Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107660
Name   oriT_7|unnamed4 in_silico
Organism   Rhizobium sp. 007
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP064191 (419386..419426 [+], 41 nt)
oriT length   41 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: 41 nt

>oriT_7|unnamed4
TCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5149 GenBank   WP_194732594
Name   traA_ISN39_RS35860_7|unnamed4 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: 123107.47 Da        Isoelectric Point: 10.0618

>WP_194732594.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. 007]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVIPADAPQWLRAMISDR
SVSGASEGFWNKVEAFEKRSDAQLAKDVTIALPIELSAEQNIALVRDFVERHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEEGFGTKKVAVLGPDGNPMRNDSGKIVYELWAGSAHDFNAFRDGWFAYQNRHLALAG
LDIRVDGRSFEKQDIELTPTIHLGVGAKAIDRKAEQTKSKASAWSPKLERLELQEDRRAENARRLQRRPE
IVLDLITREKSVFDERGVAKILYRYIDDAGLFQSLMVRILQSPETLRLDRERIEFGTGIRAPAKYTTRAL
IRLEAQMSNRAIWLAAPTSHGVKESVLEATFAHHSRLSEEQRSAIAHVAAGERIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNEGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIANRIGYAELETIYRQREQWMRDASLDLARGNVAKA
VDAYRANGGLLGSELKAQAVDNLIADWNRDYDPAKTTLILAHLRRDVRMLNELARVKLVERGIVAEGFVF
RTDDGNRRFAAGDQIVFLKNEGSLGVKNGMIGKVVEAAPNRIVAEVGEGEHRRQVTVEQRFYNNVDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSIAKAGGLIPILSRTNAKETTLDYG
KGSLYRQALQFAEARGMHLMNVARTIARDRLDWTVRQKQKLADLGARLVAIGTMFGLVDRITKSPLPNAI
KESKPMVSGISTFPKSIEQGVEEKLAADPGLKKQWEDVSTRFHLVYVQPEAAFKTVNVDAMLKDQNIAKA
TLVKIAGEPDSFGALKGKTGVFASRSDKQDRERAIVNVPALARNLERYLRQRAEAERKHEVEERGVRLKI
WVDIPALSPAARQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSKRFGERTFLGIASKDASG
ETFKSVTAGMNPIQKAEVQTAWNSMRTIQQLSAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-569)

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   5386 GenBank   WP_194732645
Name   virD4_ISN39_RS35525_7|unnamed4 insolico UniProt ID   _
Length   565 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 565 a.a.        Molecular weight: 62512.57 Da        Isoelectric Point: 8.3288

>WP_194732645.1 type IV secretion system ATPase VirD4 [Rhizobium sp. 007]
MSNKTTPSSIALSILCSLAAGFCAASLYATFRHGISGEALMAFDILAFWYETPFYLGYTTLAFYHGLAVV
VSTSGIVLLIQQMLSEGNREHHGTARWAGVDEMRRAGYLQRYSRIRGPVFGKTSGPFWSDYYLTNGEQPH
SLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKADGDSVLKFAPLDPERRTSCYNPLL
DIIALPPERQFTEARRLAANLITTKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKYR
LFARLAEETQNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPLVKAATSRSDFSIYDLRRRRTCV
YLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAVETAITTIAGYKGRF
MFIIQSLSALSGTYDEAGKQNFLSNTGVQVFMATADDETPNYISKAIGEYTFQARSTSHTQGRMFDRNIQ
SSNQGAPLLRPEQVRLLDDKCQIVLIKGQPPLQLRKVRYYSDRALKRIFENQTGGLPEPARLIITEEGVG
ANFQA

  Protein domains


Predicted by InterproScan.

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

(96-537)

  Protein structure



No available structure.



ID   5387 GenBank   WP_194732591
Name   traG_ISN39_RS35845_7|unnamed4 insolico UniProt ID   _
Length   668 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 668 a.a.        Molecular weight: 71706.74 Da        Isoelectric Point: 9.5765

>WP_194732591.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. 007]
MTANKIALVTAPIVLMILVTIGVTGIEHWLSGFGKTEAARLMLRRAGIALPYIVAAAIGIIVLLASAGSV
NIKPAGWGVVAGSGATVLIAALRETVRLASLAGQLPAAQSALSYADPATMIGAGAALMSAGFALRVALVG
NAAFARSEPRRIRGRRALHGEAEWMKSTEAGKLFPDAGGIVIGERYRVDKASTAAQSFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVVLDPSNEVAPMVIEHRSDAGRDVRVLD
PRTRDTGFNALDWIGLHGGTKEEDIAAVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTKK
EHQTLRQVRKNLAEPEPKLRERLQSIHGNSKSDFVKENVASFVNMTPETFSGVYANAVKETHWLSYSHYA
ALVSGSSFSTDELARGDIDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQMKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGTTT
VEIDQVSRSFQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
ENRFRSLSSGEKKSSNPIDPAKTDETTSGVSSIGIEGE

  Protein domains


Predicted by InterproScan.

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

(164-637)

  Protein structure



No available structure.



ID   5388 GenBank   WP_194732606
Name   t4cp2_ISN39_RS35935_7|unnamed4 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91484.38 Da        Isoelectric Point: 5.6831

>WP_194732606.1 conjugal transfer protein TrbE [Rhizobium sp. 007]
MVALKCFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGLDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTADYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTAISK
YIYSDEKSRKKSYADTVLFIFKNAIRELEQYFANTLSIRRMETREMVERGGDRIARYDELLQFVRFCITG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMALTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLIHTGNLADLIPLNSVWP
GNTIAPCPFYPPDSPPLMQVTSGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIVAQFRRYGSAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNVEEGTALAFCPLSELKSAADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASAAGRSLSDFVSGVQIRELKDALHHYTVDGPMGQLLDAEEDGLSLGAIQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSGSIPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKDDLKRIRALKSEHGDDWPIHWLQTRGVHDVASLLNFE

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 320045..329456

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ISN39_RS35450 (ISN39_35450) 316848..317999 - 1152 WP_194732541 3-deoxy-7-phosphoheptulonate synthase -
ISN39_RS35455 (ISN39_35455) 318364..319068 - 705 WP_194732542 IS6 family transposase -
ISN39_RS35460 (ISN39_35460) 319126..319281 + 156 Protein_318 IS110 family transposase -
ISN39_RS35465 (ISN39_35465) 320045..320743 + 699 WP_194732543 type IV secretion system lytic transglycosylase VirB1 virB1
ISN39_RS35470 (ISN39_35470) 320758..321120 + 363 WP_194732544 pilin major subunit VirB2 virB2
ISN39_RS35475 (ISN39_35475) 321120..321446 + 327 WP_194732545 type IV secretion system protein VirB3 virB3
ISN39_RS35480 (ISN39_35480) 321446..323815 + 2370 WP_194732546 VirB4 family type IV secretion/conjugal transfer ATPase virb4
ISN39_RS35485 (ISN39_35485) 323829..324509 + 681 WP_194732547 pilin minor subunit VirB5 -
ISN39_RS35490 (ISN39_35490) 324590..325477 + 888 WP_194732548 type IV secretion system protein virB6
ISN39_RS35495 (ISN39_35495) 325511..325678 + 168 WP_194732549 type IV secretion system lipoprotein VirB7 -
ISN39_RS35500 (ISN39_35500) 325665..326378 + 714 WP_194732550 type IV secretion system protein VirB8 virB8
ISN39_RS35505 (ISN39_35505) 326375..327256 + 882 WP_194732551 P-type conjugative transfer protein VirB9 virB9
ISN39_RS35510 (ISN39_35510) 327253..328377 + 1125 WP_194732552 type IV secretion system protein VirB10 virB10
ISN39_RS35515 (ISN39_35515) 328416..329456 + 1041 WP_194732553 P-type DNA transfer ATPase VirB11 virB11
ISN39_RS35520 (ISN39_35520) 329935..332445 - 2511 WP_281438364 two-component system VirA-like sensor kinase -

