Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113932
Name   oriT_pGDD25-16 in_silico
Organism   Salmonella enterica subsp. enterica serovar Indiana strain GDD25-16
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH316135 (91092..91177 [-], 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_pGDD25-16
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8946 GenBank   WP_000948354
Name   traI_HTS37_RS00720_pGDD25-16 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   5233 GenBank   WP_001354030
Name   WP_001354030_pGDD25-16 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   5234 GenBank   WP_000089263
Name   WP_000089263_pGDD25-16 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   10392 GenBank   WP_000069777
Name   traC_HTS37_RS00620_pGDD25-16 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   10393 GenBank   WP_000009332
Name   traD_HTS37_RS00715_pGDD25-16 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: 90524..119007

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTS37_RS00500 86496..86930 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTS37_RS00505 86927..87646 + 720 WP_001276217 plasmid SOS inhibition protein A -
HTS37_RS00800 87868..88017 + 150 Protein_102 plasmid maintenance protein Mok -
HTS37_RS00510 87959..88084 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTS37_RS00770 88403..88699 - 297 Protein_104 hypothetical protein -
HTS37_RS00525 88999..89295 + 297 WP_001272251 hypothetical protein -
HTS37_RS00530 89406..90227 + 822 WP_001234445 DUF932 domain-containing protein -
HTS37_RS00535 90524..91114 - 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
HTS37_RS00540 91449..91832 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTS37_RS00545 92026..92697 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTS37_RS00550 92834..93061 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTS37_RS00555 93094..93453 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTS37_RS00560 93468..93779 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTS37_RS00565 93801..94367 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTS37_RS00570 94354..95082 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTS37_RS00575 95082..96533 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTS37_RS00580 96523..97089 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTS37_RS00585 97076..97396 + 321 WP_001057307 conjugal transfer protein TrbD -
HTS37_RS00590 97393..97908 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTS37_RS00595 98043..98264 + 222 WP_001278683 conjugal transfer protein TraR -
HTS37_RS00600 98257..98670 + 414 WP_000549589 hypothetical protein -
HTS37_RS00605 98663..99136 + 474 WP_000549568 hypothetical protein -
HTS37_RS00610 99216..99434 + 219 WP_000556745 hypothetical protein -
HTS37_RS00615 99462..99809 + 348 WP_000836682 hypothetical protein -
HTS37_RS00620 99935..102565 + 2631 WP_000069777 type IV secretion system protein TraC virb4
HTS37_RS00625 102562..102948 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTS37_RS00630 102945..103577 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTS37_RS00635 103574..104566 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTS37_RS00640 104596..104901 + 306 WP_000224416 hypothetical protein -
HTS37_RS00645 104910..105548 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTS37_RS00650 105545..107395 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTS37_RS00655 107422..107679 + 258 WP_000864353 conjugal transfer protein TrbE -
HTS37_RS00660 107672..108415 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HTS37_RS00665 108429..108773 + 345 WP_000556796 conjugal transfer protein TrbA -
HTS37_RS00670 108892..109176 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HTS37_RS00675 109163..109708 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTS37_RS00680 109638..109985 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HTS37_RS00685 109966..110358 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HTS37_RS00690 110345..111718 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HTS37_RS00695 111715..114537 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HTS37_RS00700 114553..115038 + 486 WP_000605870 hypothetical protein -
HTS37_RS00705 115087..115818 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HTS37_RS00710 116021..116758 + 738 WP_000199905 hypothetical protein -
HTS37_RS00715 116809..119007 + 2199 WP_000009332 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   14367 GenBank   NZ_MH316135
Plasmid name   pGDD25-16 Incompatibility group   IncFIB
Plasmid size   129455 bp Coordinate of oriT [Strand]   91092..91177 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Indiana strain GDD25-16

Cargo genes

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