Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103343
Name   oriT_pGDD25-3 in_silico
Organism   Salmonella enterica subsp. enterica serovar Indiana strain GDD25-3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH316133 (89371..89456 [-], 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_pGDD25-3
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2501 GenBank   WP_000948354
Name   traI_HTS43_RS00715_pGDD25-3 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   1067 GenBank   WP_001354030
Name   WP_001354030_pGDD25-3 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   1068 GenBank   WP_000089263
Name   WP_000089263_pGDD25-3 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   2273 GenBank   WP_000069777
Name   traC_HTS43_RS00615_pGDD25-3 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: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   2274 GenBank   WP_000009332
Name   traD_HTS43_RS00710_pGDD25-3 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: 88803..117286

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTS43_RS00495 84775..85209 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTS43_RS00500 85206..85925 + 720 WP_001276217 plasmid SOS inhibition protein A -
HTS43_RS00795 86147..86296 + 150 Protein_100 plasmid maintenance protein Mok -
HTS43_RS00505 86238..86363 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTS43_RS00765 86682..86978 - 297 Protein_102 hypothetical protein -
HTS43_RS00520 87278..87574 + 297 WP_001272251 hypothetical protein -
HTS43_RS00525 87685..88506 + 822 WP_001234445 DUF932 domain-containing protein -
HTS43_RS00530 88803..89393 - 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
HTS43_RS00535 89728..90111 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTS43_RS00540 90305..90976 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTS43_RS00545 91113..91340 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTS43_RS00550 91373..91732 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTS43_RS00555 91747..92058 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTS43_RS00560 92080..92646 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTS43_RS00565 92633..93361 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTS43_RS00570 93361..94812 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTS43_RS00575 94802..95368 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTS43_RS00580 95355..95675 + 321 WP_001057307 conjugal transfer protein TrbD -
HTS43_RS00585 95672..96187 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTS43_RS00590 96322..96543 + 222 WP_001278683 conjugal transfer protein TraR -
HTS43_RS00595 96536..96949 + 414 WP_000549589 hypothetical protein -
HTS43_RS00600 96942..97415 + 474 WP_000549568 hypothetical protein -
HTS43_RS00605 97495..97713 + 219 WP_000556745 hypothetical protein -
HTS43_RS00610 97741..98088 + 348 WP_000836682 hypothetical protein -
HTS43_RS00615 98214..100844 + 2631 WP_000069777 type IV secretion system protein TraC virb4
HTS43_RS00620 100841..101227 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTS43_RS00625 101224..101856 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTS43_RS00630 101853..102845 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTS43_RS00635 102875..103180 + 306 WP_000224416 hypothetical protein -
HTS43_RS00640 103189..103827 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTS43_RS00645 103824..105674 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTS43_RS00650 105701..105958 + 258 WP_000864353 conjugal transfer protein TrbE -
HTS43_RS00655 105951..106694 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HTS43_RS00660 106708..107052 + 345 WP_000556796 conjugal transfer protein TrbA -
HTS43_RS00665 107171..107455 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HTS43_RS00670 107442..107987 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTS43_RS00675 107917..108264 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HTS43_RS00680 108245..108637 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HTS43_RS00685 108624..109997 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HTS43_RS00690 109994..112816 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HTS43_RS00695 112832..113317 + 486 WP_000605870 hypothetical protein -
HTS43_RS00700 113366..114097 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HTS43_RS00705 114300..115037 + 738 WP_000199905 hypothetical protein -
HTS43_RS00710 115088..117286 + 2199 WP_000009332 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3786 GenBank   NZ_MH316133
Plasmid name   pGDD25-3 Incompatibility group   IncFIB
Plasmid size   127734 bp Coordinate of oriT [Strand]   89371..89456 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Indiana strain GDD25-3

Cargo genes

Drug resistance gene   qepA1, rmtB, blaTEM-1B, blaCTX-M-27
Virulence gene   -
Metal resistance gene   pcoE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -