Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116911
Name   oriT_p-2 in_silico
Organism   Ensifer adhaerens strain E-60
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084488 (1226356..1226396 [+], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      20..25, 30..35  (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_p-2
ATCAAAGTGCGCAATTATACGTCGCCGATGCGACGCTTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10790 GenBank   WP_218685710
Name   traA_LDL63_RS32900_p-2 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: 122378.56 Da        Isoelectric Point: 9.8756

>WP_218685710.1 Ti-type conjugative transfer relaxase TraA [Ensifer adhaerens]
MAVPHFSVSVVARGSGRSAVMSAAYRHCAKMDYEREARTIDYRAKQGLLHEEFAIPADAPAWLRSMIADR
PVSGAAEAFWNKVEQFEKRGDAQLAKDVTIALPLELTAEQNVALIRDFVEHYVTSRGMVADWVYHDAPGN
PHVHLMTTLRPLTENGFGGKKIAVLGVDGNPIRNDHGKIVYELWAGNLDDFNAFRDGWFACQNRHLGLAG
LGIRIDGRSFDKQGIELAPTIHLGVGTKAIERKSAADEQAASLERLALQEERRSENGRRIQGRPEIVLDL
ISREKSVFDERDIAKILHRYIDDPGLFQSLMARILQSPDALCLDRERLAFATGLRVPAKYATRELIRLEA
EMASRAVWLSRRSSHGVRDAVLKAAFTRHSRLSKEQISAIEHVAGPERIAAVIGRAGAGKTTMMKAAREA
WETAGYRVVGGALAGKAAEGLEKDAGIVSRTLSAWELRWKEGRNPLDNKTVFVLDEAGMVSSRQMALFVE
VATKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELQTIYRQRERWMRDASLDLARGDVGKAVEAYR
ANGRIVASELKAQAVQNLIADWERDYDPTRTMLILAHLRRDVRMLNDMARARLVERGLLNDGFMFRTEDG
NRHFAPGDQIIFLKNEGSLGVKNGMLGKVVDAAQNRIVAEIGGGQHRRQVTVESRFYNNIDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLDVYYGQRSFAKAGGLTEMLSQKNSKETTLDYEKATFY
RQALHFAEARGLHLVNVARTIARDRLDWTVRQKQKLTDLAHRLASIGEQLGFAVGAKTMNAQRLKETRPM
VAGIATFPKSMEQSVIDKIEADPGLKKIWEDVSTRFHLVYAQPEAAFKAVNVGEMLKDDTVASATLAKVA
SQPDTYGALKGRTGILASRADKQDRERAECNVPALVQSLGDYVGQRSRIEQRYRTEEVALRRRVAIDIPE
LSAGARQTLERVRDAINRNELPAALGFALADRQVKAELDGFAKAVTERFGERTFLPLAAKDTNGETFKTI
AAGLKPGETAEVRLAWNMMRAAQQLSAHERTVEALKQAETLRQTKGQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

MobA/MobL family (MobA_MobL)

(17-243)

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

(858-953)


  Protein structure



No available structure.




T4CP

ID   12610 GenBank   WP_218685713
Name   traG_LDL63_RS32885_p-2 insolico UniProt ID   _
Length   641 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 641 a.a.        Molecular weight: 69087.84 Da        Isoelectric Point: 8.8831

>WP_218685713.1 Ti-type conjugative transfer system protein TraG [Ensifer adhaerens]
MTTDKLALATIPVALMTLTVSGMHGIEHWLSAFGKTDAARDTLGRIGVAAPYVSAAALGVIFLFASAGAV
SIKLAGWSVLFGAAATLLTATLREAARLSAFAGDVPPGMSVASYLDPATMVGAAAALLAGGYALRVALIG
NAAFRRPEPKRVKGQRALHGEADWMKMGQAAKLFSDTGGIVIGECYRVDQDSTAAEPFRADDRETWGAGG
KPPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSSEVAPMVCRHRKAAARFLRILD
PKEPETGFNALDWIGRFGGTKEEDIASVASWIISDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDQ
ENQTLRQARTNLAEPEPKLRERLQSIYHNSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGSTFSTDALASGKTDVFINIDLKTLETHAGLARVIIGSFLNAIYNRDGQVKGRALFLLDEVARLGY
MQILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPDTADYISKRCGMTT
VEIDQVSRSFQSKGASRTRSKQLAARALIQPHEVLRMRTDEQIVFTAGNPPLRCGRAIWFRRKDMKACVD
ANRFHKIAQDV

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   12611 GenBank   WP_218685701
Name   t4cp2_LDL63_RS32970_p-2 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: 91663.38 Da        Isoelectric Point: 5.8697

>WP_218685701.1 conjugal transfer protein TrbE [Ensifer adhaerens]
MVALKQFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
NGWMIQVEAIRVPTVDYPLEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHVLILTHRPPESKKTALSK
YIYSDESSRKKTYADTVLAIFRNSVREIEQYFANTLSIQRMETREVSERGGERTARYDELLQFVRFCITG
ENHPIRLPDVPMYLDWIATAELQHGLTPTVENRFLGVVAIDGFPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRALDQDAMSMVAETEDAIAQASSQLVAYGYYTPVVIL
FDDDRERLQEKAEAIRRLVQAEGFGARIETLNATDAFLGSLPGNWYCNVREPLINTSNLADLVPLNSVWS
GSPVAPCPFFPTNSPPLMQVATGSTPFRFNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEFAQIFA
FDKGNSLLPLTLATGGEHYEIGGDHEEGRALAFCPLFDLSTDGDRAWASEWIEMLVALQGTTITPDHRNA
ISRQLCLMAKATGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLTLGTFQTFEIEHLMNLGE
RHLVPVLTYLFRLIEKRLDGSPSLIVLDEAWLMLGQPVFRNKIREWLKVLRKANCAVVLATQSISDAERS
GIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSGAIPKREYYVVTSEGRRLFDMALGPV
ALSFAGASGKEDLKRIRALKSEHGQNWPSHWLATRGVPDAASILNIA

  Protein domains


Predicted by InterproScan.

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

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1231508..1243523

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LDL63_RS32905 (LDL63_32905) 1229847..1230341 + 495 WP_256939196 conjugative transfer signal peptidase TraF -
LDL63_RS32910 (LDL63_32910) 1230331..1231491 + 1161 WP_218685708 conjugal transfer protein TraB -
LDL63_RS32915 (LDL63_32915) 1231508..1232110 + 603 WP_218685707 TraH family protein virB1
LDL63_RS32920 (LDL63_32920) 1232366..1232575 - 210 WP_060529727 helix-turn-helix domain-containing protein -
LDL63_RS32925 (LDL63_32925) 1232750..1233121 + 372 WP_060585894 transcriptional repressor TraM -
LDL63_RS32930 (LDL63_32930) 1233074..1233784 - 711 WP_218685706 autoinducer binding domain-containing protein -
LDL63_RS32935 (LDL63_32935) 1234049..1235332 - 1284 WP_218685705 IncP-type conjugal transfer protein TrbI virB10
LDL63_RS32940 (LDL63_32940) 1235343..1235777 - 435 WP_090428444 conjugal transfer protein TrbH -
LDL63_RS32945 (LDL63_32945) 1235780..1236592 - 813 WP_218685704 P-type conjugative transfer protein TrbG virB9
LDL63_RS32950 (LDL63_32950) 1236609..1237271 - 663 WP_113293051 conjugal transfer protein TrbF virB8
LDL63_RS32955 (LDL63_32955) 1237287..1238468 - 1182 WP_218685703 P-type conjugative transfer protein TrbL virB6
LDL63_RS32960 (LDL63_32960) 1238462..1238659 - 198 WP_113293053 entry exclusion protein TrbK -
LDL63_RS32965 (LDL63_32965) 1238656..1239459 - 804 WP_218685702 P-type conjugative transfer protein TrbJ virB5
LDL63_RS32970 (LDL63_32970) 1239431..1241884 - 2454 WP_218685701 conjugal transfer protein TrbE virb4
LDL63_RS32975 (LDL63_32975) 1241893..1242192 - 300 WP_060529729 conjugal transfer protein TrbD virB3
LDL63_RS32980 (LDL63_32980) 1242185..1242556 - 372 WP_060529730 TrbC/VirB2 family protein virB2
LDL63_RS32985 (LDL63_32985) 1242546..1243523 - 978 WP_218685700 P-type conjugative transfer ATPase TrbB virB11
LDL63_RS32990 (LDL63_32990) 1243534..1244160 - 627 WP_218685699 acyl-homoserine-lactone synthase TraI -
LDL63_RS32995 (LDL63_32995) 1244518..1245750 + 1233 WP_218685777 plasmid partitioning protein RepA -
LDL63_RS33000 (LDL63_33000) 1245801..1246814 + 1014 WP_218685698 plasmid partitioning protein RepB -

Host bacterium

ID   17344 GenBank   NZ_CP084488
Plasmid name   p-2 Incompatibility group   -
Plasmid size   1568420 bp Coordinate of oriT [Strand]   1226356..1226396 [+]
Host baterium   Ensifer adhaerens strain E-60

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   silP, nia, arsC
Degradation gene   RPYSC3_16500, linJ, dxnH, LinG
Symbiosis gene   fixB, fixA
Anti-CRISPR   AcrIIA7, AcrIIA1