Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106951
Name   oriT_LMG 27395|unnamed in_silico
Organism   Sinorhizobium numidicum strain LMG 27395
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP120372 (136214..136253 [+], 40 nt)
oriT length   40 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 40 nt

>oriT_LMG 27395|unnamed
TCCAAGGGCGCAATTATACGTCGCTGCCGCGACGTCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4592 GenBank   WP_280736468
Name   traA_PYH38_RS29785_LMG 27395|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: 122318.05 Da        Isoelectric Point: 9.6543

>WP_280736468.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium numidicum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYRAKQGLLHEEFVMPADSPEWLRSMIADR
SVAGASEAFWNEVEDFEKRADAQLAKDVTIALPIELSAEQNIALIRDFVELHVTAKGMVADWVYHDAPGN
PHVHLMTTLRPLTDDGFGGKKIAALGPDGNPLRNDAGKIVYELWAGGLDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKSATDEQAASLERLELQEEKRAENARRIQRRPGIVLGV
ITREKSVFDERDVAKVLYRYIDDPGIFQSLMARILQSPETLRLEREQVVFATGVRTPAKYTTRGLILLEG
EMANRAIWLSTRSSHGVRKEVLEATFTRHSRLSTEQKTAIEHMAGAERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAESLEKEAGIVSRTLSSWELRWSEGRNQLDDKAVFVLDEAGMVSSRQMALFVE
AATKAGAKLVLIGDPEQLQPIEAGAAFRAIADRLGYAELETIYRQREQWMRDASLDLARGNVGKAVDAYR
ANGKMMGSELKAQAVENLIADWDRDYDPTKTTLILAHLRRDVRMLNEMARAKLVERGIVGEGFVFRTEDG
NRRFAPGDQIVFLKNEGSLGVKNGMLGKVVDASKNRIVAEIGEGEHRRQVTVEQRFYNNLDHGYATTIHK
SQGATVDRLKVLASLSLDRHLTYVAMTRHREDLGVYYGARSFAKSGGLIPILSRENSKETTLDYERATFY
RQALHFAEARGLHLVNVARTIARDRLEWTVRQKQKLADLAHRLVAIGARLGLAVGAKPTRSQSIKETRPM
VAGIATFPKSIEQAVADKLEADPGLKKQWEDVSTRFRLVYAQPEAAFKAVNVDAVLKDDTVARSTLATIA
SQPESYGALKGKTGLLTSRADKQDRERAERNAPALAQSLSDYMRQRSQAEQRYQAEELAARRKVAIDIPA
LSSSARQTLERVRDAIDRNDLPAALEFALADREVKAELEGFAKTVTERFGERTFLPLAAKDTNGETFRTI
TAGMKPGQKAEVQSAWNTMRTVQQLSAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)

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

(858-954)


  Protein structure



No available structure.




T4CP

ID   4685 GenBank   WP_280736383
Name   virD4_PYH38_RS29250_LMG 27395|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: 63582.95 Da        Isoelectric Point: 8.8049

>WP_280736383.1 type IV secretion system ATPase VirD4 [Sinorhizobium numidicum]
MISTETRPLSIAVSIVCSLAAGFCGASLYSTFRYGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGTILLLQQMIPGRNRQHHGTARWARVDEMRRAGYLQRYNRISGPVFGKTSARFWSDYYLTNSEQP
HSLVVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKARGDSIFKLAPLDPERRTNCYNPL
LDIIAMSPERQFTEARRLAANLITAKGQGAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
RLFARLAEETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPLVKAATSRSDFSIYDLRRRRTC
VYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDEAGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYSQGRMFDRNI
QNSDQGAPLLRPEQVRLLSDKYEIVLIKGQPPLQLQKVRYYSDRALKHIFESQTGDLPEPAPLMIEEGKL
GVNSSFNDC

  Protein domains


Predicted by InterproScan.

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

(97-538)

  Protein structure



No available structure.



ID   4686 GenBank   WP_280736465
Name   traG_PYH38_RS29770_LMG 27395|unnamed insolico UniProt ID   _
Length   660 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 660 a.a.        Molecular weight: 71251.27 Da        Isoelectric Point: 9.0510

>WP_280736465.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium numidicum]
MTANRLALVAVPVVLMILAVIGMTGIEQWLSAFGKTDAARLTLGRVGIAAPYVTAAAIGLIFLFASAGST
SIKFAGWGALAGSAATMLVAAIREATRLAGFAGQVPADKSIASYLDPATIIGAASALIAGCFALRVALIG
NVAFARAEPKRIRGQRALHGQADWMKMQDAAKLFPDTGGIVVGERYRVDKDSTAARPFRADDPETWATGG
NSPLLCFDGSFGSSHGIVFAGSGGFKTTSATIPTALKWGGGLVVLDPSNEVAPMVYEHRKNAARFIRILD
PKEPETGFNALDWIGRFGGTKEEDIASVASWIMSDSGGPRGVRDDFFRASALQLLTALIADVCLSGHTDT
ENQTLRQVRVNLSEPEPKLRERLQSIYDNSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGSTFSTDALAAGDTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGELKGRALFLLDEVARLGY
MRILETARDAGRRYGISLTMIYQSIGQMRETYGGRDAASKWFESASWISFASINDPDTADYISRRCGMTT
VEIDQVSRTFQAKGSSRTRSKQLAARPLIQAHEVLRMRADEQIVFTAGNPPLRCGRAIWFRREDMKACVG
TNRFHRIGKPSDARVIEPARCATSKADPGK

