Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115788
Name   oriT_pWSM1592_2 in_silico
Organism   Rhizobium sullae strain WSM1592
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP104145 (450266..450299 [+], 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_pWSM1592_2
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10112 GenBank   WP_027513360
Name   traA_N2599_RS36320_pWSM1592_2 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: 122779.64 Da        Isoelectric Point: 9.5327

>WP_027513360.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sullae]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRNMIADH
SVAGASEAFWNKAEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVEQHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTENGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGCTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQERRRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDAALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHDLREAVLQATLARHARLSDEQRTAIEHVAGGERIAAVVGRAGAGKTTMMR
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMASSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELDTIYRQRQQWMRDASLDLARGNVGKA
VDAYRAHGHVRGLDLKAQAVESLIADWDREYDPSKTSLILAHLRRDVRMLNEMARAKLVERGVIADGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEIGEGEHRRQVTIEQRFYNNLDHGYA
TSIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAINVDAMVKDQSVAQS
TLARIAGEPESFGALNGKTGLLASRADKQDREKAVANVAALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVHDAIDRNDLPAGVEYALADKMVKAELEGFAKAVSERFGERTFLPLSAKDTDG
KTFETVTAGMTAGQKAEVQSAWNSMRTVQQLAAYERTTEALKHAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-572)

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

(864-960)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   11815 GenBank   WP_037144402
Name   virD4_N2599_RS35200_pWSM1592_2 insolico UniProt ID   _
Length   571 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 571 a.a.        Molecular weight: 63052.21 Da        Isoelectric Point: 8.2537

>WP_037144402.1 type IV secretion system ATPase VirD4 [Rhizobium sullae]
MSSKTTFSNKTTPSSIALSILCSLAAGFCAASLYATFRHGISGEALMAFDILAFWYETPFYLGYTTLAFY
YGLAVVVSTSGIVLLVQQMLSEGSREHHGTARWAGVGEMRRTGYLQRYSRISGPIFGKTSGPFWSDYYLT
NGEQPHSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKADGDSVLKFAPLDPERRTS
CYNPLLDIIALPPERQFTEARRLAANLITTKGQGAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQ
PGEKYRLFARLAEETQNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPLVKAATSRSDFSIYDLR
RRRTCIYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAVETAITTIA
GYKGRFMFIIQSLSALSGTYDEAGKQNFLSNTGVQVFMATADDETPNYISKAIGEYTFQARSTSHTQGRM
FDRNIQISDQGSPLLRPEQVRLLDDKCQIVLIKGQPPLQLRKVRYYSDRALKRIFESQTGGLPEPARLII
TEEGLGANCQS

  Protein domains


Predicted by InterproScan.

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

(102-542)

  Protein structure



No available structure.



ID   11816 GenBank   WP_027513377
Name   t4cp2_N2599_RS36405_pWSM1592_2 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: 91854.61 Da        Isoelectric Point: 5.7886

>WP_027513377.1 conjugal transfer protein TrbE [Rhizobium sullae]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKTTALSK
YIYSDEESRKKSYADTVLFIFKNAVREIEQYFANTLSVRRMETRETVERGGERIARYDELLQFVRFCITG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSFDQDAMTMVTETEDAIAQASSQLVAYGYYTPVVVL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNTVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYESAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAGEGRALAFCPLSDLKSDADRAWATEWIEMLVGLQRVTITPDHRN
AISRQVGLMASAAGRSLSDFVSGVQMREIKDALHHYTVDGPMGLLLDAEEDGLSLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNVAAREPGTREFYERIGFNERQIEIVSNSIPKREYYVATPEGRRLFDMSLGP
AALSFVGASGKDDLKRIRALRSEHGFDWPIHWLQTRGVHDAASLLNFE

