Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116996
Name   oriT_YSD YN2|unnamed in_silico
Organism   Siccibacter colletis strain YSD YN2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP074353 (608..708 [-], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      80..85, 91..96  (AAAAAA..TTTTTT)
 34..41, 44..51  (AGCGTGAT..ATCACGCT)
 21..26, 38..43  (AAATCA..TGATTT)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 101 nt

>oriT_YSD YN2|unnamed
TTTAGTGTTTTTATCTTTTAAAATCATTTGGATAGCGTGATTTATCACGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10843 GenBank   WP_264386232
Name   mobF_KFZ77_RS19450_YSD YN2|unnamed insolico UniProt ID   _
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120281.47 Da        Isoelectric Point: 6.6237

>WP_264386232.1 MULTISPECIES: MobF family relaxase [Enterobacteriaceae]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTQMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTHKGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELLRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRGFSRRSEQIEKGLAEMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPHEADIARNTAPDFTSPQVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHASMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDEGIKNGRLKKTSHRVTTVEGIRLERTILTIESRGRGQMPRQLTAEIAAQLLAGKTLKPEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKSKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKDEAPRLAKLADRYLALSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGATFTLLDRVDSTQAERRDSRYFSKDQIIIPEQDYKNGMKRGESYRVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKSQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTTLETRSAEKGLTEVMGESMAFNQKPDEHNMTSGSDYQPVNNA
EDAFHLKQNPMDDSVGLRRHEAHHNDAELAHDYAAADDQQWSEQDYADYEHYAEAAEYDFDSSIYEDYAM
PQTSQAEQRQAGKEHSHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-287)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

AAA domain (AAA_30)

(477-653)


  Protein structure



No available structure.




Auxiliary protein

ID   6374 GenBank   WP_137486135
Name   WP_137486135_YSD YN2|unnamed insolico UniProt ID   _
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15323.51 Da        Isoelectric Point: 5.9716

>WP_137486135.1 MULTISPECIES: traK protein [Enterobacteriaceae]
MPTITAKVSDELLAYIDRVSGGNRSEYLRRCLEAGPGDRESGLKIVADQLGDVNRKLDYLFDRVSDADFG
SLRDELKAITETLSGVKFPPAGQMMLHESLAVETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   12658 GenBank   WP_137486136
Name   t4cp2_KFZ77_RS19445_YSD YN2|unnamed insolico UniProt ID   _
Length   509 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57584.63 Da        Isoelectric Point: 9.7339

>WP_137486136.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacteriaceae]
MDERERGLAFLFAITLPPIMVWFLVAKFTYGIDPSTAKYLVPYLVKNTFSLWPLWSALIAGWIIGIAGLV
AFILYDKSRVFKGERFKKIYRGTELVRARTLADKTRQRGVSQLTVANIPIPVEAENLHFSIAGTTGTGKT
TIFNELLFKSIKRGGKNIVLDPNGGFLKNFYRPGDAILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLTGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKKSLNPLISCWLDSIFSIVLGMGEKDGR
INVFIDELESLQYLPNLNDALTKGRKSGLCVFAGYQTFSQLVKVYGRDMAQTILANLRSNIVLGGSRLGE
DTLDHMSRSLGEIEGEVERKESDPQKPWIIRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDTPVAKFKA
KYIKYQRKNPVAGIEQREI

  Protein domains


Predicted by InterproScan.

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

(113-489)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1276..17708

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KFZ77_RS19440 (KFZ77_19420) 858..1274 + 417 WP_137486135 traK protein -
KFZ77_RS19445 (KFZ77_19425) 1276..2805 + 1530 WP_137486136 type IV secretion system DNA-binding domain-containing protein virb4
KFZ77_RS19450 (KFZ77_19430) 2805..6041 + 3237 WP_264386232 MobF family relaxase -
KFZ77_RS19455 (KFZ77_19435) 6041..6667 + 627 WP_137486176 DUF6710 family protein -
KFZ77_RS19460 (KFZ77_19440) 6841..7371 - 531 WP_137486177 phospholipase D family protein -
KFZ77_RS19465 (KFZ77_19445) 7371..8366 - 996 WP_137486178 P-type DNA transfer ATPase VirB11 virB11
KFZ77_RS19470 (KFZ77_19450) 8408..9568 - 1161 WP_137486179 type IV secretion system protein VirB10 virB10
KFZ77_RS19475 (KFZ77_19455) 9568..10452 - 885 WP_178897582 TrbG/VirB9 family P-type conjugative transfer protein virB9
KFZ77_RS19480 (KFZ77_19460) 10463..11161 - 699 WP_137486182 virB8 family protein virB8
KFZ77_RS19485 (KFZ77_19465) 11380..12429 - 1050 WP_178897584 type IV secretion system protein virB6
KFZ77_RS19490 (KFZ77_19470) 12445..12672 - 228 WP_137486231 IncN-type entry exclusion lipoprotein EexN -
KFZ77_RS19495 (KFZ77_19475) 12680..13372 - 693 WP_264386233 type IV secretion system protein virB5
KFZ77_RS19500 (KFZ77_19480) 13411..16011 - 2601 WP_178897586 VirB4 family type IV secretion/conjugal transfer ATPase virb4
KFZ77_RS19505 (KFZ77_19485) 16011..16328 - 318 WP_178897587 VirB3 family type IV secretion system protein virB3
KFZ77_RS19510 (KFZ77_19490) 16381..16674 - 294 WP_137486198 TrbC/VirB2 family protein virB2
KFZ77_RS19515 (KFZ77_19495) 16684..16965 - 282 WP_032734186 transcriptional repressor KorA -
KFZ77_RS19520 (KFZ77_19500) 16974..17708 - 735 WP_137486199 lytic transglycosylase domain-containing protein virB1
KFZ77_RS19525 (KFZ77_19505) 17817..18122 + 306 WP_170983088 H-NS family nucleoid-associated regulatory protein -
KFZ77_RS19530 (KFZ77_19510) 18138..18482 + 345 WP_264386234 hypothetical protein -
KFZ77_RS19535 (KFZ77_19515) 18479..18793 + 315 WP_137486223 TrbM/KikA/MpfK family conjugal transfer protein -
KFZ77_RS19540 (KFZ77_19520) 18839..19150 + 312 WP_032734181 hypothetical protein -
KFZ77_RS19545 (KFZ77_19525) 19276..19980 + 705 WP_001067848 IS6-like element IS26 family transposase -
KFZ77_RS19550 (KFZ77_19530) 20032..20193 + 162 Protein_23 IS91 family transposase -
KFZ77_RS19555 (KFZ77_19535) 20423..21910 + 1488 Protein_24 3-phosphoshikimate 1-carboxyvinyltransferase -
KFZ77_RS19560 (KFZ77_19540) 22020..22403 + 384 WP_148570043 hypothetical protein -

Host bacterium

ID   17429 GenBank   NZ_CP074353
Plasmid name   YSD YN2|unnamed Incompatibility group   -
Plasmid size   41462 bp Coordinate of oriT [Strand]   608..708 [-]
Host baterium   Siccibacter colletis strain YSD YN2

Cargo genes

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