Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107944
Name   oriT_YIC4027|unnamed in_silico
Organism   Sinorhizobium alkalisoli strain YIC4027
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP034911 (333658..333686 [-], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_YIC4027|unnamed
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5331 GenBank   WP_069460873
Name   traA_EKH55_RS28615_YIC4027|unnamed insolico UniProt ID   A0A1E3V5C0
Length   1538 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1538 a.a.        Molecular weight: 170233.49 Da        Isoelectric Point: 9.5172

>WP_069460873.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium alkalisoli]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAAELMHEELALPEDIPAWLKAALDG
QSVAKASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVRDNLTSRGMVADWVYHDKDG
NAHIHLITTLRPLTEEGFGPKKVAVTGEDGEPLRVVTPDRSNGKIVYRLWAGDKETMKSWKIAWAETANR
HLALAGHEVRLDGRSYAEQGLDGIAQQHLGPEKAALARKGVEMYFAPADLARRQEMADRLLVEPELLLKQ
LANERSTFDERDIAKALHRYVDDPTGFANIRARLMASDDLVLLRPQQVDGQYGKVSEPAIFTTRDILRIE
YDMAQSAEHLAKQKGFGVSPRHVSAAVASIETANPEKAFKLDAEQVDAVRHVTGDNGIAAVVGLAGAGKS
TLLASARVAWESEHRRVIGAALAGKAAEGLEDNSGIRSRTLASWELAWAGGRELLHRGDVLVIDEAGMVS
SGQMARVLKTVEDAGAKAVLVGDAMQLQPIQAGAAFRAISERIGFAELAGVRRQRDEWARDASRLFARGN
VERGLDAYAQRGHITEAERRDEIIGRIVADWTEARRDLLQKITDGGTAPRLRGDELLVLAHTNEDVKRLN
QSLRKVMMEESALTDAREYQTARGLREFAAGDRIIFLENARFLEPRARRHGPQYVKNGMLGTVVSTGDKQ
GDTLLTVRLDNGRDVVLSEDSYRNIDHGYAATIHKSQGATVDRTFILATGMMDQHLTYVAMTRHRDRADL
YAAREDFEGKPGWGHRPRVDHAAGVTGELVATGFARFRPEDEDSENPFADVRKNDGTVHRLWGVSLPKAL
KEAVVSDGDTVTLRKDGVEKVKVTIPVIDENTGEKLFEEREVDRNVWTAKLIESAKARVERIERENHRPE
LFGELVERLGRSGAKTTTLEFESEEGYRTLRQDFARRRGIDTLAGVAAGMEEGVSRQLAWIAEKREKVAK
LWERASVALGFAIAHERRTAYTEEPRVSLASDIPATGKYLIPPTTMFVRSVNEDARRAQLASPRWKERDA
ILRPVLKKIHRDPEAALVRLNTLVSDTMIEPRKLVDDLGVKPERLGRLHGSNLMVDGRAERDKRAAATAA
IKDLLPLARAHATEFCRTAGQFIERERTRRKYMAQSIPALSKPAMARLVEIEAIRERGGEDAYKTAFAYA
GEDRALVQEVKAVNDALTARFGWSAFTAKADAVAERNITDRMPDVLSPERRDKLTRLFAVIRRFAEEQHL
AEKQDRSKIVAGASVAAAPETVTVLPMLAAVTEFKTPVEEEARIRAIAAAHYRHHRAAFAETAMRVWRDP
AGGIEKIEALLAKGFAGDRIAEAVNNDPSAYGALRGSGRLVDKLLAPGRERKEALLAVPEAASRIRSLGA
SYASALDAEIRGIVEERRRMAVAIPGLSKAAEDALYRLTAEMSKKGSKLDVAAGSLDPAIAREFAIVSRA
LDERFGPKAILRGEKDVINRVAPAQRRAFEAMREKMKVLQQTVRHQGSEQVLSERRLRTIDRARGLSR

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-578)

MobA/MobL family (MobA_MobL)

(17-249)

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

(1308-1399)


  Protein structure



No available structure.




T4CP

ID   5600 GenBank   WP_151614005
Name   traG_EKH55_RS28630_YIC4027|unnamed insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 70380.30 Da        Isoelectric Point: 9.6752

>WP_151614005.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium alkalisoli]
MALKWKLHPSLLLIFVPVAVTAFAVYVTGWRWQGLTAGLSGKAEYWFLRTAPLPALLFGPLSGLLTVWAL
PMHRRRPIAIASLACFLTVAGFYGLREFGRLSPFVKSGAVTWERALSFLDMVAVLGTVTAFMAVVVAARI
STVVPAPVKRARHGTFGDADWLPMSAAARVFPPDGEIVVGERYRVDREIVHKLPFDPNDPATWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALRYSGPLICLDPSTEVAPMVVEHRTSGLGREVMVLDPT
NPVMGFNVLDGIETSKQKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPDYEGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFRSSDIVSGKKDVFLNIPASILRSYPGIGRVIIGSLINAMVQADGAFQRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVKA
SSRNIGWDTKNSASRKSESVNFQRRPLIMPHEITQSMRKDEQIIIVQGQAPLRCGRAIYFRRKDMHAAAK
RNRFVKN

  Protein domains


Predicted by InterproScan.

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

(171-635)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 358469..368021

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EKH55_RS28725 (EKH55_5914) 353609..354046 - 438 WP_069460891 hypothetical protein -
EKH55_RS28730 (EKH55_5915) 354120..356255 - 2136 WP_151614006 ParB/RepB/Spo0J family partition protein -
EKH55_RS28735 (EKH55_5916) 356494..356826 + 333 WP_069460894 integration host factor subunit beta -
EKH55_RS28740 (EKH55_5917) 357458..357814 + 357 WP_069460895 hypothetical protein -
EKH55_RS28745 (EKH55_5918) 357811..358398 + 588 WP_069460896 AAA family ATPase -
EKH55_RS28750 (EKH55_5919) 358469..359491 - 1023 WP_069460897 P-type DNA transfer ATPase VirB11 virB11
EKH55_RS28755 (EKH55_5920) 359500..360672 - 1173 WP_069460898 type IV secretion system protein VirB10 virB10
EKH55_RS28760 (EKH55_5921) 360688..361539 - 852 WP_069460899 P-type conjugative transfer protein VirB9 virB9
EKH55_RS28765 (EKH55_5922) 361536..362207 - 672 WP_069460900 virB8 family protein virB8
EKH55_RS28770 362209..362466 - 258 WP_069460901 hypothetical protein -
EKH55_RS28775 (EKH55_5924) 362501..363433 - 933 WP_069460902 type IV secretion system protein virB6
EKH55_RS28780 (EKH55_5925) 363437..363670 - 234 WP_069460903 EexN family lipoprotein -
EKH55_RS28785 (EKH55_5926) 363667..364359 - 693 WP_245314752 P-type DNA transfer protein VirB5 virB5
EKH55_RS28790 (EKH55_5927) 364365..366731 - 2367 WP_069460905 VirB4 family type IV secretion system protein virb4
EKH55_RS28795 (EKH55_5928) 366724..367062 - 339 WP_069460906 type IV secretion system protein VirB3 virB3
EKH55_RS28800 (EKH55_5929) 367066..367365 - 300 WP_069460907 TrbC/VirB2 family protein virB2
EKH55_RS28805 (EKH55_5930) 367362..368021 - 660 WP_151614007 lytic transglycosylase domain-containing protein virB1
EKH55_RS28810 (EKH55_5931) 368024..368563 - 540 WP_069460908 hypothetical protein -
EKH55_RS28815 (EKH55_5932) 368665..369018 + 354 WP_069460909 MarR family transcriptional regulator -
EKH55_RS28820 (EKH55_5933) 369184..370086 + 903 WP_069460910 hypothetical protein -
EKH55_RS28825 (EKH55_5934) 370150..371121 + 972 WP_069460911 quinolinate synthase NadA -
EKH55_RS28830 (EKH55_5935) 371118..372413 + 1296 Protein_367 L-aspartate oxidase -

Host bacterium

ID   8379 GenBank   NZ_CP034911
Plasmid name   YIC4027|unnamed Incompatibility group   -
Plasmid size   456424 bp Coordinate of oriT [Strand]   333658..333686 [-]
Host baterium   Sinorhizobium alkalisoli strain YIC4027

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodJ, nodI, nodU, nodC, nodA, nodE, nodD, nolX, nolW, nolT, nolU, nolV, nodZ, nifX, nifN, nifE, nifD, nifH, nifS, fixA, fixB, fixC, fixX, nifB, nifZ, fixU
Anti-CRISPR   -