Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104877
Name   oriT_pRSpC104g in_silico
Organism   Rhizobium sp. C104
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP092347 (176070..176111 [+], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      22..28, 33..39  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pRSpC104g
GGATCCGAAGGGCGCAATTATACGTCGCTGGTGCGACGTCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   3393 GenBank   WP_096772214
Name   t4cp2_MF410_RS00055_pRSpC104g insolico UniProt ID   _
Length   567 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 567 a.a.        Molecular weight: 62800.99 Da        Isoelectric Point: 7.1079

>WP_096772214.1 MULTISPECIES: ATP-binding protein [Rhizobium]
MIKHSLVDPDRYVGTISVVTASTVQVNLPYATARPERRALARGAVGDFVFVDCELVKLLGRLVEVKLPDA
ERLTVEPTLGTQPDPHPVGRVQLLASVDQRQSKLIRGIRHHPRVGDAVYLADPSMFGELMANSLVASGTS
ALDIGTLDAGSGVHLRLPPEKLFGRHCGVFGATGGGKSWTLATILQQVKAAGGKCILFDPTGEFAEIPAI
SEHYAFDHEEAGSQQVHFPYQFMTEDDLFALFRPSGQSQGPKLREAIKSLKLVKKSEGQLEGVTIYEKKL
LLKKQKDRRPFLKALEVHSDVIHSPLCHFDIENLPDQVQQECVQPTDWDNPTHWGKVNEQAVGYCESLIA
RMRTLIHTPELECLFGNRGQSLVKVLEAFFASERQDILRISFKNVRFEHNTREILLNVIGRFLLARARQN
TFRDKPMITLLDEAHQFLGRTIGDEYASVKLEAFGLIAKEGRKYGLTTILATQRPRDIPADVLSQLGTLI
VHRLTNEDDRNAVEKACGDLDRNAALFIPTLAPGEAIIVGPDLPAPVPVLIHEPPSPPDSKGPKYTSYWA
SRQPRAD

  Protein domains


Predicted by InterproScan.

Helicase HerA, central domain (DUF87)

(143-289)

Helicase HerA-like C-terminal (HerA_C)

(424-528)

  Protein structure



No available structure.



ID   3394 GenBank   WP_096771503
Name   traG_MF410_RS00795_pRSpC104g insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 70846.75 Da        Isoelectric Point: 9.1951

>WP_096771503.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MSRIMLFIAPVALMILVAAGLTGIEHWLSGLGKTEAARQTLGRAGIALPYVSAGLVGIVFLFASAGAIRI
KTAGWGVVAGGAATILIAAIRETMRLSALTDKVPAGMSIFSYVDPATLIGAAAAAIAACFALRVALAGNA
AFASAEPKRVRGKRALHGEAEWMKLPEAANLFSDTGGIVIGERYRVDKDSTAARSFRADEPETWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLIVLDPSNEVAPMVSAHRTSANRDLFVLDPK
NPATGFNALDWIGKFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTAMIADVCLSGHTEKEN
QTLRQVRANLSEPEPKLRQRLQEIYDNSDSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYSNYAAL
VSGRTFSTGDLADGNTDVFINIDLKTLETHAGLARVIIGSFLNGIYNRNGTMPGRALFLLDEVARLGYMR
ILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGTTTVE
IDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGTN
RFHRLRGTPEASRIEPARSATSKADPEQ

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(162-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 187156..194921

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MF410_RS00835 (MF410_00835) 182204..182836 - 633 WP_088395887 DUF433 domain-containing protein -
MF410_RS00840 (MF410_00840) 182938..183159 - 222 WP_088395888 helix-turn-helix transcriptional regulator -
MF410_RS00845 (MF410_00845) 183388..183708 + 321 WP_088395889 transcriptional repressor TraM -
MF410_RS00850 (MF410_00850) 183712..184416 - 705 WP_088395890 autoinducer binding domain-containing protein -
MF410_RS00855 (MF410_00855) 184496..185236 - 741 WP_096764645 LuxR family transcriptional regulator -
MF410_RS00860 (MF410_00860) 185407..186701 - 1295 Protein_172 IncP-type conjugal transfer protein TrbI -
MF410_RS00865 (MF410_00865) 186713..187153 - 441 WP_088395893 conjugal transfer protein TrbH -
MF410_RS00870 (MF410_00870) 187156..187968 - 813 WP_088395894 P-type conjugative transfer protein TrbG virB9
MF410_RS00875 (MF410_00875) 187986..188648 - 663 WP_088395895 conjugal transfer protein TrbF virB8
MF410_RS00880 (MF410_00880) 188669..189850 - 1182 WP_088395896 P-type conjugative transfer protein TrbL virB6
MF410_RS00885 (MF410_00885) 189844..190044 - 201 WP_081284279 entry exclusion protein TrbK -
MF410_RS00890 (MF410_00890) 190041..190844 - 804 WP_064843797 P-type conjugative transfer protein TrbJ virB5
MF410_RS00895 (MF410_00895) 190816..193271 - 2456 Protein_179 conjugal transfer protein TrbE -
MF410_RS00900 (MF410_00900) 193282..193581 - 300 WP_064843799 conjugal transfer protein TrbD virB3
MF410_RS00905 (MF410_00905) 193574..193954 - 381 WP_064843801 TrbC/VirB2 family protein virB2
MF410_RS00910 (MF410_00910) 193944..194921 - 978 WP_064843803 P-type conjugative transfer ATPase TrbB virB11
MF410_RS00915 (MF410_00915) 194932..195555 - 624 WP_141399552 acyl-homoserine-lactone synthase -
MF410_RS00920 (MF410_00920) 195932..197156 + 1225 Protein_184 plasmid partitioning protein RepA -
MF410_RS00925 (MF410_00925) 197153..198190 + 1038 WP_064843806 plasmid partitioning protein RepB -
MF410_RS00930 (MF410_00930) 198376..199590 + 1215 WP_239619760 plasmid replication protein RepC -

Host bacterium

ID   5315 GenBank   NZ_CP092347
Plasmid name   pRSpC104g Incompatibility group   -
Plasmid size   237978 bp Coordinate of oriT [Strand]   176070..176111 [+]
Host baterium   Rhizobium sp. C104

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -