Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120082
Name   oriT_pPttDSM50252-1 in_silico
Organism   Pseudomonas syringae pv. aptata str. DSM 50252
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AEAN02000003 (24774..24877 [+], 104 nt)
oriT length   104 nt
IRs (inverted repeats)      63..70, 73..80  (CCACCAAT..ATTGGTGG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 104 nt

>oriT_pPttDSM50252-1
GCCTCGCAGAGCAAGATTCCCCGTTGAGCACGAAGTGCGAATAAGGGGTAGTGAAGAAGGATCCACCAATTTATTGGTGGGCCTACTTCACCTATCTTGCCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12650 GenBank   WP_306093011
Name   traI_PSYAP_RS25640_pPttDSM50252-1 insolico UniProt ID   _
Length   828 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 828 a.a.        Molecular weight: 90429.47 Da        Isoelectric Point: 10.9169

>WP_306093011.1 TraI/MobA(P) family conjugative relaxase [Pseudomonas syringae]
MPMREAKLSSYAGLAKYITSAQNKQERVGEIRLTNFQSESLDWAVTEALHVQQLNQRAEGDKTYHLLISF
APGEQPSADILRDVEDRICASIGFGEHQRISAVHNDTDNLHIHIAINKIHPERHTIHEPYRAYKTMGDMA
SILEREHGLHLTNHTAKKSGSENRADDMEQHAGVESLLGWIKKECAAQLTQATTWNELHAVMRSNGLELQ
SRGNGFVITDGRGVGVKASSVSRDLSKSKLEKRLGIFELDAKREAGSKRGPGASNRRPPPVKPVGGRPPP
MRRGRLAALSQLAVLEGEPAKRYQGRPIRGTGNPETTELYARYKASQGIANHARAKDWDLAKDRKNRAIE
NAKRSGRAKRAAIKILDAPGITKKLLYSQVSKSVHAEIQRINAAYLAERQHIHTHYPKRTWADWLQAQAK
EGDQAALKALRGRKAVKPRVGDAVAGNGPVRRSGPVPLKVDSVTKDGTVIHRFGTSAIRDDGDALQVSRG
SGQVGIEAVLRMAVHRYGESLTVNGSDQFKEQVAHVAANSNLKIIFKDAALEARRLELVALQTKENGNDR
SRKSNRRTNERGRTARGNDGTARSERGGAAARAGVRRGPGHTNKSGAGGAGGPKPPPLSRNSLRELPELG
VVRIPNRREMLLPSDVPHNVQHEGAKHAGGMRRGVPEPGRGLGQGQRGPGRSNRPGVTPVGGKPPSMLRG
KLQPMSKLRALPVTDPADAKKNEPVPEMTPVPNNKSAAAKYIDERMSKQAKGFDIPNHRGYTDADKGPSL
FAGTRQIEGETLALLKRDEEIIVLPVDPATARRIKRYSLGDEVTVNAKGTLTKKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(9-245)

Large polyvalent protein-associated domain 7 (LPD7)

(462-546)


  Protein structure



No available structure.




T4CP

ID   14850 GenBank   WP_003396610
Name   t4cp2_PSYAP_RS25635_pPttDSM50252-1 insolico UniProt ID   _
Length   648 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 648 a.a.        Molecular weight: 71867.19 Da        Isoelectric Point: 8.2840

>WP_003396610.1 type IV secretory system conjugative DNA transfer family protein [Pseudomonas syringae]
MSKANNDVGPQTRKKKKSIGSKVVPALGIASFVAASQAATQFFAWKFEYQAVLGAHINHVYAPWAIYDWW
NKWYGVYPEALTAAGSVGTLVAAGGLIGTALAKIVAANSSKGNEYLHGSARWADREDIEQASLLGNEGRD
GGVYVGAWRDKYGKLQYLRHNGPEHVLCYAPTRSGKGVGLVLPTLLSWPHSAVITDLKGELWAMTAGWRK
KHAGNKVIRFEPASANGCAEWNALDEIRIGTEAEVGDVQNLATLVVDPDGKGLKDHWQKTAQALLVGVIL
HALYKAKDEGTIASLPSVDGMLADPNRDVSELWMEMTQYGHVNGENHPVIGRAGRDMMDRPEEEAGSVLS
SAKSYLSLYRDPVVARNVSKSTWRIKDLMNHDDPVSLYIVTQPVDKERLKPLVRVLVNMIVRLLADKMEF
ERIKAKMPLWRRILDRIGFKQQADTYVRSKKSYKHRLLMQLDEFPSMGKLSIIQESLAFLAGYGVKFYLI
CQDINQLKSQEEGYGADESISSNCHVQNAYPPNRIETAQHLSKLTGVTTVLQEQVTTSGKRAGIFMGQVS
KTIQAVQRPLLTDDECMRMPGPKKDAEGQIKEPGDMVVYVAGFPAIYGEQPLYFQDPIFTARAAVEEPKD
TDRLRLQNELSERELVAI

  Protein domains


Predicted by InterproScan.

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

(450-627)

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

(122-422)

  Protein structure



No available structure.



ID   14851 GenBank   WP_306093012
Name   trbB_PSYAP_RS25755_pPttDSM50252-1 insolico UniProt ID   _
Length   324 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 324 a.a.        Molecular weight: 35639.75 Da        Isoelectric Point: 5.4938

>WP_306093012.1 P-type conjugative transfer ATPase TrbB [Pseudomonas syringae]
MTEPDENSDAQLDTYRKRNTERLRRDLGDEIMGALNDAKTTDILVNADGKIWLKRLGEPSRVIGRIEPWR
ATSAMKTLAGLLGKTISGRQPILDGELPFRGERFAGQLPPVVSAPCFAIRKKAIKVFPLDAYVEQGIMTQ
AQCDTIKKAVQDHKNILVVGGTGSGKTTLINAIIQAMVDFDPNERIFIIEDTGEIQCVAVNCVQYHTTEE
VDMTGLLRTTLRMLPDRIIVGEVRGGEALDLLDSWNTGHDGGAGTLHANDVDSALSRFRSLVTRNKDAPS
DIEPLIAEAVNVIVHIRRTPEGRKVEGIIEILGYENGKYITNAI

  Protein domains


Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(34-298)

  Protein structure



No available structure.



ID   14852 GenBank   WP_003396563
Name   t4cp2_PSYAP_RS25770_pPttDSM50252-1 insolico UniProt ID   _
Length   850 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 850 a.a.        Molecular weight: 94633.43 Da        Isoelectric Point: 6.0142

>WP_003396563.1 conjugal transfer protein TrbE [Pseudomonas syringae]
MIETMLVAIAALGITLVVFLLLRVRQVNADLRMKKHRAKDAGLADLLNYAAVVDDGVIVCKNGSLMAAWL
YKGSDNASASDVERELNSFRLNQAFARMGSGWMIHVDSARRAAPSYSDPNDSYFPDPVSAAIDEERRRTF
ETLGNLYEGFFILTVTWFPPMLAERKFVELMFHDDDVKPNKKAQTLHLLDFFKREVRNIESRCSGAISLE
RLCGQRVMNENGTTVTHDEFLQWLQFCITGLNHPVMLPNNPIYIDNLIGGQELYTGVTPKLGRKFIQVVT
IEGFPLDSVPGILTRLGEQPAEYRWSNRFIFMDHHEAVSHLETFRKKWKQKVRGFYDQLFNSNSGHIDED
AQNMVADANQAIAETNSGMVAQGYYTSVVVLMDESRAVVEAAALQIEKTINAMAFTARVETINTMDAFMG
SLPGHGVENVRRPLINTMNLADLIPTSTIWTGEAYAPNPMMAPNSPPLLYGLTSGNSAFRVNLDVRDLGH
TMIFGPTRAGKSTLLALLALSWRRYSDARLFTFDKGMAMYPSCKAAGGSHYVVAGANDTLAFAPLSGLVT
RARRAWAAQWIDDLLALNGVKTTADQRNEIASAIRDMGKVEADTGRVGTISEFSAMVQDVDIRAALLDYT
IDGEMGHLMDAESDNLSISDFITFEIEQLMNLGNKFALPVLLYIFMRIEEALDGRPTLIILDEAWLMLGH
EVFRAKIREWLKTLAKKNCRVVMATQNLTDASESGILDVIDESTATKIYLPNPSAREEKASALYQRLGLN
LRQIEILATARKQNDYYLVSEKGSRLFSLALGPLAKSFVAKTSLEDIGAIKALEATHGPKWVDIWLRDRG
LSLDNYRGAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(625-785)

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

(220-431)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40603..51047

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PSYAP_RS25730 (PSYAP_025730) 35951..36520 - 570 WP_003396573 hypothetical protein -
PSYAP_RS25735 (PSYAP_025735) 36568..36996 - 429 WP_003396572 antirestriction protein -
PSYAP_RS25740 (PSYAP_025740) 37141..37452 - 312 WP_003396571 hypothetical protein -
PSYAP_RS25745 (PSYAP_025745) 38570..39733 - 1164 WP_003396569 plasmid replication initiator TrfA -
PSYAP_RS25750 (PSYAP_025750) 39966..40292 + 327 Protein_48 transcriptional regulator -
PSYAP_RS25755 (PSYAP_025755) 40603..41577 + 975 WP_306093012 P-type conjugative transfer ATPase TrbB virB11
PSYAP_RS25760 (PSYAP_025760) 41588..42022 + 435 WP_003396565 TrbC/VirB2 family protein virB2
PSYAP_RS25765 (PSYAP_025765) 42027..42338 + 312 WP_306092991 conjugal transfer protein TrbD virB3
PSYAP_RS25770 (PSYAP_025770) 42335..44887 + 2553 WP_003396563 conjugal transfer protein TrbE virb4
PSYAP_RS25775 (PSYAP_025775) 44884..45639 + 756 WP_003396562 VirB8/TrbF family protein virB8
PSYAP_RS25780 (PSYAP_025780) 45658..46554 + 897 WP_003396561 P-type conjugative transfer protein TrbG virB9
PSYAP_RS25785 (PSYAP_025785) 46554..47015 + 462 WP_003396560 conjugal transfer protein TrbH -
PSYAP_RS25790 (PSYAP_025790) 47021..48451 + 1431 WP_003396558 TrbI/VirB10 family protein virB10
PSYAP_RS25795 (PSYAP_025795) 48469..49239 + 771 WP_306092992 P-type conjugative transfer protein TrbJ virB5
PSYAP_RS25800 (PSYAP_025800) 49258..49497 + 240 WP_306092993 EexN family lipoprotein -
PSYAP_RS25805 (PSYAP_025805) 49500..51047 + 1548 WP_306092994 P-type conjugative transfer protein TrbL virB6
PSYAP_RS25810 (PSYAP_025810) 51055..51354 + 300 WP_003396553 TrbM/KikA/MpfK family conjugal transfer protein -
PSYAP_RS25815 (PSYAP_025815) 51365..52030 + 666 WP_003396552 transglycosylase SLT domain-containing protein -
PSYAP_RS25820 (PSYAP_025820) 52039..52770 + 732 WP_003396551 TraX family protein -
PSYAP_RS25825 (PSYAP_025825) 52799..53398 + 600 WP_306092995 hypothetical protein -

Host bacterium

ID   20512 GenBank   NZ_AEAN02000003
Plasmid name   pPttDSM50252-1 Incompatibility group   -
Plasmid size   53430 bp Coordinate of oriT [Strand]   24774..24877 [+]
Host baterium   Pseudomonas syringae pv. aptata str. DSM 50252

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   klaB/telA/kilB
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -