Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118957
Name   oriT_pSymA in_silico
Organism   Sinorhizobium medicae strain ml42
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140901 (234433..234466 [-], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      20..25, 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_pSymA
ATCCAAGGGCGCAATTATACGTCGCAGGGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12014 GenBank   WP_322884401
Name   traA_U8C35_RS21260_pSymA insolico UniProt ID   _
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 122380.39 Da        Isoelectric Point: 10.3031

>WP_322884401.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium medicae]
MAVPHFSVSLITRGSGRSAVLSAAYRHCAKMAYQREARTIDYTRKTGLLHEEFVIPDNAPEWLQSMITDR
SVSDAAEAFWNKVEDFEKRSDAQLAKEVTIALPIELTSAQNIALVRDFVEQHISAKGMVADWVYHDAPGN
PHVHLMTTLRPLTQQGFGAKKVAVLGPDGYPIRNDAGKIVYELWAGSLDDFNALRDGWFACQNRHLTLAG
LDIRIDGRSFEKQGIELAPTLHLGAGTKAIERKATAEAKTLSLERLQLQEDLRSENARRLQRRPEIVLDL
ITRERSVFDERDVAKILHRYVDDPAVFRSLMARILQSPETLQLERERTAFATGIRAPAKYTTRALIRLEA
EMANRAIWLSRRSSHRLREAVLEATLARHSRLSDEQKTAIEHVAKAGRIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIISRTLSAWELRWSQGRNQLDARTVFILDEAGMVSSRQMACFIE
AATRTGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGNVGKAVEAYR
ANGRMIGAELKAEAVRNLVADWNRDYDPTKTTLILAHLRRDVRMLNEMARSKLVERGIVGEGFAFRTADG
NRNFAAGDQIVFLKNEGSLGVKNGMLGKIVEASPNRVVAEIGAGEHHRQVIIEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLVYVAMTRHRDNLDVYYGARSFARAGGLIQVLSRKNSKETTLDYEKATFY
RQALRFAEARGLHLLNVARTIARDRLAWTARQSSRLADLAHRLVRIGRKLGLAAGTNPINSQNSKETRPM
VAGIATHPGSVEQAVADKLAADPGLKKQWDDVSTRFHLVYAHPAAAFKAVNIDVMLKDETAAKATLSKIA
KQPDSYGALKGKTGLLASRADRQDRERAERNVPALVQSLDGYMRQRGSAERRYRAEESEARRKVAIDIPA
LSPGARQILERVRDAIDRNDLSAALEFARADRHVKAELDGFANAVEARFGKRTFLPLSARDTNGDTFTSV
TAGMNPGQRLEVESAWKAMRTVQQLRAHERTTEALKLSETLRLSKSQGLSLG

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

AAA domain (AAA_30)

(382-565)

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

(858-954)


  Protein structure



No available structure.




T4CP

ID   14069 GenBank   WP_101778059
Name   t4cp2_U8C35_RS21190_pSymA insolico UniProt ID   _
Length   817 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 817 a.a.        Molecular weight: 91666.67 Da        Isoelectric Point: 6.2518

>WP_101778059.1 conjugal transfer protein TrbE [Sinorhizobium medicae]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDCESATDLERNGLSRQINSVLSRLG
SGWMIQVEAIRIPTVDYPSDDHCHFPDPVTRAIDAERRAHFAHTQGHFESKHALILTYRPLESRKAALSK
YIYSDEESRKKSYADTVLFVFKNAVREIEQYFANTLSIKRMETRETVKRGGERVARYDELLQFVRFCITG
ESHPVRLPDIPMYLDWLATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARAKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAQASSQLVAYGYYTPVVVL
FDDDRNTLQEKAESVRRLVQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNAVAPCPYYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYDRAQIFA
FDKGNSLLSLTLAAGGYHYDLCGDDAEERNALAFCPLSELKSDADRAWATEWIEMLIALQGVIITPDHRN
AISHQVSLMASATGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLGALQTFEIEQLMNMG
ERNLVPVLTYIFRRIEKRLDGSPSLIILDEAWLMLGHPIFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSIAIPKREYYVATPEGRRLFEMALGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLETRGVQDAAAILKK

  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.



ID   14070 GenBank   WP_127628307
Name   traG_U8C35_RS21275_pSymA insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 68577.37 Da        Isoelectric Point: 9.3577

>WP_127628307.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium medicae]
MIANRIGLAVAPVVLMAFPVIGMTGFEQWLSALGKTDAARLTLGQAGIAVPYVSAAAIGVIFLFASAGSA
SIRFAGWGALTGSTATVLVAAIRETTRLAALAAEVPGGKSAASYIDPATMIGAAAVLMAGCFALRVAMIG
NAAFAPAEPKRVRGKRALHGQADWMRMHEASKLFPARGGVIIGERYRVDKDSTAAQPFRADDPETWGTGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTVPTALKWGGALVVLDPSSEVAPMVCKHRRDAGRFIRILD
PKVPETGFNALDWLGRYGGTKEEDISSVASWIMSDSGGMRAMRDDFFRASALQLLTALIADVCLSGHTDR
ENQTLRQVRANLSEPEPKLRERLQSIYDNSGSDFVRENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGSTFTTDAVAAGGTDVFINIGLKTLETHSGLARVIIGSFLNALYNRDGAAQGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETAEYISKRCGMTT
VEIDQISRSSQSNGSSRTRSKQLAARPLIQAHEVLRMRADEQIVFTVGNAPLRCGRAIWFRRDDMKACVG
TNRFQGPLG

  Protein domains


Predicted by InterproScan.

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

(163-633)

  Protein structure



No available structure.



ID   14071 GenBank   WP_024312635
Name   virD4_U8C35_RS25155_pSymA insolico UniProt ID   _
Length   563 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 563 a.a.        Molecular weight: 63029.39 Da        Isoelectric Point: 9.2858

>WP_024312635.1 MULTISPECIES: type IV secretion system ATPase VirD4 [Sinorhizobium/Ensifer group]
MISSKTRPLRIAGSIMCSLAVGYCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSAAILLVQQMVSVRDRQHHGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTFEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDILALPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QHSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPAPLMIADERF
SHV

  Protein domains


Predicted by InterproScan.

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

(97-537)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 217333..229312

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8C35_RS21150 (U8C35_21155) 213307..213453 + 147 WP_011970249 DUF1127 domain-containing protein -
U8C35_RS21155 (U8C35_21160) 213789..213998 - 210 WP_011970250 hypothetical protein -
U8C35_RS21160 (U8C35_21165) 214057..214740 - 684 WP_318890129 5-formyltetrahydrofolate cyclo-ligase -
U8C35_RS21165 (U8C35_21170) 215143..215985 - 843 WP_011970252 LysR family transcriptional regulator -
U8C35_RS21170 (U8C35_21175) 216702..217322 + 621 WP_101778058 acyl-homoserine-lactone synthase -
U8C35_RS21175 (U8C35_21180) 217333..218310 + 978 WP_011970254 P-type conjugative transfer ATPase TrbB virB11
U8C35_RS21180 (U8C35_21185) 218300..218680 + 381 WP_011970255 TrbC/VirB2 family protein virB2
U8C35_RS21185 (U8C35_21190) 218673..218969 + 297 WP_011970256 conjugal transfer protein TrbD virB3
U8C35_RS21190 (U8C35_21195) 218980..221433 + 2454 WP_101778059 conjugal transfer protein TrbE virb4
U8C35_RS21195 (U8C35_21200) 221408..222208 + 801 WP_101778060 P-type conjugative transfer protein TrbJ virB5
U8C35_RS21200 (U8C35_21205) 222202..222375 + 174 WP_101778061 entry exclusion protein TrbK -
U8C35_RS21205 (U8C35_21210) 222420..223601 + 1182 WP_101806960 P-type conjugative transfer protein TrbL virB6
U8C35_RS21210 (U8C35_21215) 223579..224241 + 663 WP_024325225 conjugal transfer protein TrbF virB8
U8C35_RS21215 (U8C35_21220) 224258..225070 + 813 WP_024325224 P-type conjugative transfer protein TrbG virB9
U8C35_RS21220 (U8C35_21225) 225074..225514 + 441 WP_322884400 conjugal transfer protein TrbH -
U8C35_RS21225 (U8C35_21230) 225527..226819 + 1293 WP_101778063 IncP-type conjugal transfer protein TrbI virB10
U8C35_RS21230 (U8C35_21235) 227076..227780 + 705 WP_024311808 autoinducer binding domain-containing protein -
U8C35_RS21235 (U8C35_21240) 227784..228107 - 324 WP_101798698 transcriptional repressor TraM -
U8C35_RS21240 (U8C35_21245) 228326..228538 + 213 WP_011970267 helix-turn-helix domain-containing protein -
U8C35_RS21245 (U8C35_21250) 228716..229312 - 597 WP_101778065 TraH family protein virB1
U8C35_RS21250 (U8C35_21255) 229329..230492 - 1164 WP_101778066 conjugal transfer protein TraB -
U8C35_RS21255 (U8C35_21260) 230482..231048 - 567 WP_024325218 conjugative transfer signal peptidase TraF -

Region 2: 995218..1004632

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8C35_RS25190 (U8C35_25195) 990370..990543 - 174 WP_162305702 hypothetical protein -
U8C35_RS25195 (U8C35_25200) 991317..991477 - 161 Protein_1004 integrase -
U8C35_RS25200 (U8C35_25205) 991975..992175 - 201 WP_102764985 IS66 family insertion sequence element accessory protein TnpB -
U8C35_RS25205 (U8C35_25210) 992221..992899 - 679 Protein_1006 IS110 family transposase -
U8C35_RS25210 (U8C35_25215) 993016..994530 + 1515 WP_018209585 ISNCY family transposase -
U8C35_RS25215 (U8C35_25220) 994700..994918 - 219 Protein_1008 IS110 family transposase -
U8C35_RS25220 (U8C35_25225) 995218..996258 - 1041 WP_011970871 P-type DNA transfer ATPase VirB11 virB11
U8C35_RS25225 (U8C35_25230) 996298..997416 - 1119 WP_028054757 type IV secretion system protein VirB10 virB10
U8C35_RS25230 (U8C35_25235) 997413..998294 - 882 WP_011970873 P-type conjugative transfer protein VirB9 virB9
U8C35_RS25235 (U8C35_25240) 998291..999003 - 713 Protein_1012 type IV secretion system protein VirB8 -
U8C35_RS25240 (U8C35_25245) 998990..999157 - 168 WP_080665920 type IV secretion system lipoprotein VirB7 -
U8C35_RS25245 (U8C35_25250) 999190..1000077 - 888 WP_088896200 type IV secretion system protein virB6
U8C35_RS25250 (U8C35_25255) 1000160..1000843 - 684 WP_018009784 pilin minor subunit VirB5 traI
U8C35_RS25255 (U8C35_25260) 1000857..1003226 - 2370 WP_028054760 VirB4 family type IV secretion/conjugal transfer ATPase virb4
U8C35_RS25260 (U8C35_25265) 1003226..1003552 - 327 WP_003537077 type IV secretion system protein VirB3 virB3
U8C35_RS25265 (U8C35_25270) 1003549..1003911 - 363 WP_014528518 pilin major subunit VirB2 virB2
U8C35_RS25270 (U8C35_25275) 1003925..1004632 - 708 WP_028054762 type IV secretion system lytic transglycosylase VirB1 virB1
U8C35_RS25275 (U8C35_25280) 1005264..1005443 + 180 Protein_1020 transposase -
U8C35_RS25280 (U8C35_25285) 1005684..1005866 - 183 Protein_1021 Lrp/AsnC ligand binding domain-containing protein -
U8C35_RS25285 (U8C35_25290) 1005901..1006724 + 824 Protein_1022 type IV secretory system conjugative DNA transfer family protein -
U8C35_RS25290 (U8C35_25295) 1007121..1008209 + 1089 WP_153417059 IS630 family transposase -
U8C35_RS25295 (U8C35_25300) 1008248..1008730 - 483 WP_322884370 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme -
U8C35_RS25300 (U8C35_25305) 1008908..1009426 + 519 WP_028054765 hypothetical protein -

Host bacterium

ID   19389 GenBank   NZ_CP140901
Plasmid name   pSymA Incompatibility group   -
Plasmid size   1291908 bp Coordinate of oriT [Strand]   234433..234466 [-]
Host baterium   Sinorhizobium medicae strain ml42

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   nia, silP, arsC
Degradation gene   RPYSC3_16500
Symbiosis gene   fixG, fixO, fixN, nodD, nodM, nifN, nodA, nodB, nodC, nodI, nodJ, nodE, nodF, nodH, mLTONO_5203, nifE, nifK, nifD, nifH, fixA, fixB, fixC, fixX, nifB, fixU
Anti-CRISPR   -