  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: 257454..266833

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N2599_RS35275 (N2599_35275) 253139..254692 - 1554 WP_027513949 IS21 family transposase -
N2599_RS35280 (N2599_35280) 254889..256509 + 1621 Protein_242 Tn3 family transposase -
N2599_RS35285 (N2599_35285) 257454..258494 - 1041 WP_027513742 P-type DNA transfer ATPase VirB11 virB11
N2599_RS35290 (N2599_35290) 258533..259642 - 1110 WP_027513743 type IV secretion system protein VirB10 virB10
N2599_RS35295 (N2599_35295) 259639..260520 - 882 WP_027513744 P-type conjugative transfer protein VirB9 virB9
N2599_RS35300 (N2599_35300) 260517..261230 - 714 WP_027513745 type IV secretion system protein VirB8 virB8
N2599_RS35305 (N2599_35305) 261217..261384 - 168 WP_084606758 type IV secretion system lipoprotein VirB7 -
N2599_RS35310 (N2599_35310) 261418..262308 - 891 WP_027513746 type IV secretion system protein virB6
N2599_RS35315 (N2599_35315) 262360..263040 - 681 WP_027513747 type IV secretion system protein VirB5 traI
N2599_RS35320 (N2599_35320) 263054..265423 - 2370 WP_027513748 VirB4 family type IV secretion/conjugal transfer ATPase virb4
N2599_RS35325 (N2599_35325) 265423..265749 - 327 WP_027513749 type IV secretion system protein VirB3 virB3
N2599_RS35330 (N2599_35330) 265749..266111 - 363 WP_027513750 pilin major subunit VirB2 virB2
N2599_RS35335 (N2599_35335) 266141..266833 - 693 WP_027513751 type IV secretion system lytic transglycosylase VirB1 virB1
N2599_RS35340 (N2599_35340) 267209..267457 + 249 Protein_254 transposase -
N2599_RS35345 (N2599_35345) 267867..268337 + 471 WP_027513752 transposase -
N2599_RS35350 (N2599_35350) 268334..268618 + 285 Protein_256 IS66 family insertion sequence element accessory protein TnpB -
N2599_RS35355 (N2599_35355) 268672..269422 - 751 Protein_257 IS6 family transposase -
N2599_RS35360 (N2599_35360) 269428..270057 + 630 Protein_258 bifunctional folylpolyglutamate synthase/dihydrofolate synthase -
N2599_RS35365 (N2599_35365) 270106..270426 - 321 WP_132568927 thioredoxin -
N2599_RS35370 (N2599_35370) 270479..270847 - 369 WP_027513883 hypothetical protein -

Region 2: 455432..469712

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N2599_RS36325 (N2599_36325) 453702..454265 + 564 WP_027513361 conjugative transfer signal peptidase TraF -
N2599_RS36330 (N2599_36330) 454255..455415 + 1161 WP_027513362 conjugal transfer protein TraB -
N2599_RS36335 (N2599_36335) 455432..456052 + 621 WP_027513363 TraH family protein virB1
N2599_RS36340 (N2599_36340) 456224..456598 - 375 WP_027513364 DUF5615 family PIN-like protein -
N2599_RS36345 (N2599_36345) 456595..457227 - 633 WP_027513365 DUF433 domain-containing protein -
N2599_RS36350 (N2599_36350) 457515..457907 - 393 Protein_456 adenylate cyclase -
N2599_RS36355 (N2599_36355) 458434..458646 - 213 WP_027513367 helix-turn-helix domain-containing protein -
N2599_RS36360 (N2599_36360) 458864..459187 + 324 WP_027513368 transcriptional repressor TraM -
N2599_RS36365 (N2599_36365) 459191..459895 - 705 WP_027513369 autoinducer binding domain-containing protein -
N2599_RS36370 (N2599_36370) 460208..461506 - 1299 WP_027513370 IncP-type conjugal transfer protein TrbI virB10
N2599_RS36375 (N2599_36375) 461518..461958 - 441 WP_027513371 conjugal transfer protein TrbH -
N2599_RS36380 (N2599_36380) 461962..462774 - 813 WP_027513372 P-type conjugative transfer protein TrbG virB9
N2599_RS36385 (N2599_36385) 462791..463453 - 663 WP_027513373 conjugal transfer protein TrbF virB8
N2599_RS36390 (N2599_36390) 463474..464622 - 1149 WP_245209322 P-type conjugative transfer protein TrbL virB6
N2599_RS36395 (N2599_36395) 464658..464831 - 174 WP_311319516 entry exclusion protein TrbK -
N2599_RS36400 (N2599_36400) 464828..465631 - 804 WP_027513376 P-type conjugative transfer protein TrbJ virB5
N2599_RS36405 (N2599_36405) 465603..468059 - 2457 WP_027513377 conjugal transfer protein TrbE virb4
N2599_RS36410 (N2599_36410) 468070..468369 - 300 WP_027513378 conjugal transfer protein TrbD virB3
N2599_RS36415 (N2599_36415) 468362..468745 - 384 WP_027513379 TrbC/VirB2 family protein virB2
N2599_RS36420 (N2599_36420) 468735..469712 - 978 WP_027513380 P-type conjugative transfer ATPase TrbB virB11
N2599_RS36425 (N2599_36425) 469732..470346 - 615 WP_027513381 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   16221 GenBank   NZ_CP104145
Plasmid name   pWSM1592_2 Incompatibility group   -
Plasmid size   470679 bp Coordinate of oriT [Strand]   450266..450299 [+]
Host baterium   Rhizobium sullae strain WSM1592

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodD, nifT, nifZ, nifB, fixX, fixC, fixB, fixA, nifW, nifS, nodC, nodB, nodA, a9174_31165, nodF, nodE, nodJ, nodI, nifH, nifD, nifK, nifE, nifN, nifX, mLTONO_5203
Anti-CRISPR   -