Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121181
Name   oriT_punamed3 in_silico
Organism   Pantoea agglomerans strain CFBP8774
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP143405 (114562..114639 [-], 78 nt)
oriT length   78 nt
IRs (inverted repeats)      28..35, 38..45  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 78 nt

>oriT_punamed3
CTCACCACCAAAAGCACCACACCCCACGCAAAATTAAAATTTTGCTGATTGGCCTTACAAGTCATGCACTTATGTTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13372 GenBank   WP_191924853
Name   traI_IFU02_RS03340_punamed3 insolico UniProt ID   _
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189420.68 Da        Isoelectric Point: 6.1445

>WP_191924853.1 conjugative transfer relaxase/helicase TraI [Pantoea agglomerans]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLCGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHGDEWRTLSSDRVGKTGFIENIYANQIAFGRLYRAALKDDVTA
MGYETETVGRHGMWEFKGVPVAPFSSRSRTIGEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMSEWMQT
LKETGFDIKAYREAADQRVVQGNIPVTAPEAIDINSSVGQSIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDTAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMSRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSDEYITDRRG
LTEGMTFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVNTLAWQD
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVSGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLKGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSARVFASLSQRELDNTTLNRLALSGPVVQLYSAQTAQKTTEKLSRQSAWSIVSEQIKD
AAGRERLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQI
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSILRHVLEGKEAVTPLMAGVPEAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DMAVMQAIVRQTPELKPAVYSLINRDIGSALTTIESVAPAQVPRRADAWRPDSSVMEFSREREDAIAKAV
AAGDMIPGGQPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQDTGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYNIEALDREAHLVTLKDAQGNTRSLSPAQAATEGVTLYCQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVQG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDSRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALCEVPAGRAALRQAGLQPEGSMAKFIAPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLGSEGRVMGSGDAAFAGLQASRNGESLLARNMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADSLPDSAGTQPGETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGHGPAGGADVAV
QDVVRDMDRVKETPASPLTLPDAPDARRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1430-1551)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(967-1151)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(631-710)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(573-625)


  Protein structure



No available structure.




T4CP

ID   15670 GenBank   WP_191919512
Name   traD_IFU02_RS03355_punamed3 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 80186.60 Da        Isoelectric Point: 5.1640

>WP_191919512.1 type IV conjugative transfer system coupling protein TraD [Pantoea agglomerans]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGVIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGRELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVIAPEVSAENAGQPQPPAARAA
DAASASASVAGAGGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAEQDELSPQERQRREEVN
INVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

  Protein structure



No available structure.



ID   15671 GenBank   WP_191919501
Name   traC_IFU02_RS03425_punamed3 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 98951.67 Da        Isoelectric Point: 5.7676

>WP_191919501.1 type IV secretion system protein TraC [Pantoea agglomerans]
MSNPLDTVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRRRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDVLYPTVRELDPLKDLNYQCVDDSFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVEQEAKEWGD
LRQRLSSGQSSLVSYFLNVTVFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVVQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANITDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFRNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKIIS

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(470-765)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 90252..121527

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IFU02_RS03345 (IFU02_003345) 89618..89845 + 228 WP_191919514 toxin-antitoxin system antitoxin VapB -
IFU02_RS03350 (IFU02_003350) 89845..90297 + 453 WP_191919513 type II toxin-antitoxin system VapC family toxin -
IFU02_RS03355 (IFU02_003355) 90252..92405 - 2154 WP_191919512 type IV conjugative transfer system coupling protein TraD virb4
IFU02_RS03360 (IFU02_003360) 92582..93313 - 732 WP_191919511 conjugal transfer complement resistance protein TraT -
IFU02_RS03365 (IFU02_003365) 93409..93720 + 312 WP_191919510 hypothetical protein -
IFU02_RS03370 (IFU02_003370) 93722..96541 - 2820 WP_191919509 conjugal transfer mating-pair stabilization protein TraG traG
IFU02_RS03375 (IFU02_003375) 96541..97911 - 1371 WP_191919508 conjugal transfer pilus assembly protein TraH traH
IFU02_RS03380 (IFU02_003380) 97898..98326 - 429 WP_191919507 conjugal transfer protein TrbF -
IFU02_RS03385 (IFU02_003385) 98319..98873 - 555 WP_191919506 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IFU02_RS03390 (IFU02_003390) 98863..99111 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
IFU02_RS03395 (IFU02_003395) 99128..99883 - 756 WP_191919505 type-F conjugative transfer system pilin assembly protein TraF traF
IFU02_RS03400 (IFU02_003400) 99894..101774 - 1881 WP_191919504 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IFU02_RS03405 (IFU02_003405) 101771..102400 - 630 WP_191919503 type-F conjugative transfer system pilin assembly protein TrbC trbC
IFU02_RS03410 (IFU02_003410) 102416..103402 - 987 WP_191919521 conjugal transfer pilus assembly protein TraU traU
IFU02_RS03415 (IFU02_003415) 103405..104052 - 648 WP_191919502 type-F conjugative transfer system protein TraW traW
IFU02_RS03420 (IFU02_003420) 104052..104399 - 348 WP_049047524 type-F conjugative transfer system protein TrbI -
IFU02_RS03425 (IFU02_003425) 104396..107026 - 2631 WP_191919501 type IV secretion system protein TraC virb4
IFU02_RS03430 (IFU02_003430) 107019..107585 - 567 WP_191919500 conjugal transfer pilus-stabilizing protein TraP -
IFU02_RS03435 (IFU02_003435) 107575..107871 - 297 WP_191919499 hypothetical protein -
IFU02_RS03440 (IFU02_003440) 108041..108265 - 225 WP_016674195 TraR/DksA C4-type zinc finger protein -
IFU02_RS03445 (IFU02_003445) 108385..108924 - 540 WP_191919498 type IV conjugative transfer system lipoprotein TraV traV
IFU02_RS03450 (IFU02_003450) 108946..110340 - 1395 WP_191919497 F-type conjugal transfer pilus assembly protein TraB traB
IFU02_RS03455 (IFU02_003455) 110327..111070 - 744 WP_011201807 type-F conjugative transfer system secretin TraK traK
IFU02_RS03460 (IFU02_003460) 111057..111623 - 567 WP_191919496 type IV conjugative transfer system protein TraE traE
IFU02_RS03465 (IFU02_003465) 111638..111943 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
IFU02_RS03470 (IFU02_003470) 112094..112444 - 351 WP_191919495 type IV conjugative transfer system pilin TraA -
IFU02_RS03475 (IFU02_003475) 112510..112884 - 375 WP_191919494 TraY domain-containing protein -
IFU02_RS03480 (IFU02_003480) 112993..113697 - 705 WP_191919493 hypothetical protein -
IFU02_RS03485 (IFU02_003485) 113884..114279 - 396 WP_191919492 conjugal transfer relaxosome DNA-binding protein TraM -
IFU02_RS03490 (IFU02_003490) 114653..115185 + 533 Protein_116 transglycosylase SLT domain-containing protein -
IFU02_RS03495 (IFU02_003495) 115233..115763 - 531 WP_191919490 antirestriction protein -
IFU02_RS03500 (IFU02_003500) 116113..117036 + 924 WP_330451442 IS5 family transposase -
IFU02_RS03505 (IFU02_003505) 117109..117516 - 408 Protein_119 recombinase family protein -
IFU02_RS03510 (IFU02_003510) 117855..118531 - 677 Protein_120 M91 family zinc metallopeptidase -
IFU02_RS03515 (IFU02_003515) 118740..119693 - 954 WP_191919638 Rpn family recombination-promoting nuclease/putative transposase -
IFU02_RS03520 (IFU02_003520) 119759..119962 - 204 WP_191919637 hemolysin expression modulator Hha -
IFU02_RS03525 (IFU02_003525) 120141..121064 - 924 WP_330451442 IS5 family transposase -
IFU02_RS03530 (IFU02_003530) 121144..121527 - 384 WP_191919635 conjugal transfer protein TraH traH
IFU02_RS03535 (IFU02_003535) 121771..121983 + 213 WP_191919636 hypothetical protein -
IFU02_RS03540 (IFU02_003540) 122307..122867 - 561 WP_191919634 disulfide bond formation protein B -
IFU02_RS03545 (IFU02_003545) 122879..123037 - 159 WP_244631168 DUF5993 family protein -
IFU02_RS03550 (IFU02_003550) 123118..124065 - 948 WP_191919633 DMT family transporter -
IFU02_RS03555 (IFU02_003555) 124199..124752 - 554 Protein_129 IS1 family transposase -
IFU02_RS03560 (IFU02_003560) 124828..125082 + 255 Protein_130 transposase -
IFU02_RS03565 (IFU02_003565) 125138..126061 - 924 WP_330451442 IS5 family transposase -

Host bacterium

ID   21609 GenBank   NZ_CP143405
Plasmid name   punamed3 Incompatibility group   IncFII
Plasmid size   149927 bp Coordinate of oriT [Strand]   114562..114639 [-]
Host baterium   Pantoea agglomerans strain CFBP8774

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -