Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104823
Name   oriT_pUSP3 in_silico
Organism   Aminobacter sp. MSH1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP028971 (12953..12989 [+], 37 nt)
oriT length   37 nt
IRs (inverted repeats)      22..27, 32..37  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 37 nt

>oriT_pUSP3
GGATCCAAGGGCGCAGTAATACGTCGCTGATGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3420 GenBank   WP_108610784
Name   traA_DCS14_RS30395_pUSP3 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123759.27 Da        Isoelectric Point: 10.0608

>WP_108610784.1 Ti-type conjugative transfer relaxase TraA [Aminobacter sp. MSH1]
MAITHFTPQLIGRGNGRSAVLSAAYRHCAKMTYEMEARTVDYSNKRNLAYEEFLLPADAPDWARKLIADR
SVSGAVEAFWNRVEAFEKREDAQFAKEFIIALPAELTKEQNIALMRQFVFEQVLARGQVADWVYHDEPGN
PHVHLMTTLRPLTESGFGAKKVAVLGQDGQPVRTKTGKIQYRLWAGEKQDFLEQRNSWLDLQNQHLALGG
VEIRVDGRSYAERGIDLVPTVHIGVGAKAIQRKGVQQGWTPSLDRIEQFEAQRQENARRILRRPEIVLDL
LSSEKSVFDSQDIAKVLHRYVDDAGTFQHLMTRIVQSPDLLRIEREGVEFATGERVRARYTTRELIRVEA
EMAKRAIWLSERTSHGVRQKVLDATFARHERLSQEQRVAIEHVAGAARIAAVVGRAGAGKTTMMKAAREA
WESAGYRVVGGALAGKAAEGLEKEAGIASRTLASWELRWKEGRDALDGKTVFVLDEAGMVASKQMALFVE
AALRTGAKLVLVGDPEQLQPIEAGAAFRAIVERIGYAELETIYRQREDWMRKASLDLARSRVDQAISAYR
GRGRVMGSDLKAQAVENLIADWNSDYDATKSTLILAHLRRDVRMLNVMAREKLVERGIVGEGHVFRTEDG
MRRFDAGDQIVFLKNDGSLGVKNGMIAKVVEVAPNRIVAEIGEGDQRHRVSVDQRFYRNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVALTRHREDMALYYGRRSFGMNGGLVKVLSRRNAKETTLDYERGTLY
RQALRFAENRGLHIARVARTLVRDRVDWTLRQKQRLADLGLRLRGFGERLGLLDTPQTQTLKECAPMVKG
VTQFPYSVQDTVEEKLLADPAVKKQWEEVSTRFRFVFADPETAFRAMNFDAVLTDPSTAKATLERLVSEP
ATIGPLKGRVGLLAGKADREDRHIAQVTAPALKRDIERYLRLRQTAVQKVEAEEQTLRRRFSIDIPALSP
AAIQVLERVRDAIDRNDLPTALGYALADRMAKAEIDGFNKAITERFGERTLLTNAAREPSGKLFDRAAEG
LAPDERQKLAEAWPVMRAAQQIAAHERTVETLKQAENLRLSQRQTPVLKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-734)


  Protein structure



No available structure.




T4CP

ID   3358 GenBank   WP_108610716
Name   traG_DCS14_RS30380_pUSP3 insolico UniProt ID   _
Length   641 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 641 a.a.        Molecular weight: 68781.66 Da        Isoelectric Point: 9.1176

>WP_108610716.1 Ti-type conjugative transfer system protein TraG [Aminobacter sp. MSH1]
MTANKLLLAGSAAALMLGACIGISGVETWLAGFGTSDAARLMLGRTGIALPYIAAAVIGVIFLFASAGAS
AIRAAGWGVAAGTVGVVAIAIAREAVRLSALADRVPAGRTILSYVDPATMAGATIAMICGGFAMRVAMRG
NAAFAVATPRRIRGKRAVHGEADWMSLPAAARLFPDSGGIAIGERYRVDRDSVAAEPFRADARETWGGGG
RSPLICFDGSFGSSHGIVFAGSGGFKTTSITVPTALKWGGSLVVLDPSSEVAPMVIGHRRRAGRNVFLLD
PGNAAIGFNALDWIGRFGSTKEEDIVAVATWIITDNPRQASARDDFFRASALQLLTVLIADVCLSGHTEE
KDQTLRRVRSNLSEPEPKLRERLTAIHDQSESAFVKENVAPFIAMTPETFSGVYANAVKETHWLSYSNYA
ALVSGSSFTTDELAAGETDIFIALDLKVLETHPGLARVIIGALMNAIYNRNGEVKGRTLFLLDEVARLGF
LRVLETARDAGRKYGITMTLLYQSIGQMREAYGGRDATSKWFESASWVSFAAINDPETADYISKRCGDTT
VEVDQTSRSSQMSGSSRTRSKQLTRRPLILPHEVMQMRADEQIVFTAGNPPLRCGRAIWFRRADMKACVG
ENRFHRKETEA

  Protein domains


Predicted by InterproScan.

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

(164-639)

  Protein structure



No available structure.



