Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115837
Name   oriT_NZLR24|p4 in_silico
Organism   Rhizobium ruizarguesonis strain NZLR24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP071682 (158964..158997 [-], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_NZLR24|p4
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10146 GenBank   WP_207580365
Name   traA_J3P73_RS35050_NZLR24|p4 insolico UniProt ID   _
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 122803.82 Da        Isoelectric Point: 9.7932

>WP_207580365.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYELWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASLGVREAVLEATFARHSRLSDEQRTAIEHVAGATRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDQTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRNASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNNMARAKLVERGVVAHGFAF
KTEDGTRVFATGDQIVFLKNEGSLGVKNGMLAKVLEAVAGRIVAEIGDGEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIAHDRLQWAVRQSSRLADLGARLAAIGAALGLVRDSNKHSVPDTI
KETKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAELKHETEERAVRLKV
SVDIPALSPSAKRTLERVRDAIDRNDLPSGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTSGMTAGQKAEVRSAWNSMRTVQQLGSHERTTEAAKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   11853 GenBank   WP_207580341
Name   t4cp2_J3P73_RS34465_NZLR24|p4 insolico UniProt ID   _
Length   907 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 907 a.a.        Molecular weight: 101280.51 Da        Isoelectric Point: 8.2223

>WP_207580341.1 type IV secretory system conjugative DNA transfer family protein [Rhizobium ruizarguesonis]
MASVSTHTETDRPKWTGLQRASLFTLPIALFGVVLLWLAFFTLIYDAYITSFGSSSYFDYVGQARLIDAV
RYTWSIIHVRNTVGLSLLAFVLALPFLSFMTCLWMLKGGRALSRKILYLLHIRSMFSLIAHTALIFAAAY
AGVIVYGVAFYLVATRAGEHAEIASYYGNHLAAMYQAPFGATDAAGAYQKPSRQTVLAALAGLAAAGAIV
GFPIVAAIQKRQRMIMGKARLATLKDAADFRLRDKHGIVLGLKQGLLLRNDGDQHVMVIGSPGQGKSRGF
VIPTMMSFQGSQVVLDMSGELFEETSGYLKDKGYEVFLLAPGSRYTDGYNPLDLISDEPNQRITDLQKLT
QMLLPERLRSDSSDFWEESARILLTAMLGFVLECPDTRKSLSELYRILNSMSDERKAIIQLLENYEPVLS
DQTRMQLTKFAGRHEKLGEGIAAEIVAKLNFLQNPLVEALTSITTIPIGTIRKRKLAIYIQADWNAMQIY
ERLISMFIQQMADKLVQMGPLRNGEHEVLMMLDEFGNGGRIDTVLTLAPLIRKNGVRFVFILQDGAQLER
LYQRSGQKILMGASTIKLFMNFQNQEDATAVSMAAGKTTEWVEQSSYSHRHGRRQRSISKVPVSVDLLPI
NTLMMMKPEEAILQVTGMPLMRIMKLDSGGERMFSKVRKFKPVKRPCMEPVEWTIADSRSAAAAPPATGA
HIHFDRSVVKDAVRHVYISSLDELRHRLDLDETREAGVTEKEAPEEEKKQPGGKRKGDPANGKRKRSMPK
TSGAARESDNDLNIDEEKLSRNVYSGSPAHRSVRSKQTNGPTDHIVPRPVAPVLQRQEVRDAFGEDLNAL
NDVIFQQAEENALEPVELNADVELLIESLSNRLTEDSSRAYLYQFANLARDPLGEDREQYETEAHAD

  Protein domains


Predicted by InterproScan.

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

(218-655)

  Protein structure



No available structure.



ID   11854 GenBank   WP_164580028
Name   virB11_J3P73_RS34470_NZLR24|p4 insolico UniProt ID   _
Length   349 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 349 a.a.        Molecular weight: 39031.31 Da        Isoelectric Point: 7.1229

>WP_164580028.1 P-type DNA transfer ATPase VirB11 [Rhizobium ruizarguesonis]
MNARPSISAEQHFLSEAIEPIRPFLDDPNVVEISCQRSNEIWLERIGQLSMVRQDVDGLDQDAIRHMASR
AASFTKQTVNAQHPLLSATLVNGERVQFVLNPTSATGHAFSIRKQFIRRFDLNDYEKAGAFRFTKVTGDD
YIDDVDIELSRLLRAGKVRAFLELAAINHRSMLISGGTSTGKTTFLNTMLTAIPNHERFILMQDTAELKP
RQENVVSLLISKGGQGEARVTMGDLLATALRLRPDRIFMGELRGDEAFDFLNAINTGHPGSMSTIHANSP
HHAFNRLSTLVLNSNVRMERDDIIRYIRSIIPIVVQLKKSDGAGGRGVSEIYFADEVDENGKRIHAHRD

  Protein domains


Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(27-319)

  Protein structure



No available structure.



ID   11855 GenBank   WP_207580361
Name   t4cp2_J3P73_RS34970_NZLR24|p4 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91350.99 Da        Isoelectric Point: 5.5804

>WP_207580361.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERTELSRQINAVLSRLG
SGWMIQVDAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRTKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVEGGGERIARYDELLQFARFCTTG
ESHPIRLPDIPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSDLKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTIDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLEGSPTLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFDMALGP
VALSFVGASGKEDLKRIRGLKSEHGHEWPIHWLETRGIHDAASLLK

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.



ID   11856 GenBank   WP_207580369
Name   traG_J3P73_RS35090_NZLR24|p4 insolico UniProt ID   _
Length   643 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 643 a.a.        Molecular weight: 69246.37 Da        Isoelectric Point: 9.2306

>WP_207580369.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTINRIALVVVPGTLMILVVIGMTGIEQWLSGFGKTEAARLAWGRTGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSAFMTVPADKTVWAFLDPATSIGASAALLCAGFALRVALIGN
AAFARAEPKRIQGKRALHGEAGWMKLTEAAKLFPDAGGIIIGERYRVDKDSVGSQAFRADSAETWGAGGK
SPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSGHRGGAGRDVFVLDP
RKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDGGGVRGVRDDFFRASALQLLTALIADVCLSGHTDGH
DQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAA
LVSGKKFATNEIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNHDGQIKGRALFLLDEVARLGYM
RIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTV
EIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRIRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGT
NRFHMVGDTPKPA

  Protein domains


Predicted by InterproScan.

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

(163-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 30965..41411

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J3P73_RS34450 (J3P73_34450) 26119..26412 + 294 WP_164580024 hypothetical protein -
J3P73_RS34455 (J3P73_34455) 26423..27811 + 1389 WP_164580025 hypothetical protein -
J3P73_RS34460 (J3P73_34460) 27815..28090 - 276 WP_245002799 hypothetical protein -
J3P73_RS34465 (J3P73_34465) 28273..30996 - 2724 WP_207580341 type IV secretory system conjugative DNA transfer family protein -
J3P73_RS34470 (J3P73_34470) 30965..32014 - 1050 WP_164580028 P-type DNA transfer ATPase VirB11 virB11
J3P73_RS34475 (J3P73_34475) 32011..33018 - 1008 WP_245002800 type IV secretion system protein VirB10 virB10
J3P73_RS34480 (J3P73_34480) 33359..34177 - 819 WP_245002801 TrbG/VirB9 family P-type conjugative transfer protein virB9
J3P73_RS34485 (J3P73_34485) 34186..34920 - 735 WP_164579990 virB8 family protein virB8
J3P73_RS34490 (J3P73_34490) 34949..36022 - 1074 WP_164579989 type IV secretion system protein virB6
J3P73_RS34495 (J3P73_34495) 36231..37022 - 792 WP_164579988 conjugal transfer protein -
J3P73_RS34500 (J3P73_34500) 37046..38221 - 1176 WP_164579987 lytic transglycosylase domain-containing protein -
J3P73_RS34505 (J3P73_34505) 38199..40718 - 2520 WP_164579986 VirB4 family type IV secretion/conjugal transfer ATPase virb4
J3P73_RS34510 (J3P73_34510) 40722..41048 - 327 WP_164579985 VirB3 family type IV secretion system protein virB3
J3P73_RS34515 (J3P73_34515) 41052..41411 - 360 WP_164579984 TrbC/VirB2 family protein virB2
J3P73_RS34520 (J3P73_34520) 41411..42484 - 1074 WP_164579983 lytic transglycosylase domain-containing protein -
J3P73_RS34525 (J3P73_34525) 42650..43153 - 504 WP_164579982 hypothetical protein -
J3P73_RS37855 43165..43659 - 495 WP_245002802 hypothetical protein -
J3P73_RS37860 44333..44515 + 183 WP_245002803 hypothetical protein -
J3P73_RS37865 44626..44724 + 99 Protein_50 LysR family transcriptional regulator -
J3P73_RS34535 (J3P73_34535) 45785..46267 - 483 WP_164579981 hypothetical protein -

Region 2: 140028..153828

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J3P73_RS34935 (J3P73_34935) 135355..136569 - 1215 WP_207580407 plasmid replication protein RepC -
J3P73_RS34940 (J3P73_34940) 136759..137796 - 1038 WP_164021417 plasmid partitioning protein RepB -
J3P73_RS34945 (J3P73_34945) 137793..139016 - 1224 WP_032991837 plasmid partitioning protein RepA -
J3P73_RS34950 (J3P73_34950) 139393..140031 + 639 WP_131624136 acyl-homoserine-lactone synthase -
J3P73_RS34955 (J3P73_34955) 140028..141005 + 978 WP_131624138 P-type conjugative transfer ATPase TrbB virB11
J3P73_RS34960 (J3P73_34960) 140995..141378 + 384 WP_164021416 TrbC/VirB2 family protein virB2
J3P73_RS34965 (J3P73_34965) 141371..141670 + 300 WP_027668110 conjugal transfer protein TrbD virB3
J3P73_RS34970 (J3P73_34970) 141681..144131 + 2451 WP_207580361 conjugal transfer protein TrbE virb4
J3P73_RS34975 (J3P73_34975) 144109..144906 + 798 WP_131624147 P-type conjugative transfer protein TrbJ virB5
J3P73_RS34980 (J3P73_34980) 144903..145103 + 201 WP_207580408 entry exclusion protein TrbK -
J3P73_RS34985 (J3P73_34985) 145097..146278 + 1182 WP_207580362 P-type conjugative transfer protein TrbL virB6
J3P73_RS34990 (J3P73_34990) 146299..146961 + 663 WP_131624151 conjugal transfer protein TrbF virB8
J3P73_RS34995 (J3P73_34995) 146979..147791 + 813 WP_131624153 P-type conjugative transfer protein TrbG virB9
J3P73_RS35000 (J3P73_35000) 147795..148235 + 441 WP_131624155 conjugal transfer protein TrbH -
J3P73_RS35005 (J3P73_35005) 148247..149545 + 1299 WP_207580363 IncP-type conjugal transfer protein TrbI virB10
J3P73_RS35010 (J3P73_35010) 149856..150560 + 705 WP_077988209 autoinducer binding domain-containing protein -
J3P73_RS35015 (J3P73_35015) 150564..150854 - 291 WP_077988208 transcriptional repressor TraM -
J3P73_RS35020 (J3P73_35020) 151114..151362 + 249 WP_027668121 helix-turn-helix domain-containing protein -
J3P73_RS35025 (J3P73_35025) 151605..152222 + 618 WP_077988207 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
J3P73_RS35030 (J3P73_35030) 152215..153080 + 866 Protein_149 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
J3P73_RS35035 (J3P73_35035) 153211..153828 - 618 WP_164021400 TraH family protein virB1
J3P73_RS35040 (J3P73_35040) 153845..155008 - 1164 WP_168334974 conjugal transfer protein TraB -
J3P73_RS35045 (J3P73_35045) 154998..155561 - 564 WP_207580364 conjugative transfer signal peptidase TraF -

Host bacterium

ID   16270 GenBank   NZ_CP071682
Plasmid name   NZLR24|p4 Incompatibility group   -
Plasmid size   643193 bp Coordinate of oriT [Strand]   158964..158997 [-]
Host baterium   Rhizobium ruizarguesonis strain NZLR24

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   hupE
Degradation gene   -
Symbiosis gene   nodM, nodE, nodF, nodD, nodA, nodC, nodI, nodJ, nifB, fixX, fixC, fixB, fixA, nifH, nifD, nifE, nifN, fixQ, fixO, fixN
Anti-CRISPR   -