Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113931
Name   oriT_pGDD25-5 in_silico
Organism   Salmonella enterica subsp. enterica serovar Indiana strain GDD25-5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH316134 (62572..62657 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_pGDD25-5
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8945 GenBank   WP_000948354
Name   traI_HTS99_RS00560_pGDD25-5 insolico UniProt ID   A0AA36L3I8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


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

>WP_000948354.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
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.




Auxiliary protein

ID   5231 GenBank   WP_001354030
Name   WP_001354030_pGDD25-5 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3

ID   5232 GenBank   WP_000089263
Name   WP_000089263_pGDD25-5 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9


T4CP

ID   10390 GenBank   WP_172693526
Name   traC_HTS99_RS00460_pGDD25-5 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: 99147.82 Da        Isoelectric Point: 6.1126

>WP_172693526.1 type IV secretion system protein TraC [Salmonella enterica]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEVAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(469-772)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   10391 GenBank   WP_000009332
Name   traD_HTS99_RS00555_pGDD25-5 insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


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

>WP_000009332.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
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



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 62004..90487

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTS99_RS00340 57976..58410 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTS99_RS00345 58407..59126 + 720 WP_001276217 plasmid SOS inhibition protein A -
HTS99_RS00630 59348..59497 + 150 Protein_71 plasmid maintenance protein Mok -
HTS99_RS00350 59439..59564 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTS99_RS00610 59883..60179 - 297 Protein_73 hypothetical protein -
HTS99_RS00365 60479..60775 + 297 WP_001272251 hypothetical protein -
HTS99_RS00370 60886..61707 + 822 WP_001234445 DUF932 domain-containing protein -
HTS99_RS00375 62004..62594 - 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
HTS99_RS00380 62929..63312 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTS99_RS00385 63506..64177 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTS99_RS00390 64314..64541 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTS99_RS00395 64574..64933 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTS99_RS00400 64948..65259 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTS99_RS00405 65281..65847 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTS99_RS00410 65834..66562 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTS99_RS00415 66562..68013 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTS99_RS00420 68003..68569 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTS99_RS00425 68556..68876 + 321 WP_001057307 conjugal transfer protein TrbD -
HTS99_RS00430 68873..69388 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTS99_RS00435 69523..69744 + 222 WP_001278683 conjugal transfer protein TraR -
HTS99_RS00440 69737..70150 + 414 WP_000549589 hypothetical protein -
HTS99_RS00445 70143..70616 + 474 WP_000549568 hypothetical protein -
HTS99_RS00450 70696..70914 + 219 WP_000556745 hypothetical protein -
HTS99_RS00455 70942..71289 + 348 WP_000836682 hypothetical protein -
HTS99_RS00460 71415..74045 + 2631 WP_172693526 type IV secretion system protein TraC virb4
HTS99_RS00465 74042..74428 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTS99_RS00470 74425..75057 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTS99_RS00475 75054..76046 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTS99_RS00480 76076..76381 + 306 WP_000224416 hypothetical protein -
HTS99_RS00485 76390..77028 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTS99_RS00490 77025..78875 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTS99_RS00495 78902..79159 + 258 WP_000864353 conjugal transfer protein TrbE -
HTS99_RS00500 79152..79895 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HTS99_RS00505 79909..80253 + 345 WP_000556796 conjugal transfer protein TrbA -
HTS99_RS00510 80372..80656 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HTS99_RS00515 80643..81188 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTS99_RS00520 81118..81465 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HTS99_RS00525 81446..81838 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HTS99_RS00530 81825..83198 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HTS99_RS00535 83195..86017 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HTS99_RS00540 86033..86518 + 486 WP_000605870 hypothetical protein -
HTS99_RS00545 86567..87298 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HTS99_RS00550 87501..88238 + 738 WP_000199905 hypothetical protein -
HTS99_RS00555 88289..90487 + 2199 WP_000009332 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   14366 GenBank   NZ_MH316134
Plasmid name   pGDD25-5 Incompatibility group   IncFIB
Plasmid size   100935 bp Coordinate of oriT [Strand]   62572..62657 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Indiana strain GDD25-5

Cargo genes

Drug resistance gene   qepA1, rmtB, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -