Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106916
Name   oriT_YW14|4 in_silico
Organism   Pseudorhizobium flavum strain YW14
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LR723673 (55309..55353 [+], 45 nt)
oriT length   45 nt
IRs (inverted repeats)      22..27, 32..37  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 45 nt

>oriT_YW14|4
GGCTCCAAGGGCGCAATTATACGTCGCTTACGCGACGCCTTGCGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4573 GenBank   WP_077548981
Name   traA_GFD27_RS22105_YW14|4 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 124015.50 Da        Isoelectric Point: 9.7393

>WP_077548981.1 Ti-type conjugative transfer relaxase TraA [Pseudorhizobium flavum]
MAITHFSVSIVSRGDGRSAVLSAAYRHCARMEYEREARTIDYTRKEGLLHEEFLLPADAPKCARMLIADR
SIAGASETFWNKVEAYEKRSDAQLAKDLTIALPLELTPEQNIALVRDFVERHILSKGMVADWVYHDNPGN
PHIHLMTTLRPLTEDGFGAKKVAVTGEDGQPLRNKAGKIVYELWAGGTDDFNAFRDAWFERLNHHLALNG
ISLRVDGRSYEKQGIDLEATIHLGVGAKAIERKAEKQGVRPELERLELNEKRRSENARRILRKPGIVVDL
ITREKSVFDERDVAKVLHRYIDDPAVFQQLMLSIILNPKVLRLQRDTIDFATGAKVPARYSTREMIRLEA
TMARQAMWLSGRETHDVDDKVLAATFARHARLSDEQKTAIERIAGSARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIVSRTLASWELRWQQGRDTLDARTVFVMDEAGMVASKQMAGFVD
GVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREEWMRHASLDLARGNVEKALTAYN
ANARITGERLKAEAVESLIADWNRDYDPKKTMLMLAHLRRDVRMLNVMAREKLVERGIVGEGHVFRTADG
TRQFDAGDQIVFLKNEGSLGVKNGMIGHVVEAASNRIVAVVGEGDQRRQVTVESRFYNNLDYGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQVYFGRRSFEMNGGLAKVLSRKNAKETTLDYERGTLY
REALRFAENRGLHIMQVARTLLRDRLDWTLRQKSKLTDLTNRLRQLGERFGLRQSPPTQSAKESKPMVAG
ITRFENSVADTVEQKLDADLALKKQWEEVSIRFRYVFADPETAFRAMNFDAVLADRDLGRQVLQKLETEP
VSIGPLKGKTGILASKTDREARRIAEVNVPALKRDLERYLQMRESAVQRHEAEENTLRQRVSIDIPALSP
AARAVLERVRDAIDRNDLEAALAYALSNRETKLEIDEFNKAVTERFGERTLLTNAAREPSGKLFDKLSEG
LQPQEKERLAEAWPVMRTAQQLAAHERTSETLRQVEELRLSQRQAPVMKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-566)

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

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-736)


  Protein structure



No available structure.




T4CP

ID   4659 GenBank   WP_077548979
Name   traG_GFD27_RS22090_YW14|4 insolico UniProt ID   _
Length   640 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 640 a.a.        Molecular weight: 69205.36 Da        Isoelectric Point: 9.7102

>WP_077548979.1 Ti-type conjugative transfer system protein TraG [Pseudorhizobium flavum]
MNRLLLTILPAALMIAAMLAMSGIETWLSGFGTSAQAKLMLGLIGLTLPYAAAAAVGLIFLFATAGAANI
KTAGLSVLAGASVVCIAAITREGWRLHALADRVPQGQSVFAYTDPSAMLGAFAAVFSGIFALRVATRGNA
AFAKAAPRRIAGKRAVHGEADWMKMADAVKLFPDAGGIVIGERYRVDKDSVAGVTFRASEARSWGAGGRS
PLLCFDGSFGSSHGIIFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVIDHRRKAGRNVIVLDPA
TPAIGFNALDWIGRHGNTKEEDIVAVATWIMTDNARTASARDDFFRASAMQLLTALIADVCLSGHTDEKD
QTLRRVRANLSEPEPKLRERLTRIYEQSESDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGDSFSTDNLAEGSADLFIALNLKVLEAHPGLARVVIGSLLNAIYNRNGKVKGRTLFLLDEVARLGYLR
ILETARDAGRKYGITLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTTVE
VEQTNRSTGMKGSSRSRSKQLSRRPLIMPHEVLRMRSDEQIVFTSGNPPLRCGRAIWFRRDDMMTCVGQN
RFHREGEKSG

  Protein domains


Predicted by InterproScan.

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

(161-633)

  Protein structure



No available structure.



ID   4660 GenBank   WP_003501273
Name   t4cp2_GFD27_RS22305_YW14|4 insolico UniProt ID   _
Length   822 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 822 a.a.        Molecular weight: 91864.77 Da        Isoelectric Point: 5.4885

>WP_003501273.1 conjugal transfer protein TrbE [Pseudorhizobium flavum]
MVALKSFRHPGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAVRVLTGDYPAEDDCHFPDPVTRAIDAERRAHFQKERGHFESRHALILTWRPPEPRRSGLTR
YIYSDPASRSATYADKTLETFLTSIREVEQYLANVVSIRRMMTRETQERGGFRVARYDELFQFIRFCITG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMMMVAETEDAIAEASSQLVACGYYTPVIVI
FDENQARLQENCEAVRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSIWS
GSPTAPCPFYPPGSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYASAQVFA
FDKGSSMLPLTLGLNGDHYQIGGDIGPSAEGEVKALAFCPLAELSTDGDRAWATEWIETLVALQGVTITP
DYRNAISRQIELMAESRGRSLSDFVSGVQMREIKEALHHYTVDGPMGQLLDAEEDGLALGAFQCFEIEEL
MNMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVVSPEGRRLFDM
ALGPVALSFVGASGKEDLKRIRALHSEHGAGWPLHWLQQRGIAHADTLFPAE

  Protein domains


Predicted by InterproScan.

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

(188-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 93038..102739

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GFD27_RS22245 (RFYW14_04503) 88576..89343 + 768 WP_003501297 glucose 1-dehydrogenase -
GFD27_RS22250 (RFYW14_04504) 89354..90124 + 771 WP_003501296 enoyl-CoA hydratase-related protein -
GFD27_RS22255 (RFYW14_04505) 90168..90983 + 816 WP_003501295 alpha/beta hydrolase -
GFD27_RS22260 (RFYW14_04506) 91050..91697 + 648 WP_210187336 MarR family transcriptional regulator -
GFD27_RS23465 91719..92517 - 799 Protein_95 3-methyl-2-oxobutanoate hydroxymethyltransferase -
GFD27_RS22270 (RFYW14_04510) 93038..94354 - 1317 WP_077549915 IncP-type conjugal transfer protein TrbI virB10
GFD27_RS22275 (RFYW14_04511) 94366..94839 - 474 WP_035243671 conjugal transfer protein TrbH -
GFD27_RS22280 (RFYW14_04512) 94839..95693 - 855 WP_035243803 P-type conjugative transfer protein TrbG virB9
GFD27_RS22285 (RFYW14_04513) 95711..96388 - 678 WP_003501288 conjugal transfer protein TrbF virB8
GFD27_RS22290 (RFYW14_04514) 96406..97602 - 1197 WP_077549914 P-type conjugative transfer protein TrbL virB6
GFD27_RS22295 (RFYW14_04515) 97596..97826 - 231 WP_003501277 entry exclusion protein TrbK -
GFD27_RS22300 (RFYW14_04516) 97823..98632 - 810 WP_035243669 P-type conjugative transfer protein TrbJ virB5
GFD27_RS22305 (RFYW14_04517) 98604..101072 - 2469 WP_003501273 conjugal transfer protein TrbE virb4
GFD27_RS22310 (RFYW14_04518) 101082..101381 - 300 WP_003501271 conjugal transfer protein TrbD virB3
GFD27_RS22315 (RFYW14_04519) 101374..101778 - 405 WP_077549913 conjugal transfer pilin TrbC virB2
GFD27_RS22320 (RFYW14_04520) 101768..102739 - 972 WP_003501268 P-type conjugative transfer ATPase TrbB virB11
GFD27_RS22325 (RFYW14_04521) 102736..103371 - 636 WP_077549912 acyl-homoserine-lactone synthase TraI -
GFD27_RS22330 (RFYW14_04522) 103747..104937 + 1191 WP_077549911 plasmid partitioning protein RepA -
GFD27_RS22335 (RFYW14_04523) 105022..106017 + 996 WP_077549910 plasmid partitioning protein RepB -
GFD27_RS22340 (RFYW14_04524) 106174..107418 + 1245 WP_077549909 plasmid replication protein RepC -

Host bacterium

ID   7353 GenBank   NZ_LR723673
Plasmid name   YW14|4 Incompatibility group   -
Plasmid size   150934 bp Coordinate of oriT [Strand]   55309..55353 [+]
Host baterium   Pseudorhizobium flavum strain YW14

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixB, fixA
Anti-CRISPR   -