Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   109510
Name   oriT_pT2-4-4-ndm in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain YT2-4-4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OM179752 (102768..102891 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pT2-4-4-ndm
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTTAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   6348 GenBank   WP_221829827
Name   traI_NBU52_RS00810_pT2-4-4-ndm 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: 191875.45 Da        Isoelectric Point: 5.9767

>WP_221829827.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVGDSPFTALKL
ESGWVETPGHSVSHSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTSFVDLGREINA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWVDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPESVLREPQREREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

AAA domain (AAA_30)

(969-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   3356 GenBank   WP_000124981
Name   WP_000124981_pT2-4-4-ndm insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   3357 GenBank   WP_001254386
Name   WP_001254386_pT2-4-4-ndm insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   6955 GenBank   WP_001064243
Name   traC_NBU52_RS00710_pT2-4-4-ndm insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99191.87 Da        Isoelectric Point: 5.8486

>WP_001064243.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.



ID   6956 GenBank   WP_034169381
Name   traD_NBU52_RS00805_pT2-4-4-ndm insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83846.52 Da        Isoelectric Point: 5.2346

>WP_034169381.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 102196..129524

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NBU52_RS00620 97805..99472 - 1668 WP_012372796 group II intron reverse transcriptase/maturase -
NBU52_RS00625 100201..100374 - 174 Protein_124 hypothetical protein -
NBU52_RS00630 100671..100967 + 297 WP_001272251 hypothetical protein -
NBU52_RS00635 101078..101899 + 822 WP_001234445 DUF932 domain-containing protein -
NBU52_RS00640 102196..102798 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
NBU52_RS00645 103120..103503 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
NBU52_RS00650 103694..104380 + 687 WP_015059009 PAS domain-containing protein -
NBU52_RS00655 104474..104701 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
NBU52_RS00660 104735..105097 + 363 WP_000340273 type IV conjugative transfer system pilin TraA -
NBU52_RS00665 105102..105413 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
NBU52_RS00670 105435..106001 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
NBU52_RS00675 105988..106716 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
NBU52_RS00680 106716..108143 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
NBU52_RS00685 108133..108705 + 573 WP_063078161 conjugal transfer pilus-stabilizing protein TraP -
NBU52_RS00690 108702..108899 + 198 WP_001324648 conjugal transfer protein TrbD -
NBU52_RS00695 108911..109162 + 252 WP_001038341 conjugal transfer protein TrbG -
NBU52_RS00700 109159..109674 + 516 WP_000809906 type IV conjugative transfer system lipoprotein TraV traV
NBU52_RS00705 109809..110030 + 222 WP_001278689 conjugal transfer protein TraR -
NBU52_RS00710 110190..112817 + 2628 WP_001064243 type IV secretion system protein TraC virb4
NBU52_RS00715 112814..113200 + 387 WP_000214096 type-F conjugative transfer system protein TrbI -
NBU52_RS00720 113197..113829 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
NBU52_RS00725 113826..114818 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
NBU52_RS00730 114844..115305 + 462 WP_000277845 hypothetical protein -
NBU52_RS00735 115335..115787 + 453 WP_000069427 hypothetical protein -
NBU52_RS00740 115857..116453 + 597 WP_232610088 type-F conjugative transfer system pilin assembly protein TrbC trbC
NBU52_RS00745 116450..118258 + 1809 WP_000821844 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NBU52_RS00750 118285..118545 + 261 WP_000864323 conjugal transfer protein TrbE -
NBU52_RS00755 118538..119281 + 744 WP_001030376 type-F conjugative transfer system pilin assembly protein TraF traF
NBU52_RS00760 119297..119644 + 348 WP_001287893 conjugal transfer protein TrbA -
NBU52_RS00765 119766..120047 + 282 WP_077917747 type-F conjugative transfer system pilin chaperone TraQ -
NBU52_RS00770 120034..120579 + 546 WP_105078375 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NBU52_RS00775 120509..120871 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
NBU52_RS00780 120868..122244 + 1377 WP_000982842 conjugal transfer pilus assembly protein TraH traH
NBU52_RS00785 122241..125066 + 2826 WP_221262076 conjugal transfer mating-pair stabilization protein TraG traG
NBU52_RS00790 125063..125572 + 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
NBU52_RS00795 125586..126317 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
NBU52_RS00800 126520..127257 + 738 WP_000199911 hypothetical protein -
NBU52_RS00805 127308..129524 + 2217 WP_034169381 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   9945 GenBank   NZ_OM179752
Plasmid name   pT2-4-4-ndm Incompatibility group   -
Plasmid size   138709 bp Coordinate of oriT [Strand]   102768..102891 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain YT2-4-4

Cargo genes

Drug resistance gene   qnrS1, tet(A), blaTEM-1B, aph(6)-Id, aph(3'')-Ib, sul2, dfrA14, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -