Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114632
Name   oriT_FDAARGOS_506|unnamed in_silico
Organism   Serratia sp. FDAARGOS_506
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP033830 (3097..3197 [-], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      80..85, 91..96  (AAAAAA..TTTTTT)
 20..26, 38..44  (TAAATCA..TGATTTA)
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_FDAARGOS_506|unnamed
TATTTATTTTTTTATCTTTTAAATCAGTACGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9384 GenBank   WP_012561142
Name   mobF_EGY12_RS00040_FDAARGOS_506|unnamed insolico UniProt ID   A0A1S6KKJ9
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120195.37 Da        Isoelectric Point: 6.5230

>WP_012561142.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKADMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

AAA domain (AAA_30)

(477-653)

TrwC relaxase (TrwC)

(16-287)


  Protein structure


Source ID Structure
AlphaFold DB A0A1S6KKJ9


Auxiliary protein

ID   5506 GenBank   WP_001749975
Name   WP_001749975_FDAARGOS_506|unnamed insolico UniProt ID   A0A5C2CVS6
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15332.60 Da        Isoelectric Point: 5.9670

>WP_001749975.1 MULTISPECIES: hypothetical protein [Gammaproteobacteria]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A5C2CVS6


T4CP

ID   10893 GenBank   WP_000342688
Name   t4cp2_EGY12_RS00035_FDAARGOS_506|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: 57762.87 Da        Isoelectric Point: 9.6551

>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI

  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: 3764..21628

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EGY12_RS00005 (EGY12_00005) 111..290 + 180 WP_012561134 protein CcgAI -
EGY12_RS00010 (EGY12_00010) 752..1096 - 345 WP_012561137 hypothetical protein -
EGY12_RS00015 (EGY12_00015) 1297..1665 - 369 WP_012561138 plasmid stabilization protein StbC -
EGY12_RS00020 (EGY12_00020) 1667..2383 - 717 WP_012561139 StbB family protein -
EGY12_RS00025 (EGY12_00025) 2392..2778 - 387 WP_013279398 plasmid stabilization protein StbA -
EGY12_RS00030 (EGY12_00030) 3346..3762 + 417 WP_001749975 hypothetical protein -
EGY12_RS00035 (EGY12_00035) 3764..5293 + 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
EGY12_RS00040 (EGY12_00040) 5293..8529 + 3237 WP_012561142 MobF family relaxase -
EGY12_RS00045 (EGY12_00045) 8529..8927 + 399 WP_012561143 DUF6710 family protein -
EGY12_RS00050 (EGY12_00050) 8991..9281 + 291 WP_001247892 nucleotidyltransferase family protein -
EGY12_RS00055 (EGY12_00055) 9278..9679 + 402 WP_001293886 DUF86 domain-containing protein -
EGY12_RS00060 (EGY12_00060) 9669..10025 + 357 WP_000215515 cupin domain-containing protein -
EGY12_RS00065 (EGY12_00065) 10280..10594 + 315 WP_000091613 hypothetical protein -
EGY12_RS00070 (EGY12_00070) 10767..11300 - 534 WP_000792636 phospholipase D family protein -
EGY12_RS00075 (EGY12_00075) 11300..12295 - 996 WP_012561144 ATPase, T2SS/T4P/T4SS family virB11
EGY12_RS00080 (EGY12_00080) 12337..13497 - 1161 WP_012561145 type IV secretion system protein VirB10 virB10
EGY12_RS00085 (EGY12_00085) 13497..14381 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
EGY12_RS00090 (EGY12_00090) 14392..15090 - 699 WP_000646594 virB8 family protein virB8
EGY12_RS00100 (EGY12_00100) 15309..16349 - 1041 WP_001749958 type IV secretion system protein virB6
EGY12_RS00105 (EGY12_00105) 16365..16592 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
EGY12_RS00110 (EGY12_00110) 16600..17313 - 714 WP_001749960 type IV secretion system protein virB5
EGY12_RS00115 (EGY12_00115) 17331..19931 - 2601 WP_012561149 VirB4 family type IV secretion/conjugal transfer ATPase virb4
EGY12_RS00120 (EGY12_00120) 19931..20248 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
EGY12_RS00125 (EGY12_00125) 20298..20591 - 294 WP_001749962 hypothetical protein virB2
EGY12_RS00130 (EGY12_00130) 20601..20882 - 282 WP_016338364 transcriptional repressor KorA -
EGY12_RS00135 (EGY12_00135) 20891..21628 - 738 WP_013279384 lytic transglycosylase domain-containing protein virB1
EGY12_RS00140 (EGY12_00140) 21737..22042 + 306 WP_012561154 H-NS family nucleoid-associated regulatory protein -
EGY12_RS00145 (EGY12_00145) 22058..22402 + 345 WP_012561155 hypothetical protein -
EGY12_RS00150 (EGY12_00150) 22399..22713 + 315 WP_016338363 TrbM/KikA/MpfK family conjugal transfer protein -
EGY12_RS00155 (EGY12_00155) 22749..23060 + 312 WP_013279382 hypothetical protein -
EGY12_RS00160 (EGY12_00160) 23116..23757 + 642 WP_012561158 restriction endonuclease -
EGY12_RS00170 (EGY12_00170) 24991..25200 + 210 WP_123892201 hypothetical protein -
EGY12_RS00175 (EGY12_00175) 25211..25483 - 273 Protein_33 IS1 family transposase -

Host bacterium

ID   15067 GenBank   NZ_CP033830
Plasmid name   FDAARGOS_506|unnamed Incompatibility group   IncN
Plasmid size   43953 bp Coordinate of oriT [Strand]   3097..3197 [-]
Host baterium   Serratia sp. FDAARGOS_506

Cargo genes

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