975) 25040..25549 - 510 WP_021553190 transglycosylase SLT domain-containing protein virB1
PQP79_RS22980 (PQP79_22980) 25963..26349 + 387 WP_000124826 conjugal transfer relaxosome DNA-binding protein TraM -
PQP79_RS22985 (PQP79_22985) 26538..27227 + 690 WP_000332474 PAS domain-containing protein -
PQP79_RS22990 (PQP79_22990) 27315..27542 + 228 WP_096936277 conjugal transfer relaxosome protein TraY -
PQP79_RS22995 (PQP79_22995) 27576..27941 + 366 WP_097178401 type IV conjugative transfer system pilin TraA -
PQP79_RS23000 (PQP79_23000) 27956..28267 + 312 WP_097178400 type IV conjugative transfer system protein TraL traL
PQP79_RS23005 (PQP79_23005) 28289..28855 + 567 WP_021553195 type IV conjugative transfer system protein TraE traE
PQP79_RS23010 (PQP79_23010) 28842..29570 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
PQP79_RS23015 (PQP79_23015) 29570..31000 + 1431 WP_097178399 F-type conjugal transfer pilus assembly protein TraB traB
PQP79_RS23020 (PQP79_23020) 30990..31574 + 585 WP_096936312 conjugal transfer pilus-stabilizing protein TraP -
PQP79_RS23025 (PQP79_23025) 31561..31881 + 321 WP_001057302 conjugal transfer protein TrbD virb4
PQP79_RS23030 (PQP79_23030) 31874..32125 + 252 WP_096936314 conjugal transfer protein TrbG -
PQP79_RS23035 (PQP79_23035) 32122..32637 + 516 WP_097178398 type IV conjugative transfer system lipoprotein TraV traV
PQP79_RS23040 (PQP79_23040) 32772..32993 + 222 WP_097178397 conjugal transfer protein TraR -
PQP79_RS23045 (PQP79_23045) 32986..33459 + 474 WP_097178396 hypothetical protein -
PQP79_RS23050 (PQP79_23050) 33456..33842 + 387 WP_274881628 hypothetical protein -
PQP79_RS23055 (PQP79_23055) 33922..34170 + 249 WP_097178395 hypothetical protein -
PQP79_RS23060 (PQP79_23060) 34167..34514 + 348 WP_021553203 hypothetical protein -
PQP79_RS23065 (PQP79_23065) 34645..37275 + 2631 WP_097178394 type IV secretion system protein TraC virb4
PQP79_RS23070 (PQP79_23070) 37272..37658 + 387 WP_021553205 type-F conjugative transfer system protein TrbI -
PQP79_RS23075 (PQP79_23075) 37655..38287 + 633 WP_021569944 type-F conjugative transfer system protein TraW traW
PQP79_RS23080 (PQP79_23080) 38284..39276 + 993 WP_000817325 conjugal transfer pilus assembly protein TraU traU
PQP79_RS23085 (PQP79_23085) 39303..39635 + 333 WP_021553224 hypothetical protein -
PQP79_RS23090 (PQP79_23090) 39763..40401 + 639 WP_021553225 type-F conjugative transfer system pilin assembly protein TrbC trbC
PQP79_RS23095 (PQP79_23095) 40398..42248 + 1851 WP_097231216 type-F conjugative transfer system mating-pair stabilization protein TraN traN
PQP79_RS23100 (PQP79_23100) 42275..42532 + 258 WP_063113354 conjugal transfer protein TrbE -
PQP79_RS23105 (PQP79_23105) 42525..43268 + 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
PQP79_RS23110 (PQP79_23110) 43282..43647 + 366 WP_021572669 hypothetical protein -
PQP79_RS23115 (PQP79_23115) 43777..44178 + 402 WP_021572668 hypothetical protein -
PQP79_RS23120 (PQP79_23120) 44245..44526 + 282 WP_000049684 type-F conjugative transfer system pilin chaperone TraQ -
PQP79_RS23125 (PQP79_23125) 44513..45058 + 546 WP_040084549 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
PQP79_RS23130 (PQP79_23130) 44988..45335 + 348 WP_097178392 P-type conjugative transfer protein TrbJ -
PQP79_RS23135 (PQP79_23135) 45316..45708 + 393 WP_244578643 F-type conjugal transfer protein TrbF -
PQP79_RS23140 (PQP79_23140) 45695..47068 + 1374 WP_123000941 conjugal transfer pilus assembly protein TraH traH
PQP79_RS23145 (PQP79_23145) 47065..49911 + 2847 WP_096936249 conjugal transfer mating-pair stabilization protein TraG traG
PQP79_RS23150 (PQP79_23150) 49908..50417 + 510 WP_096936248 conjugal transfer entry exclusion protein TraS -
PQP79_RS23155 (PQP79_23155) 50431..51162 + 732 WP_089700085 conjugal transfer complement resistance protein TraT -
PQP79_RS23160 (PQP79_23160) 51365..52096 + 732 WP_122997022 hypothetical protein -
PQP79_RS23165 (PQP79_23165) 52152..54413 + 2262 WP_274881681 type IV conjugative transfer system coupling protein TraD prgC

Host bacterium

ID   13644 GenBank   NZ_CP117333
Plasmid name   pRM055_1 Incompatibility group   -
Plasmid size   66452 bp Coordinate of oriT [Strand]   25613..25734 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Muenster strain RM055

Cargo genes

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