Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107621
Name   oriT_HDIAp1 in_silico
Organism   Hartmannibacter diazotrophicus strain E19T
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LT960615 (14915..14951 [+], 37 nt)
oriT length   37 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 37 nt

>oriT_HDIAp1
AAGGGCGCAGTAATACGTCGCTGGCACGACGACCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5122 GenBank   WP_099559158
Name   traA_HDIA_RS24590_HDIAp1 insolico UniProt ID   _
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 121795.97 Da        Isoelectric Point: 9.9932

>WP_099559158.1 Ti-type conjugative transfer relaxase TraA [Hartmannibacter diazotrophicus]
MAITHFTPQLISRGNGRSAVLSAAYRHCAKMEHQREARYVDYSNKPNLAHEAFLLPPYAPAWARALIADR
SVAGASEAFWNAVEAFEKRSDAQLAKEFIVALPVELSAEQNIVLVNQFVSEQVLSRGQVADWVFHDDPGN
PHIHLMTTLRPLTEGGFGSKKVPMLDSGGSPVRSKSGKIQYKLWSGEKAEFLEQRQGWLDLQNRHLAMAG
LDIRVDGRSYAERGIDLVPTTHIGVGAKALQRKAGEKGRVIDLERLDRHEAERRDNAKRIKARPETVLDL
VTSERSVFDERDIAKVLHRYIDDVETFQRLLARIVQSPECLKLADETIDLATARRLPARLTTRAMIRLEA
EMVSRADWLSKRNEFAVTSKVLETVFSRHARLSDEQKAAIAHVAGPERIAAVVGRAGAGKTTMMKAAREA
WELAGYTVVGGALAGKAAEGLQKEAGIASRTLASWELGWSKGSGRLDEKTIFALDEAGMVASKQMATFVE
AVTKASAKLVLVGDAEQLQPIEAGAAFRAIAERTGYAELQTIYRQNEGWMRAASLDLARGQVANALKAYA
ARGKLVGMRLKAEAVDRLIADWNRDYDPAKSSLILAHLRRDVRLLNTLARQTLIERGLIEEGHVFKTEDG
TRNFATGDQIVFLKNEGSLGVKNGMIAKVVEASPGRMVAKVGEGEAARRVEIDQRFYRNLDHGYATTIHK
SQGATVDRIKVLASLSLDRHLTYVAMTRHREDMSLYYGSRSFAIAGGLETLLSRKNAKEVTLDYADGRFY
GQALRFANNRGLHLMRVARTLMRDRLQWTLRQKQRLAELGARLRAAGARLGLVDSALQPSRTSATRLEPM
VKGVTSFSLSVADTAEQKLQSDPALQRQWNEVSHRIRLVYADPEKAFAAMGMDTVAADKNVAATRLAQIN
EDPTHFGAMRGSKGLFADNESREDRRIAMLNVPALCRDLERYLEMREKTRQTLAAAEEAQRERVSIDIPA
LSPVAGAVLAKVRDAIDRNDLPAALGFALADNMVKAEIDAFNTAVSERFGERTLLPLDAKDAKGPAFEKA
ATGLGSAEREQLAAAWPVMRAGQQLAAEERTQAALKEAETLRHTQRQSPALKQ

  Protein domains


Predicted by InterproScan.

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

(858-953)

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5356 GenBank   WP_099559155
Name   traG_HDIA_RS24575_HDIAp1 insolico UniProt ID   _
Length   638 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 638 a.a.        Molecular weight: 68788.87 Da        Isoelectric Point: 9.1000

>WP_099559155.1 Ti-type conjugative transfer system protein TraG [Hartmannibacter diazotrophicus]
MTPSRLLLLIVPVALMVVSCLGLTGIEAWLAACGSTANAKLLLGRIGLALPYSAAASIGVIFLFAARGAV
AIRSAGSGTLIGCSVIAAIAVSREITRLDDLADRVPDGRQLLDYVDPATSIGTAIAFIAGLFAMRVALKG
DAAFAPTKPRRITGKRAIHGAADWMSISEAKALFGAAGGIVVGEAYRVDKDSIASRRFEADQKESWGVGG
KALLLCFDTSFGSTHGLVFAGSGGFKTTSVTVPTALKWGGGLVTLDPSNEVAPMVMDHRRKAGRSVFVLS
PRDPSVGFNVLDWIGKFGGTKEEDVVAVASWVVTDMGGRTSIRDDFFRASALQLITALIADVCLSGHTAK
ENQTLRQVRMNLSEPEPKLRGRLQAIHDNSASLFVRENVAAFVNMTPETFSGVYANAIKETHWLSYPNYA
ALVSGSSFATDDLANGKTDIFVNLDLKTLEAHPGLARTIIGALLNAIYNRNGETQDRTLFLLDEVARLGY
LRILETARDAGRKYGISLLLLFQSIGQMRETYGGRDAASKWFESASWVSFAAINDPETADYISRRCGNTT
IEVDQTSRTSQMSGSSRTRSKQLAARPLILPEEVLRMRGDEQIVFTAGNPPLRCGRAIWFRREDMKSVVA
ENRFHREV

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   5357 GenBank   WP_099559205
Name   t4cp2_HDIA_RS24905_HDIAp1 insolico UniProt ID   _
Length   814 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 814 a.a.        Molecular weight: 90908.39 Da        Isoelectric Point: 5.1855

>WP_099559205.1 conjugal transfer protein TrbE [Hartmannibacter diazotrophicus]
MIALKQFRNRNPSFSDLLPYAGLVEDGIILLKDGSLMAGWYFAGPDSESSTNSERNEVSRQLNAVLSRLG
SGWMIQVEAVRVPTTAYPARETCHFPDCVTRAIDEERRAHFEAERGHYESQHALILTYRPPEPRQSALVR
YVYSDEGSRSETYADGVLKSFQTSIREVEQYLANVLVIRRMVTRTVLDPETGIEARYDELFQFIRFCLVG
ENHPVRLPAIPMYLDWLVTAEFHHGLSPMVDGNYLAVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFIF
LDEQEARQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAEASSQLVAYGYYTAVIVM
FDTNEARLQDHAEAVRRLIQAEGFVARIETLNATEAYLGSLPGVTYANIREPLINTRNLADLIPVNSVWA
GSAVAPCPFYPPNAPPLMQVASGSSPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGKSLYPLTLAAGGDHYDVGAGEGALAFCPLSELSTDGDRAWASEWIETLIAMQGVTIAPDHRNAISR
QAGLMATAPGKSLSDFVSGVQMREIKTALRHYTLDGPMAQLLDAEEDGLTLGTFQTFEIEELMNMGERNL
VPVLLYLFRRIEKRLTGAPSLIILDEAWLMLGHPTFRDKIRDWLKVLRKANCAVVLATQSISDAEQSGII
DVLKESCPTKICLPNGAAREAGTREFYERIGFNERQIEIVATATPKREYYVASPEGRRLFDMALGPIALA
FVGASGKDDLKRIEELGTAHGADWPVHWLRTRGVDNAERILAAD

  Protein domains


Predicted by InterproScan.

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

(194-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 80629..90132

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HDIA_RS24845 (HDIA_P0070) 75716..77056 + 1341 WP_099559196 cytochrome c -
HDIA_RS24850 (HDIA_P0071) 77600..78949 + 1350 WP_099559197 adenylate/guanylate cyclase domain-containing protein -
HDIA_RS24855 79042..79188 - 147 Protein_71 IS3 family transposase -
HDIA_RS24860 79190..79771 - 582 Protein_72 MFS transporter -
HDIA_RS24870 (HDIA_P0073) 80629..81945 - 1317 WP_099559198 IncP-type conjugal transfer protein TrbI virB10
HDIA_RS24875 (HDIA_P0074) 81942..82409 - 468 WP_099559199 conjugal transfer protein TrbH -
HDIA_RS24880 (HDIA_P0075) 82413..83192 - 780 WP_245884340 P-type conjugative transfer protein TrbG virB9
HDIA_RS24885 (HDIA_P0076) 83258..83920 - 663 WP_099559201 conjugal transfer protein TrbF virB8
HDIA_RS24890 (HDIA_P0077) 83929..85092 - 1164 WP_099559202 P-type conjugative transfer protein TrbL virB6
HDIA_RS24895 (HDIA_P0078) 85076..85285 - 210 WP_099559203 entry exclusion protein TrbK -
HDIA_RS24900 (HDIA_P0079) 85282..86082 - 801 WP_099559204 P-type conjugative transfer protein TrbJ virB5
HDIA_RS24905 (HDIA_P0080) 86054..88498 - 2445 WP_099559205 conjugal transfer protein TrbE virb4
HDIA_RS24910 (HDIA_P0081) 88505..88804 - 300 WP_099559206 conjugal transfer protein TrbD virB3
HDIA_RS24915 (HDIA_P0082) 88797..89171 - 375 WP_099559207 TrbC/VirB2 family protein virB2
HDIA_RS24920 (HDIA_P0083) 89161..90132 - 972 WP_099559208 P-type conjugative transfer ATPase TrbB virB11
HDIA_RS24925 (HDIA_P0084) 90510..91724 + 1215 WP_099559243 plasmid partitioning protein RepA -
HDIA_RS24930 (HDIA_P0085) 91721..92722 + 1002 WP_157775828 plasmid partitioning protein RepB -
HDIA_RS24935 (HDIA_P0086) 92950..94236 + 1287 WP_099559210 plasmid replication protein RepC -

Host bacterium

ID   8056 GenBank   NZ_LT960615
Plasmid name   HDIAp1 Incompatibility group   -
Plasmid size   122332 bp Coordinate of oriT [Strand]   14915..14951 [+]
Host baterium   Hartmannibacter diazotrophicus strain E19T

Cargo genes

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