Region 2: 424546..437582

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ISN39_RS35865 (ISN39_35865) 422821..423387 + 567 WP_194732595 conjugative transfer signal peptidase TraF -
ISN39_RS35870 (ISN39_35870) 423377..424531 + 1155 WP_194732596 conjugal transfer protein TraB -
ISN39_RS35875 (ISN39_35875) 424546..425157 + 612 WP_194732597 TraH family protein virB1
ISN39_RS35880 (ISN39_35880) 425173..425550 - 378 WP_194732598 DUF5615 family PIN-like protein -
ISN39_RS35885 (ISN39_35885) 425547..426179 - 633 WP_194732651 DUF433 domain-containing protein -
ISN39_RS35890 (ISN39_35890) 426279..426491 - 213 WP_194732599 helix-turn-helix transcriptional regulator -
ISN39_RS35895 (ISN39_35895) 426706..427029 + 324 WP_194732600 transcriptional repressor TraM -
ISN39_RS35900 (ISN39_35900) 427033..427737 - 705 WP_194732601 autoinducer binding domain-containing protein -
ISN39_RS35905 (ISN39_35905) 428080..429375 - 1296 WP_194732602 IncP-type conjugal transfer protein TrbI virB10
ISN39_RS35910 (ISN39_35910) 429387..429827 - 441 WP_194732603 conjugal transfer protein TrbH -
ISN39_RS35915 (ISN39_35915) 429831..430643 - 813 WP_194732604 P-type conjugative transfer protein TrbG virB9
ISN39_RS35920 (ISN39_35920) 430660..431322 - 663 WP_194732605 conjugal transfer protein TrbF virB8
ISN39_RS35925 (ISN39_35925) 431343..432533 - 1191 WP_246763636 P-type conjugative transfer protein TrbL virB6
ISN39_RS35930 (ISN39_35930) 432698..433501 - 804 WP_194732653 P-type conjugative transfer protein TrbJ virB5
ISN39_RS35935 (ISN39_35935) 433473..435929 - 2457 WP_194732606 conjugal transfer protein TrbE virb4
ISN39_RS35940 (ISN39_35940) 435940..436239 - 300 WP_194732607 conjugal transfer protein TrbD virB3
ISN39_RS35945 (ISN39_35945) 436232..436615 - 384 WP_194732608 TrbC/VirB2 family protein virB2
ISN39_RS35950 (ISN39_35950) 436605..437582 - 978 WP_194732609 P-type conjugative transfer ATPase TrbB virB11
ISN39_RS35955 (ISN39_35955) 437595..438218 - 624 WP_194732654 acyl-homoserine-lactone synthase TraI -
ISN39_RS35960 (ISN39_35960) 438357..438799 - 443 Protein_421 transposase -
ISN39_RS35965 (ISN39_35965) 439115..440338 + 1224 WP_194732655 plasmid partitioning protein RepA -
ISN39_RS35970 (ISN39_35970) 440335..441372 + 1038 WP_194732610 plasmid partitioning protein RepB -

Host bacterium

ID   8095 GenBank   NZ_CP064191
Plasmid name   7|unnamed4 Incompatibility group   -
Plasmid size   441467 bp Coordinate of oriT [Strand]   419386..419426 [+]
Host baterium   Rhizobium sp. 007

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   dxnH, linJ
Symbiosis gene   nodM, fixN, fixO, fixG, nodD, nodA, nodB, nodC, nodI, nodJ, nifT, nifZ, nifB, fixX, fixC, fixB, fixA, nifW, nifS, nifH, nifD, nifK, nifE, nifN, nifX, mLTONO_5203, nodZ, nodF, nodE
Anti-CRISPR   -