Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118170
Name   oriT_pR28_75 in_silico
Organism   Serratia fonticola strain R28
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP072744 (2865..2937 [+], 73 nt)
oriT length   73 nt
IRs (inverted repeats)      27..33, 38..44  (GCAAAAA..TTTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 73 nt

>oriT_pR28_75
TCACCACAAAAAGCACCACACCCCACGCAAAAATTACTTTTTGCTGATTTGGTTGTTGAAACAGTGGGTTATG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11545 GenBank   WP_218520572
Name   traI_J8M99_RS26050_pR28_75 insolico UniProt ID   _
Length   1748 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1748 a.a.        Molecular weight: 189517.87 Da        Isoelectric Point: 6.4245

>WP_218520572.1 conjugative transfer relaxase/helicase TraI [Serratia fonticola]
MLSLWRVKSAGSAGNYYTDKDNYYVIGSMGERWAGEGAAELGLKGEVDQKIFTQLLEGRLPDGSDLSRMQ
EGANKHRPGYDLTFSAPKSISVMAMLGGDTRLIDAHNHAVDTAVKQVEALASTRVMTDGKSQTELTGNLV
MALFNHDTSRDQEPLLHTHAVVANLTRHGDDWRTLSSDKVGKTGFIENVYANQIAFGKIYRATLHQDVTA
LGYETEVVGKHGMWELKDVPVVEFSSRTQAIKEAVGEDASLKSRDMAALDTRRPKEKVDPEQRMSEWMHT
LKATGFDIRGYREDADQRAQAGDIPAPAVEAVDISASVGLAIGMLSDRRARFTYSELLATTIGQLPAQPG
VVAQAREGIESAIKNEQLIPLDKEKGLFTSNIHVLDELSVAALTRDLQRAGPIDTFADKAQPRTRAYSDA
VSVLAQDRLPVAIVAGQGGAAGQRERVAELAMMAHEQGREVQIVAADRRSARSLAQDERLGGEHITDRRA
LTEGMTFLPGSTLIVDQAEKLTLKETLTLLDGALRHNVQLLMTDSGQRSGTGSALTVMKESGVNTLSWQQ
GEKTRVDVISEPDRRQRYDRLATDFARSIRAGEHSVAQVSGVREQAALTGAVRNALRAERVLGEKEHTIT
ALEPVWLDSRHQQVRDHYRDGMVMERWDAQARRHERFVIDRVTARNNSLTLRNAQGESQVIRLASLDSSW
SLLRATQIPVSEGDRLAVLGKTPGARLKGGDTVTVTGFDDKGIAVTLPGRKGTVTLPSGDSPFTAPKVGQ
GWVGSPGRSVSDNATVFASLSLREMDTTTLNKLALSGSQVRLYSAQTEAKTTEKLARQSAFSVVSAQIKE
AAGHDRLEEALTHQKNALHTPAQQAIHLAIPELESRNLAFTKPQLMAAASEAAPTGPGLAAIEREIDQQA
REGALMSVPVSPGNGLQLLVARASYNAEKSIIRHVLEGKDAVAPLMHRVPGAQMEGLTSGQRNATRMILE
SSDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEEQRPRVIGVAPTHRAVSEMRDAGVPESQTLAAFIHDTQ
QQLRGGEKPDFRNVLFLVDESSMVGNADMARAYGLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPALKPAVYSLIDRDIDSALNTLEQVAPAQVPRQAGAWQPESSVVEFGAAQEKAIEKGL
ADGSLTPGAQPATLYEAIVRDYTGRTPQAQAQTIVVTTLNADRRALNAQIHEARQAAGELGEQEARLPIL
TSANLRDGELRKMATWQAAHDNLVLLDSTYYRIDSLDKEGQLVTLKDEQGNTRSLSPTQAVTEGVTLYRP
DTLTVSPGDRMRFSKSDNDRGFVANSVWTVSEIDGDRVTLSDGHQTRTVNPAAERAEQHIDLAYAVTAHG
AQGASEPFAIALQGTEGARKAMVSFESAYVALSRMKQHAQVYTDNRAAWVEAMGKSRARSTAHDILEPRG
DRAVSNAERLMGTAKPLGEVAAGRAVLRQAGLSPDGSMARFISPGRKYPQPHVALPAFDGNGKPAGIWLS
SLMPVEGEVRGLTDEGRVMGSEAATFAGLQVSRNGESLLAADMPAALKLARENPHSGVVVRLPGSEGRPW
NPGAITGGRIWADGVSNDAVTGTQHGEKLPPEIVAQQAQAEQQRREMEERAAQAVREMARGGDKGREGTD
PVREVARELERTQEPTPDAVRVLDNHEERRRDDAVALVAHENVQRERLQQMEREVVRDLDREKTLSGD

  Protein domains


Predicted by InterproScan.

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

(631-710)

TrwC relaxase (TrwC)

(10-283)

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

(573-625)

AAA domain (AAA_30)

(967-1155)

DNA helicase TraI (TraI_C)

(1430-1548)


  Protein structure



No available structure.




T4CP

ID   13499 GenBank   WP_218520559
Name   traC_J8M99_RS25980_pR28_75 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: 98617.14 Da        Isoelectric Point: 5.3526

>WP_218520559.1 type IV secretion system protein TraC [Serratia fonticola]
MSSNLLDAVTRTVNALVTALKMPDDSAKANDILGQMNFPQFSRLLPYRDYDAQTGLFMNDKTMGFMLEAQ
PINGANETIVSSLENLMRTKLTREVPLAIHLVSSPLVGQDIQYGLRELSWTGEEADKFNAITRAYYLRAA
EEGFPLPEHLNLPLTLRNYRVYFSCCVPRKRGSKASVMELENQVKIIRASLQGAQIVTRGVDADAFIRIV
AEMVNHNPDALYTKDRELDPLKDLNYQCVDDGFDLKVKADHMTLGLRENGKNSAARIMNFQLTRNPEMAF
LWNTADNYSNLLSPELSISSPFILTLILSVEDQVKAQNEANLKFLDLEKKSKNSYAKFFPGVVQEAQEWG
DLRQRLASGQSSLVSYFLNITVFCRDEQETALNVEQDVLNSFRKNGFELISPRFNQMRNFLANLPFTAGG
GLFKQLKASGVVQRAESFNVANLLPVVADSPLATSGLLAPTYRNQLAFIDLFSKGMGNTNFNMAVCGTSG
AGKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGESLKFNPFANITDDTINEMAERLRDQ
LSVMASPNGNLDEVHEGLLLKAVKATWLSKKNQARIDDVVDYLVMARDSEEYAGSPTLRSRLDEMVVLLT
QYTCDGVYGSYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDE
GWRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSDTASSAARAAWGNSSYKIILKQSAKEFA
KYNQLYPDQYSQMQRDMIARFGNAKDQWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFVQRRRQ
EGLTIHEAVWELAWQKSGPEMASLERWLQEHEGITL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraG P-loop domain (P-loop_TraG)

(469-773)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   13500 GenBank   WP_218520570
Name   traD_J8M99_RS26045_pR28_75 insolico UniProt ID   _
Length   723 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 723 a.a.        Molecular weight: 81720.03 Da        Isoelectric Point: 4.9585

>WP_218520570.1 type IV conjugative transfer system coupling protein TraD [Serratia fonticola]
MSFNAKDMTQGGQIASMRIRMFSQIANIIIYCLVILFAIIVALTFWVKLSWQTFVNGMLYYWCQTLSPMR
DIFKSQPVYTVRYYEKELQYNALQVLQDKYLIWCAEQVWATFLLAAIIAAVVCVVAFFVTTWVLGHQGKQ
QSEDEITGGRELTDDPKIVAKMLKRDGMASDIKIGDLPLIKNSEIQNFCLHGTVGSGKSEVIRRLMNYAR
KRGDMIVVYDRSGEFVKSYYDPSIDKILNPQDSRCAAWDLWRECLTQPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRAYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEGNGEPFTIRDWMRGVRDDGKNGTLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRNRRV
WYFGDELPTLHKIPDLVEILPEARKFGGCYVVGIQSYAQLEDIYGNKAAETLFDVLNTRAFFRSPSKSIA
EFAAGEIGEKEFRKASEQYSYGVDPVRDGTSVGKDMERQTLVSYSDIQTLPDLSCYVTLPGPYPAVKMAL
KYQPRPKVAPDFIPRFIDEKANERLNIALAAREDESRNIAVLFEPDADDIATNESSPEAEQPQQPQQPQQ
PQQVVRKATADPVSTSAATGTGGTEQDLRTKSEEAEQLPPGIDETGEVVDMEAWESWQAEQERLSGKDMQ
RREEVNINVHRSPEKDLEPGDNL

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2309..26611

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J8M99_RS25915 (J8M99_25905) 1186..2055 + 870 WP_218520551 LPD29 domain-containing protein -
J8M99_RS25920 (J8M99_25910) 2309..2791 - 483 WP_218520552 transglycosylase SLT domain-containing protein virB1
J8M99_RS25925 (J8M99_25915) 3213..3608 + 396 WP_166735224 conjugal transfer relaxosome DNA-binding protein TraM -
J8M99_RS25930 (J8M99_25920) 3845..4624 - 780 WP_218520553 helix-turn-helix domain-containing protein -
J8M99_RS25935 (J8M99_25925) 4920..5078 + 159 WP_235784873 TraY domain-containing protein -
J8M99_RS25940 (J8M99_25930) 5331..5660 + 330 WP_235784870 TraY domain-containing protein -
J8M99_RS25945 (J8M99_25935) 5725..6075 + 351 WP_218520556 type IV conjugative transfer system pilin TraA -
J8M99_RS25950 (J8M99_25940) 6225..6530 + 306 WP_065684418 type IV conjugative transfer system protein TraL traL
J8M99_RS25955 (J8M99_25945) 6545..7111 + 567 WP_065684419 type IV conjugative transfer system protein TraE traE
J8M99_RS25960 (J8M99_25950) 7098..7841 + 744 WP_218520578 type-F conjugative transfer system secretin TraK traK
J8M99_RS25965 (J8M99_25955) 7828..9222 + 1395 WP_218520557 F-type conjugal transfer pilus assembly protein TraB traB
J8M99_RS25970 (J8M99_25960) 9244..9786 + 543 WP_218520558 type IV conjugative transfer system lipoprotein TraV traV
J8M99_RS25975 (J8M99_25965) 9922..10179 + 258 WP_235784871 hypothetical protein -
J8M99_RS25980 (J8M99_25970) 10172..12802 + 2631 WP_218520559 type IV secretion system protein TraC virb4
J8M99_RS25985 (J8M99_25975) 12909..13319 + 411 WP_218520560 hypothetical protein -
J8M99_RS25990 (J8M99_25980) 13316..13663 + 348 WP_218520561 type-F conjugative transfer system protein TrbI -
J8M99_RS25995 (J8M99_25985) 13660..14316 + 657 WP_218520562 type-F conjugative transfer system protein TraW traW
J8M99_RS26000 (J8M99_25990) 14369..15316 + 948 WP_218520580 conjugal transfer pilus assembly protein TraU traU
J8M99_RS26005 (J8M99_25995) 15331..15960 + 630 WP_218520563 type-F conjugative transfer system pilin assembly protein TrbC trbC
J8M99_RS26010 (J8M99_26000) 15957..17831 + 1875 WP_218520564 type-F conjugative transfer system mating-pair stabilization protein TraN traN
J8M99_RS26015 (J8M99_26005) 17841..18584 + 744 WP_218520565 type-F conjugative transfer system pilin assembly protein TraF traF
J8M99_RS26020 (J8M99_26010) 18601..18864 + 264 WP_115160180 type-F conjugative transfer system pilin chaperone TraQ -
J8M99_RS26025 (J8M99_26015) 18854..19432 + 579 WP_218520566 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
J8M99_RS26030 (J8M99_26020) 19429..20796 + 1368 WP_218520567 conjugal transfer pilus assembly protein TraH traH
J8M99_RS26035 (J8M99_26025) 20796..23624 + 2829 WP_218520568 conjugal transfer mating-pair stabilization protein TraG traG
J8M99_RS26040 (J8M99_26030) 23633..24148 + 516 WP_218520569 hypothetical protein -
J8M99_RS26045 (J8M99_26035) 24440..26611 + 2172 WP_218520570 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   18603 GenBank   NZ_CP072744
Plasmid name   pR28_75 Incompatibility group   -
Plasmid size   75602 bp Coordinate of oriT [Strand]   2865..2937 [+]
Host baterium   Serratia fonticola strain R28

Cargo genes

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