Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106949
Name   oriT_LMG 24692|unnamed in_silico
Organism   Sinorhizobium garamanticum strain LMG 24692
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP120375 (385431..385488 [+], 58 nt)
oriT length   58 nt
IRs (inverted repeats)      25..32, 35..42  (ACGTCGCG..CGCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 58 nt

>oriT_LMG 24692|unnamed
CCCCGCCAGGGGTATCAAAGCAAGACGTCGCGACCGCGACGTATAATTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4590 GenBank   WP_280663393
Name   traA_PZN02_RS31040_LMG 24692|unnamed 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: 123029.18 Da        Isoelectric Point: 10.0185

>WP_280663393.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium garamanticum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLRHEEFVIPADAPDWLWSMIADR
SVASASEAFWNKVEDFEKRVDAQLAKDVTIALPIELTAEQSIALIRDFVEQHVTAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEGGFGAKKIAVRGPDGNPIRNDAGKIVYELWAGGLDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKSARNEQAAPLERLELQEERRSENALRIQRRPEIVLDL
ITREKSVFDERDVAKVLHRYIDDPGIFQSLMARILQSPETLRLEREQVAFATGIRVPAKYTTRGLIRLEA
EMANRAIWLSTRSSHGVRKEVLETTFTRHSRLSEEQKTAIEHIAGAERIAAVIGRAGAGKTTMMKTAREA
WEAAGYRVVGGALAGKAAEGLQKEAGIVSRTLSSWELRWTEGRNQLDDKTIFVLDEAGMVSSRQMALFVE
AATKAGAKLVLIGDPEQLQPIEAGAAFGAIADRIGYAELETIYRQREQWMRDASLDLARGKVGKAVDAYR
ANGRMMASELKAEAVQYLISDWNRDYDPTKTTLILAHLRRDVRILNEMARAKLVDRGIVGEGFVFRTEDG
NRRFAPGDQIVFLKNEGSLGVKNGMLGKVVDASKNRIVAEIGEGEHHRQVTVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGVYYGVRSFAKAGGLIQTLSRKNSKETTLDYEKATFY
RQALRFAEARGLHLVNVARTIARDRLEWTVRQKQKLTDLSYRLVAIGAKLSLAKGTKPINTQSIKETRPM
VAGISTFPKSIEQAVADKLEADPGLKKQWEDVSTRFHLVYAQPEAAFKAVNVDAMLKDETAAKSTIATIT
SQPEAYGALKGKTGLLASRADKQDRERAERNVPALAQSFSDYMRQRSQAEQRYQAEELAVRRKVAIAIPA
LSPSARQTLERVRDAIDRNDLPAALEFALANKMVKAELERFAKTLTDRFGERTLLPLAAKDTNGESFRRI
TAGMNPGRQAEVHSAWNTMRTVQQLGAYQRTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(686-735)

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   4682 GenBank   WP_280663361
Name   t4cp2_PZN02_RS30850_LMG 24692|unnamed 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: 91861.82 Da        Isoelectric Point: 6.1627

>WP_280663361.1 conjugal transfer protein TrbE [Sinorhizobium garamanticum]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
SGWMIQVEAVRIPTFDYPSEDRCHFPDAVTRAIDAERRAHFARERGHFESKHALILTHRPLESRKTTLSK
YIYSDEESRKKTYADTVLFIFKNAIREIEQYLANTLSIRRIETRGAVERGGVRVARYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQVVAYGYYTPVIIL
FDSDREALQEKAETIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLVPLNSVWS
GNPIAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYDGAQIFA
FDKGSSLLPLTLAAGGDHYEICGDNAEEGRALAFCPLSELESDADRAWATEWIEMLVALQGVTITPDHRN
AISRQVGLMARAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQCFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFGSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCRTKICLPNGAAREPGTREFYERIGFNERQIEIVSNAIPKREYYVVTPEGRRLFDMALGP
VALSFVGASGKEDLKRIRTLHSEHGRDWPIHWLQMRGVHDAALQLNVK

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.



ID   4683 GenBank   WP_280663396
Name   traG_PZN02_RS31055_LMG 24692|unnamed insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 71053.30 Da        Isoelectric Point: 9.4442

>WP_280663396.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium garamanticum]
MTANRLALVAVPVVLMILAVIGMTGIEQWLSAFGKTDAARLTLGRVGIAAPYVTAAAIGVIFLFASAGSA
SIKFAGWGVLAGSVATMLIAAIREATRLAPFAGEVPAGKSIVSYLDPATMIGAAAALMTACFSLRVGLVG
NAAFTRAEPKRIRGQRALHGEADWMKMQDAAKLFPDTGGVVIGERYRVDKDSIAARSFRADDPQTWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVYRHRKDAARFIRILD
PKEPELGFNALDWIGRFGGTKEEDIASVASWIMSDSGGPRGVRDDFFRASALQLLTALIADVCLSGHTDS
ENQTLRQVRANLAEPEPKLRERLQSIYDNSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGSTFSTDALAAGETDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGEVKGRALFLLDEVARLGY
MRILETARDAGRKYGISLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPDTADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQAHEVLRMRADEQIVFTAGNPPLRCGRAIWFRRGDMKACVG
TNRFHKIGKPSEARMIEPARSATSRADP

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   4684 GenBank   WP_280663473
Name   virD4_PZN02_RS31595_LMG 24692|unnamed insolico UniProt ID   _
Length   569 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 569 a.a.        Molecular weight: 63561.97 Da        Isoelectric Point: 9.0770

>WP_280663473.1 type IV secretion system ATPase VirD4 [Sinorhizobium garamanticum]
MISNETRPLSIAVSIVCSLAAGFCGASMYSTFRYGFDGRALLTFDIFAFWYETPFYLGYTTLSFYRGLAV
VVLTSGTILLMQQMVPGRNRQHHGTARWARVDEMRRAGYLQRYNRISGPVFGKTSARFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKARGDSVFKLAPLDPERRTSCYNPL
LDIMAMSPERQFTEARRLAANLITAKGQGAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAEETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPLVKAATSRSDFSIYDLRRRRTC
VYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGRLEAIETAITTIAGYKGR
FMLIIQSLSALTGTYDEAGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFRARSTSYNQSRMFDRNI
QNSDQGALLLRPEQVRLLPDKYEIVLIKGQPPLQLQKVRYYSDRALKRIFESQTGDLPEPVPLMIAEGKL
GANSSFNDC

  Protein domains


Predicted by InterproScan.

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

(97-538)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 338042..347552

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PZN02_RS30815 (PZN02_006164) 333292..334506 - 1215 WP_280663354 plasmid replication protein RepC -
PZN02_RS30820 (PZN02_006165) 334664..335644 - 981 WP_280663355 plasmid partitioning protein RepB -
PZN02_RS30825 (PZN02_006166) 335701..336924 - 1224 WP_280663356 plasmid partitioning protein RepA -
PZN02_RS30830 (PZN02_006167) 337408..338031 + 624 WP_280663357 acyl-homoserine-lactone synthase -
PZN02_RS30835 (PZN02_006168) 338042..339019 + 978 WP_280663358 P-type conjugative transfer ATPase TrbB virB11
PZN02_RS30840 (PZN02_006169) 339009..339392 + 384 WP_280663359 TrbC/VirB2 family protein virB2
PZN02_RS30845 (PZN02_006170) 339385..339684 + 300 WP_280663360 conjugal transfer protein TrbD virB3
PZN02_RS30850 (PZN02_006171) 339694..342150 + 2457 WP_280663361 conjugal transfer protein TrbE virb4
PZN02_RS30855 (PZN02_006172) 342122..342925 + 804 WP_280663362 P-type conjugative transfer protein TrbJ virB5
PZN02_RS30860 (PZN02_006173) 342922..343116 + 195 WP_280663363 entry exclusion protein TrbK -
PZN02_RS30865 (PZN02_006174) 343110..344285 + 1176 WP_280663364 P-type conjugative transfer protein TrbL virB6
PZN02_RS30870 (PZN02_006175) 344310..344972 + 663 WP_280663365 conjugal transfer protein TrbF virB8
PZN02_RS30875 (PZN02_006176) 344989..345801 + 813 WP_280663366 P-type conjugative transfer protein TrbG virB9
PZN02_RS30880 (PZN02_006177) 345805..346242 + 438 WP_280663367 conjugal transfer protein TrbH -
PZN02_RS30885 (PZN02_006178) 346254..347552 + 1299 WP_280663368 IncP-type conjugal transfer protein TrbI virB10
PZN02_RS30890 (PZN02_006179) 347863..348573 + 711 WP_280663779 autoinducer binding domain-containing protein -
PZN02_RS30895 (PZN02_006180) 348577..348900 - 324 WP_280663369 transcriptional repressor TraM -
PZN02_RS30900 (PZN02_006181) 349096..349335 + 240 WP_280663370 helix-turn-helix transcriptional regulator -
PZN02_RS30905 (PZN02_006182) 349552..351060 - 1509 WP_280663371 MFS transporter -
PZN02_RS30910 (PZN02_006183) 351157..351876 - 720 WP_280663372 HAD family hydrolase -

Region 2: 497725..507150

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PZN02_RS31495 (PZN02_006302) 493328..493567 + 240 WP_280663460 helix-turn-helix transcriptional regulator -
PZN02_RS31500 (PZN02_006303) 493709..494320 - 612 WP_280663461 hypothetical protein -
PZN02_RS31505 (PZN02_006304) 494577..494840 - 264 Protein_466 transposase -
PZN02_RS31510 (PZN02_006305) 494859..495185 + 327 WP_280663462 heme-binding protein -
PZN02_RS31515 (PZN02_006306) 495448..495655 - 208 Protein_468 hypothetical protein -
PZN02_RS31520 (PZN02_006307) 495862..496312 + 451 Protein_469 exonuclease domain-containing protein -
PZN02_RS31525 (PZN02_006308) 497725..498432 + 708 WP_280663463 type IV secretion system lytic transglycosylase VirB1 virB1
PZN02_RS31530 (PZN02_006309) 498452..498814 + 363 WP_280663464 pilin major subunit VirB2 virB2
PZN02_RS31535 (PZN02_006310) 498814..499140 + 327 WP_280663465 type IV secretion system protein VirB3 virB3
PZN02_RS31540 (PZN02_006311) 499140..501509 + 2370 WP_280663466 VirB4 family type IV secretion/conjugal transfer ATPase virb4
PZN02_RS31545 (PZN02_006312) 501523..502203 + 681 WP_280663467 pilin minor subunit VirB5 -
PZN02_RS31550 (PZN02_006313) 502284..503171 + 888 WP_280663468 type IV secretion system protein virB6
PZN02_RS31555 (PZN02_006314) 503205..503372 + 168 WP_194732549 type IV secretion system lipoprotein VirB7 -
PZN02_RS31560 (PZN02_006315) 503359..504072 + 714 WP_280663469 type IV secretion system protein VirB8 virB8
PZN02_RS31565 (PZN02_006316) 504069..504950 + 882 WP_280663470 TrbG/VirB9 family P-type conjugative transfer protein virB9
PZN02_RS31570 (PZN02_006317) 504947..506071 + 1125 WP_280663471 type IV secretion system protein VirB10 virB10
PZN02_RS31575 (PZN02_006318) 506110..507150 + 1041 WP_280663472 P-type DNA transfer ATPase VirB11 virB11
PZN02_RS31580 (PZN02_006319) 507223..508717 + 1495 Protein_481 ISL3 family transposase -
PZN02_RS31585 (PZN02_006320) 509314..510295 + 982 Protein_482 adenylyl-sulfate kinase -
PZN02_RS31590 (PZN02_006321) 510344..511069 + 726 WP_280663790 response regulator -

Host bacterium

ID   7386 GenBank   NZ_CP120375
Plasmid name   LMG 24692|unnamed Incompatibility group   -
Plasmid size   623165 bp Coordinate of oriT [Strand]   385431..385488 [+]
Host baterium   Sinorhizobium garamanticum strain LMG 24692

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   linJ, dxnH, LinG
Symbiosis gene   nodM, fixS, fixG, fixO, fixN, fixX, fixC, fixB, fixA, nifW, nifS, nifH, nifD, nifE, nifX, mLTONO_5203, nodD, nodH, nodF, nodE, nodJ, nodI, nodC, nodB, nodA, nifN, a9174_31165, nifB, nifZ, fixU
Anti-CRISPR   -