ID   3359 GenBank   WP_108610730
Name   t4cp2_DCS14_RS30470_pUSP3 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91435.78 Da        Isoelectric Point: 5.6624

>WP_108610730.1 conjugal transfer protein TrbE [Aminobacter sp. MSH1]
MAALRSFRHSGPSFSDLVPYAALVANGVILLKDGSLMAGWYFAGPDSESSTDTERNEVSRQINTVLSRLG
SGWMIQVEAVRVGTSDYPANDQCHFPDPVTLAIDGERRTHFQKERGHYESRHALILTWRPPEKTRSGLAR
YVYSDSESRTARYADTVLDSFQTSIREVEQYLGNVLSIRRMVTQSVEERGGFQTARYDELFQFIRFCITG
ENHPIRLPEIPMYLDWLATAEFHHGLSPMVENHYLAVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFIF
LDDQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMMMVAETEDAIAQASSQLVAYGYYTPVIVL
FDDSEARLREKAEAVRRLIQAEGFGARIETVNATEAFLGSLPGNWYANIREPLINTRNLADLIPLNSVWS
GAPAAPCPFYPPASPPLMLVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLSLVAAQFRRYAFAQIFA
FDKGRSMLPLTLAAGGDHYEIGETEGEGGPRLAFCPLSDLATDGDRAWASEWIETLVVLQGVNITPDHRN
AISRQVALMADSSGRSLSDFVSGVQLREIKEALHHYTVDGPMGQLLDAESDGLSLGSFQTFEIEQLMNMG
ERSLVPVLLYLFRRIEKRLTGAPSLIILDEAWLMLGHATFRDKIREWLKVLRKANCAVVLATQSITDAER
SGIIDVLKESCPTKICLPNGAARERGTREFYERIGFNERQIEIVATALPKREYYVVSPDGRRLFDMALGP
VALAFAGASGKEDLKRIQALSAEHGGDWPVHWLQQRGIGDAETILERG

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(188-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 10389..32859

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DCS14_RS30345 6005..6589 + 585 WP_108610712 hypothetical protein -
DCS14_RS30350 6910..7836 + 927 WP_108610713 zincin-like metallopeptidase domain-containing protein -
DCS14_RS30355 7836..8015 + 180 Protein_11 hypothetical protein -
DCS14_RS30365 8632..8946 + 315 WP_108610714 DUF736 domain-containing protein -
DCS14_RS31760 9028..9174 + 147 WP_159097927 hypothetical protein -
DCS14_RS30370 9263..9508 - 246 WP_108610715 WGR domain-containing protein -
DCS14_RS30375 9593..9979 - 387 WP_108610783 thermonuclease family protein -
DCS14_RS30380 10389..12314 - 1926 WP_108610716 Ti-type conjugative transfer system protein TraG virb4
DCS14_RS30385 12301..12516 - 216 WP_108610717 type IV conjugative transfer system coupling protein TraD -
DCS14_RS30390 12521..12817 - 297 WP_108610718 conjugal transfer protein TraC -
DCS14_RS30395 13066..16368 + 3303 WP_108610784 Ti-type conjugative transfer relaxase TraA -
DCS14_RS30400 16365..16895 + 531 WP_108610719 conjugative transfer signal peptidase TraF -
DCS14_RS30405 16912..18051 + 1140 WP_245453616 conjugal transfer protein TraB -
DCS14_RS30410 18066..18680 + 615 WP_108610721 TraH family protein virB1
DCS14_RS30415 18971..19294 + 324 WP_108610722 transcriptional repressor TraM -
DCS14_RS30420 19309..20013 - 705 WP_245453614 autoinducer binding domain-containing protein -
DCS14_RS30425 20398..22011 + 1614 WP_108610723 hypothetical protein -
DCS14_RS30430 22001..23026 + 1026 WP_108610724 dienelactone hydrolase-related enzyme -
DCS14_RS30435 23290..24594 - 1305 WP_108610725 IncP-type conjugal transfer protein TrbI virB10
DCS14_RS30440 24606..25058 - 453 WP_108610726 conjugal transfer protein TrbH -
DCS14_RS30445 25062..25901 - 840 WP_108610786 P-type conjugative transfer protein TrbG virB9
DCS14_RS30450 25919..26581 - 663 WP_108610727 conjugal transfer protein TrbF virB8
DCS14_RS30455 26600..27787 - 1188 WP_108610728 P-type conjugative transfer protein TrbL virB6
DCS14_RS30460 27781..27990 - 210 WP_245453615 entry exclusion protein TrbK -
DCS14_RS30465 27987..28787 - 801 WP_108610729 P-type conjugative transfer protein TrbJ virB5
DCS14_RS30470 28759..31215 - 2457 WP_108610730 conjugal transfer protein TrbE virb4
DCS14_RS30475 31226..31537 - 312 WP_108610731 conjugal transfer protein TrbD virB3
DCS14_RS30480 31530..31901 - 372 WP_108610732 TrbC/VirB2 family protein virB2
DCS14_RS30485 31891..32859 - 969 WP_108610733 P-type conjugative transfer ATPase TrbB virB11
DCS14_RS30490 33421..34614 + 1194 WP_067970026 plasmid partitioning protein RepA -
DCS14_RS30495 34836..35759 + 924 WP_343207477 plasmid partitioning protein RepB -
DCS14_RS30500 35934..37277 + 1344 WP_108610735 plasmid replication protein RepC -
DCS14_RS30505 37327..37854 - 528 Protein_41 recombinase family protein -

Host bacterium

ID   5261 GenBank   NZ_CP028971
Plasmid name   pUSP3 Incompatibility group   -
Plasmid size   97029 bp Coordinate of oriT [Strand]   12953..12989 [+]
Host baterium   Aminobacter sp. MSH1

Cargo genes

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