Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113599
Name   oriT_S16BD03602|p105 in_silico
Organism   Salmonella enterica strain S16BD03602
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099766 (14939..15024 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..13, 21..26  (TGATTT..AAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_S16BD03602|p105
AATTACATGATTTAAAACGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8708 GenBank   WP_253075075
Name   traI_NHV93_RS00300_S16BD03602|p105 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: 191693.21 Da        Isoelectric Point: 5.7446

>WP_253075075.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRTEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVVDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPGSERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQNGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPRADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRTATSEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   5091 GenBank   WP_001342639
Name   WP_001342639_S16BD03602|p105 insolico UniProt ID   A0A836N7B7
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: 4.7033

>WP_001342639.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISLSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A836N7B7

ID   5092 GenBank   WP_000089263
Name   WP_000089263_S16BD03602|p105 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   10082 GenBank   WP_000069752
Name   traC_NHV93_RS00195_S16BD03602|p105 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: 99572.55 Da        Isoelectric Point: 6.6265

>WP_000069752.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
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   10083 GenBank   WP_048961038
Name   traD_NHV93_RS00295_S16BD03602|p105 insolico UniProt ID   _
Length   726 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 726 a.a.        Molecular weight: 82489.07 Da        Isoelectric Point: 5.0504

>WP_048961038.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQ
QMQRREEVNINVHRERGEDVEPGDDF

  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: 14371..42330

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV93_RS00065 9755..10009 + 255 WP_001230709 hypothetical protein -
NHV93_RS00070 10006..10248 + 243 WP_000151456 hypothetical protein -
NHV93_RS00075 10430..10663 + 234 WP_000553848 hypothetical protein -
NHV93_RS00080 10795..11088 + 294 WP_112367531 hypothetical protein -
NHV93_RS00085 11396..11683 + 288 WP_000606467 hypothetical protein -
NHV93_RS00090 12111..12344 + 234 WP_000093745 hypothetical protein -
NHV93_RS00095 12420..12722 + 303 WP_000379301 hypothetical protein -
NHV93_RS00100 12994..13143 + 150 WP_000903193 hypothetical protein -
NHV93_RS00105 13254..14075 + 822 WP_073972859 DUF932 domain-containing protein -
NHV93_RS00110 14371..14973 - 603 WP_072205450 transglycosylase SLT domain-containing protein virB1
NHV93_RS00115 15296..15679 + 384 WP_001342639 conjugal transfer relaxosome DNA-binding protein TraM -
NHV93_RS00120 15870..16523 + 654 WP_001342640 conjugal transfer protein TraJ -
NHV93_RS00125 16648..16875 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
NHV93_RS00130 16908..17270 + 363 WP_023910486 type IV conjugative transfer system pilin TraA -
NHV93_RS00135 17275..17586 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
NHV93_RS00140 17608..18174 + 567 WP_000399805 type IV conjugative transfer system protein TraE traE
NHV93_RS00145 18161..18889 + 729 WP_001230809 type-F conjugative transfer system secretin TraK traK
NHV93_RS00150 18889..20316 + 1428 WP_032215882 F-type conjugal transfer pilus assembly protein TraB traB
NHV93_RS00155 20306..20890 + 585 WP_000002795 conjugal transfer pilus-stabilizing protein TraP -
NHV93_RS00160 20877..21197 + 321 WP_001057302 conjugal transfer protein TrbD virb4
NHV93_RS00165 21190..21441 + 252 WP_001038341 conjugal transfer protein TrbG -
NHV93_RS00170 21438..21953 + 516 WP_000809891 type IV conjugative transfer system lipoprotein TraV traV
NHV93_RS00175 22088..22309 + 222 WP_001278978 conjugal transfer protein TraR -
NHV93_RS00180 22302..22778 + 477 WP_001744739 hypothetical protein -
NHV93_RS00185 22858..23076 + 219 WP_072277258 hypothetical protein -
NHV93_RS00190 23104..23451 + 348 WP_160540375 hypothetical protein -
NHV93_RS00195 23577..26207 + 2631 WP_000069752 type IV secretion system protein TraC virb4
NHV93_RS00200 26204..26590 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
NHV93_RS00205 26587..27219 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
NHV93_RS00210 27216..28208 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
NHV93_RS00215 28238..28543 + 306 WP_000224411 hypothetical protein -
NHV93_RS00220 28552..29190 + 639 WP_032299189 type-F conjugative transfer system pilin assembly protein TrbC trbC
NHV93_RS00225 29187..29558 + 372 WP_000056340 hypothetical protein -
NHV93_RS00230 29583..30005 + 423 WP_001229306 HNH endonuclease -
NHV93_RS00235 30002..31810 + 1809 WP_237828321 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NHV93_RS00240 31837..32094 + 258 WP_000864319 conjugal transfer protein TrbE -
NHV93_RS00245 32087..32830 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
NHV93_RS00250 32846..32944 + 99 Protein_49 conjugal transfer protein TrbA -
NHV93_RS00255 32998..33282 + 285 WP_000623730 type-F conjugative transfer system pilin chaperone TraQ -
NHV93_RS00260 33269..33814 + 546 WP_000059832 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NHV93_RS00265 33744..34091 + 348 WP_072130275 P-type conjugative transfer protein TrbJ -
NHV93_RS00270 34072..34464 + 393 WP_001462107 F-type conjugal transfer protein TrbF -
NHV93_RS00275 34451..35824 + 1374 WP_088130027 conjugal transfer pilus assembly protein TraH traH
NHV93_RS00280 35821..38646 + 2826 WP_061089748 conjugal transfer mating-pair stabilization protein TraG traG
NHV93_RS00285 38643..39152 + 510 WP_160540419 conjugal transfer entry exclusion protein TraS -
NHV93_RS00290 39166..39897 + 732 WP_001734698 conjugal transfer complement resistance protein TraT -
NHV93_RS00295 40150..42330 + 2181 WP_048961038 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   14034 GenBank   NZ_CP099766
Plasmid name   S16BD03602|p105 Incompatibility group   IncFII
Plasmid size   52174 bp Coordinate of oriT [Strand]   14939..15024 [-]
Host baterium   Salmonella enterica strain S16BD03602

Cargo genes

Drug resistance gene   blaCTX-M-15
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -