Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118959
Name   oriT_pSymA in_silico
Organism   Sinorhizobium medicae strain ml49
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140895 (229670..229703 [-], 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   12015 GenBank   WP_322887282
Name   traA_U8C36_RS20685_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: 122464.38 Da        Isoelectric Point: 10.2757

>WP_322887282.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium medicae]
MAVPHFSVSLITRGSGRSAVLSAAYRHCAKMAYQREARTIDYTRKTGLLHEEFVIPDNAPEWLQSMITDR
SVSDAAEAFWNKVEDFEKRSDAQLAKEVTIALPIELTSAQNIALVRDFVEQHISAKGMVADWVYHDAPGN
PHVHLMTTLRPLTQQGFGAKKVAVLGPDGYPIRNDAGKIVYELWAGSLDDFNALRDGWFACQNRHLTLAG
LDIRIDGRSFEKQGIELAPTLHLGAGTKAIERKATAEAKTLSLERLQLQEDLRSENARRLQRRPEIVLDL
ITRERSVFDERDVAKILHRYVDDPAVFRSLMARILQSPETLQLERERTAFATGIRAPAKYTTRALIRLEA
EMANRAIWLSRRSSHRLREAVLEATLARHSRLSDEQKTAIEHVAKAGRIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIISRTLSAWELRWSQGRNQLDARTVFILDEAGMVSSRQMACFIE
AATRTGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGNVGKAVEAYR
ANGRMIGAELKAEAVRNLVADWNRDYDPTKTTLILAHLRRDVRMLNEMARSKLVERGIVGEGFAFRTADG
NRNFAAGDQIVFLKNEGSLGVKNGMLGKIVEASPNRVVAEIGAGEHHRQVIIEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLVYVAMTRHRDNLDVYYGARSFARAGGLIQVLSRKNSKETTLDYEKATFY
RQALRFAEARGLHLLNVARTIARDRLAWTARQSSRLADLAHRLVRIGRKLGLAAGTNPINSQNSKETRPM
VAGIATHPGSVEQAVADKLAADPGLKKQWDDVSTRFHLVYAHPAAAFKAVNIDVMLKDETAAKATLSKIA
KQPDSYGALKGKTGLLASRADRQDRERAERNVPALVQSLDGYMRQRGSAERRYRAEESEARRKVAIDIPA
LSPGARQILERVRDAIDRNDLSAALEFARADRHVKAELDGFANAVDARFGKRTFLPLSARDTNGDTFTSV
TAGMNPGQRLEVESAWKAMRTVQQLSDHERTTEALKHSETLRLSKSQGLSLR

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

MobA/MobL family (MobA_MobL)

(17-243)

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   14072 GenBank   WP_322887280
Name   t4cp2_U8C36_RS20595_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: 91748.74 Da        Isoelectric Point: 6.2518

>WP_322887280.1 conjugal transfer protein TrbE [Sinorhizobium medicae]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDCESATDLERNELSRQINSVLSRLG
SGWMIQVEAIRIPTVDYPSDDHCHFPDPVTRAIDAERRAHFAHTQGHFESKHALILTYRPLESRKAALSK
YIYSDEESRKKSYADTVLFVFKNAVREIEQYFANTLSIKRMETRETVKRGGERVARYDELLQFVRFCITG
ESHPVRLPDIPMYLDWLATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARAKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAQASSQLVAYGYYTPVVVL
FDDDRNTLQEKAESVRRLVQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNAVAPCPYYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYDRAQIFA
FDKGNSLLSLTLAAGGYHYDLCGDDAEERNALAFCPLSELKSDADRAWATEWIEMLIALQGVIITPDHRN
AISHQVSLMASATGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVFTYIFRRIEKRLDGSPSLIILDEAWLMLGHPIFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSIAIPKREYYVATPEGRRLFEMALGP
VALSFVGASGKADLKRIRALKSEHGRDWPIHWLETRGVQDAAAILKK

  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   14073 GenBank   WP_127628307
Name   traG_U8C36_RS20700_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   14074 GenBank   WP_024312635
Name   virD4_U8C36_RS25900_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: 208572..223201

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8C36_RS20555 (U8C36_20560) 204545..204691 + 147 WP_011970249 DUF1127 domain-containing protein -
U8C36_RS20560 (U8C36_20565) 205027..205236 - 210 WP_024325234 hypothetical protein -
U8C36_RS20565 (U8C36_20570) 205295..205978 - 684 WP_024325233 5-formyltetrahydrofolate cyclo-ligase -
U8C36_RS20570 (U8C36_20575) 206381..207223 - 843 WP_011970252 LysR family transcriptional regulator -
U8C36_RS20575 (U8C36_20580) 207941..208561 + 621 WP_101799598 acyl-homoserine-lactone synthase -
U8C36_RS20580 (U8C36_20585) 208572..209549 + 978 WP_011970254 P-type conjugative transfer ATPase TrbB virB11
U8C36_RS20585 (U8C36_20590) 209539..209919 + 381 WP_024325229 TrbC/VirB2 family protein virB2
U8C36_RS20590 (U8C36_20595) 209912..210208 + 297 WP_011970256 conjugal transfer protein TrbD virB3
U8C36_RS20595 (U8C36_20600) 210219..212672 + 2454 WP_322887280 conjugal transfer protein TrbE virb4
U8C36_RS20600 (U8C36_20605) 212647..213447 + 801 WP_024311807 P-type conjugative transfer protein TrbJ virB5
U8C36_RS20605 (U8C36_20610) 213444..213644 + 201 WP_011970259 entry exclusion protein TrbK -
U8C36_RS20610 (U8C36_20615) 213638..214846 + 1209 WP_011970260 P-type conjugative transfer protein TrbL virB6
U8C36_RS20615 (U8C36_20620) 214824..215486 + 663 WP_011970261 conjugal transfer protein TrbF virB8
U8C36_RS20620 (U8C36_20625) 215503..216315 + 813 WP_011970262 P-type conjugative transfer protein TrbG virB9
U8C36_RS20625 (U8C36_20630) 216319..216759 + 441 WP_011970263 conjugal transfer protein TrbH -
U8C36_RS20630 (U8C36_20635) 216772..218064 + 1293 WP_208179266 IncP-type conjugal transfer protein TrbI virB10
U8C36_RS20635 (U8C36_20640) 218320..218514 + 195 WP_322887281 hypothetical protein -
U8C36_RS20640 (U8C36_20645) 218684..220168 + 1485 WP_153445718 IS21 family transposase -
U8C36_RS20645 (U8C36_20650) 220165..221061 + 897 WP_101778737 IS21-like element helper ATPase IstB -
U8C36_RS20650 (U8C36_20655) 221111..221671 + 561 Protein_211 autoinducer binding domain-containing protein -
U8C36_RS20655 (U8C36_20660) 221675..221998 - 324 WP_208179264 transcriptional repressor TraM -
U8C36_RS20660 (U8C36_20665) 222217..222429 + 213 WP_011970267 helix-turn-helix domain-containing protein -
U8C36_RS20665 (U8C36_20670) 222605..223201 - 597 WP_208179263 conjugal transfer protein TraH virB1
U8C36_RS20670 (U8C36_20675) 223218..224351 - 1134 WP_322887330 conjugal transfer protein TraB -
U8C36_RS20675 (U8C36_20680) 224400..225596 - 1197 WP_039845999 IS256-like element ISRm5 family transposase -
U8C36_RS20680 (U8C36_20685) 225719..226285 - 567 WP_208179261 conjugative transfer signal peptidase TraF -

Region 2: 1286505..1295920

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8C36_RS25920 (U8C36_25930) 1281760..1281920 - 161 Protein_1263 integrase -
U8C36_RS25925 (U8C36_25935) 1282016..1282210 - 195 WP_024312638 hypothetical protein -
U8C36_RS25930 (U8C36_25940) 1282418..1282618 - 201 WP_102764985 IS66 family insertion sequence element accessory protein TnpB -
U8C36_RS25935 (U8C36_25945) 1282664..1283342 - 679 Protein_1266 IS110 family transposase -
U8C36_RS25940 (U8C36_25950) 1283558..1285042 + 1485 WP_153445718 IS21 family transposase -
U8C36_RS25945 (U8C36_25955) 1285039..1285935 + 897 WP_101778737 IS21-like element helper ATPase IstB -
U8C36_RS25950 (U8C36_25960) 1285987..1286205 - 219 Protein_1269 IS110 family transposase -
U8C36_RS25955 (U8C36_25965) 1286505..1287545 - 1041 WP_011970871 P-type DNA transfer ATPase VirB11 virB11
U8C36_RS25960 (U8C36_25970) 1287585..1288703 - 1119 WP_028054757 type IV secretion system protein VirB10 virB10
U8C36_RS25965 (U8C36_25975) 1288700..1289581 - 882 WP_322887265 P-type conjugative transfer protein VirB9 virB9
U8C36_RS25970 (U8C36_25980) 1289578..1290290 - 713 Protein_1273 type IV secretion system protein VirB8 -
U8C36_RS25975 (U8C36_25985) 1290277..1290444 - 168 WP_080665920 type IV secretion system lipoprotein VirB7 -
U8C36_RS25980 (U8C36_25990) 1290477..1291365 - 889 Protein_1275 type IV secretion system protein -
U8C36_RS25985 (U8C36_25995) 1291448..1292131 - 684 WP_018009784 pilin minor subunit VirB5 traI
U8C36_RS25990 (U8C36_26000) 1292145..1294514 - 2370 WP_028054760 VirB4 family type IV secretion/conjugal transfer ATPase virb4
U8C36_RS25995 (U8C36_26005) 1294514..1294840 - 327 WP_003537077 type IV secretion system protein VirB3 virB3
U8C36_RS26000 (U8C36_26010) 1294837..1295199 - 363 WP_014528518 pilin major subunit VirB2 virB2
U8C36_RS26005 (U8C36_26015) 1295213..1295920 - 708 WP_028054762 type IV secretion system lytic transglycosylase VirB1 virB1
U8C36_RS26010 (U8C36_26020) 1296552..1296731 + 180 Protein_1281 transposase -
U8C36_RS26015 (U8C36_26025) 1296972..1297154 - 183 Protein_1282 Lrp/AsnC ligand binding domain-containing protein -
U8C36_RS26020 (U8C36_26030) 1297189..1298012 + 824 Protein_1283 type IV secretory system conjugative DNA transfer family protein -
U8C36_RS26025 (U8C36_26035) 1298409..1299497 + 1089 WP_153417059 IS630 family transposase -
U8C36_RS26030 (U8C36_26040) 1299536..1300048 - 513 Protein_1285 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme -
U8C36_RS26035 (U8C36_26045) 1300196..1300714 + 519 WP_028054765 hypothetical protein -

Host bacterium

ID   19391 GenBank   NZ_CP140895
Plasmid name   pSymA Incompatibility group   -
Plasmid size   1577431 bp Coordinate of oriT [Strand]   229670..229703 [-]
Host baterium   Sinorhizobium medicae strain ml49

Cargo genes

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