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   4687 GenBank   WP_280736473
Name   t4cp2_PYH38_RS29845_LMG 27395|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: 91573.23 Da        Isoelectric Point: 5.6675

>WP_280736473.1 conjugal transfer protein TrbE [Sinorhizobium numidicum]
MVALKRFRAPGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
SGWMIQVEAVRIPTFDYASEDRCHFSDAVTHAIDAERRAHFARERGHFESKHAVILTYRPVESKKTALSK
YIYSDEESRKKTYADTVLFIFKNAIREIEQYLANTLSIRRMETREVAERGGERVARYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVENQFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIIL
FDSDREALQEKAEAIRRLIQAEGFGGRIETLNATDAYLGSLPGNWYSNIREPLINTSNLADLVPLNSVWS
GNPSAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTMIFGPTGSGKSTLLALIAAQFRRYNQAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDAHDAGPPLAFCPLSDLGSDSDRAWATEWIEMLIALQGITITPDHRN
AISRQVTLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEDDGLALGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNSAAREPGTREFYERIGFNERQIEIVSNAIPKREYYVVTPEGRRLFDMALGP
VALSFVGASGKEDLKRIRTLQSEHGRDWPVHWLQMRGVHDAASLLEVA

  Protein domains


Predicted by InterproScan.

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

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 25045..34468

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PYH38_RS29250 (PYH38_005849) 21121..22830 + 1710 WP_280736383 type IV secretion system ATPase VirD4 -
PYH38_RS29255 (PYH38_005850) 22967..23161 + 195 WP_280736384 hypothetical protein -
PYH38_RS29260 (PYH38_005851) 23270..23974 - 705 WP_280736604 response regulator -
PYH38_RS29265 (PYH38_005852) 25045..26085 - 1041 WP_280736385 P-type DNA transfer ATPase VirB11 virB11
PYH38_RS29270 (PYH38_005853) 26124..27248 - 1125 WP_280736386 type IV secretion system protein VirB10 virB10
PYH38_RS29275 (PYH38_005854) 27245..28126 - 882 WP_280736387 P-type conjugative transfer protein VirB9 virB9
PYH38_RS29280 (PYH38_005855) 28123..28836 - 714 WP_280663469 type IV secretion system protein VirB8 virB8
PYH38_RS29285 (PYH38_005856) 28823..28990 - 168 WP_194732549 type IV secretion system lipoprotein VirB7 -
PYH38_RS29290 (PYH38_005857) 29024..29911 - 888 WP_280736388 type IV secretion system protein virB6
PYH38_RS29295 (PYH38_005858) 29990..30670 - 681 WP_280736389 pilin minor subunit VirB5 -
PYH38_RS29300 (PYH38_005859) 30684..33053 - 2370 WP_280736390 VirB4 family type IV secretion/conjugal transfer ATPase virb4
PYH38_RS29305 (PYH38_005860) 33053..33379 - 327 WP_280663465 type IV secretion system protein VirB3 virB3
PYH38_RS29310 (PYH38_005861) 33379..33741 - 363 WP_280663464 pilin major subunit VirB2 virB2
PYH38_RS29315 (PYH38_005862) 33761..34468 - 708 WP_280736391 type IV secretion system lytic transglycosylase VirB1 virB1
PYH38_RS29320 (PYH38_005863) 35538..35777 + 240 WP_280736392 helix-turn-helix transcriptional regulator -
PYH38_RS29325 (PYH38_005864) 35919..36521 - 603 WP_280736393 hypothetical protein -
PYH38_RS29330 (PYH38_005865) 36778..37041 - 264 Protein_34 transposase -
PYH38_RS29335 (PYH38_005866) 37314..37661 - 348 WP_280736394 hypothetical protein -

Host bacterium

ID   7388 GenBank   NZ_CP120372
Plasmid name   LMG 27395|unnamed Incompatibility group   -
Plasmid size   629446 bp Coordinate of oriT [Strand]   136214..136253 [+]
Host baterium   Sinorhizobium numidicum strain LMG 27395

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   dxnH, linJ
Symbiosis gene   nifN, nodD, nodA, nodB, nodC, nodI, nodJ, nodE, nodF, nodH, mLTONO_5203, nifX, nifE, nifD, nifH, nifS, nifW, fixA, fixB, fixC, fixX, fixN, fixO, fixG, fixS, nodM, a9174_31165, fixU, nifZ, nifB
Anti-CRISPR   AcrIIC2, AcrIIA9