Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104063
Name   oriT_|unnamed in_silico
Organism   Citrobacter freundii
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT745953 (39928..40028 [+], 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_|unnamed
TATTTATTTTTTTATTTTTTAAATCAGTGTGATAGTGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3008 GenBank   WP_011407157
Name   mobF_MCP55_RS00230_|unnamed insolico UniProt ID   A0A740S2B6
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120179.41 Da        Isoelectric Point: 6.5766

>WP_011407157.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB A0A740S2B6


Auxiliary protein

ID   1267 GenBank   WP_001532083
Name   WP_001532083_|unnamed insolico UniProt ID   A8R734
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_001532083.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCLEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A8R734


T4CP

ID   2881 GenBank   WP_000342688
Name   t4cp2_MCP55_RS00235_|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: 13674..39361

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MCP55_RS00060 8882..9718 - 837 WP_001050931 RepB family plasmid replication initiator protein -
MCP55_RS00325 10035..10166 + 132 WP_000705922 hypothetical protein -
MCP55_RS00065 10952..11203 + 252 WP_000121743 plasmid stabilization protein -
MCP55_RS00070 11193..11474 + 282 WP_000220560 type II toxin-antitoxin system RelE/ParE family toxin -
MCP55_RS00075 11549..12246 + 698 WP_095033700 IS1-like element IS1B family transposase -
MCP55_RS00080 12392..12649 + 258 WP_105278499 hypothetical protein -
MCP55_RS00085 12686..13654 - 969 WP_077783444 IS5 family transposase -
MCP55_RS00090 13671..13964 + 294 Protein_18 peptidoglycan DD-metalloendopeptidase family protein -
MCP55_RS00095 13998..14093 - 96 Protein_19 DUF2933 domain-containing protein -
MCP55_RS00100 14158..14862 + 705 WP_001067855 IS6-like element IS26 family transposase -
MCP55_RS00105 15707..16552 + 846 WP_164538741 macrolide hydrolase EstT -
MCP55_RS00110 16542..17699 + 1158 WP_094309310 tetracycline-inactivating monooxygenase Tet(X4) -
MCP55_RS00115 18038..19480 + 1443 Protein_23 IS91-like element ISVsa3 family transposase -
MCP55_RS00120 19842..20546 + 705 WP_001067855 IS6-like element IS26 family transposase -
MCP55_RS00125 20608..20805 - 198 WP_000844102 hypothetical protein -
MCP55_RS00130 20810..21451 - 642 WP_001694850 restriction endonuclease -
MCP55_RS00135 21507..21740 - 234 WP_001191790 hypothetical protein -
MCP55_RS00140 21854..22168 - 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
MCP55_RS00145 22131..22508 - 378 WP_000504251 hypothetical protein -
MCP55_RS00150 22524..22895 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
MCP55_RS00155 22938..23672 + 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
MCP55_RS00160 23681..23962 + 282 WP_000440698 transcriptional repressor KorA -
MCP55_RS00165 23972..24265 + 294 WP_000209137 TrbC/VirB2 family protein virB2
MCP55_RS00170 24315..24632 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
MCP55_RS00175 24632..27232 + 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
MCP55_RS00180 27250..27963 + 714 WP_000749362 type IV secretion system protein virB5
MCP55_RS00185 27971..28198 + 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
MCP55_RS00190 28214..29254 + 1041 WP_000886022 type IV secretion system protein virB6
MCP55_RS00195 29325..29483 + 159 WP_012561180 hypothetical protein -
MCP55_RS00200 29473..30171 + 699 WP_000646594 type IV secretion system protein virB8
MCP55_RS00205 30182..31066 + 885 WP_185229345 TrbG/VirB9 family P-type conjugative transfer protein virB9
MCP55_RS00210 31066..32226 + 1161 WP_000101711 type IV secretion system protein VirB10 virB10
MCP55_RS00215 32268..33263 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
MCP55_RS00220 33263..33796 + 534 WP_000731968 phospholipase D family protein -
MCP55_RS00225 33970..34596 - 627 WP_000434930 DUF6710 family protein -
MCP55_RS00230 34596..37832 - 3237 WP_011407157 MobF family relaxase -
MCP55_RS00235 37832..39361 - 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
MCP55_RS00240 39363..39779 - 417 WP_001532083 hypothetical protein -
MCP55_RS00245 40292..40711 + 420 WP_000802909 plasmid stabilization protein StbA -
MCP55_RS00250 40720..41436 + 717 WP_000861577 StbB family protein -
MCP55_RS00255 41438..41806 + 369 WP_000414913 plasmid stabilization protein StbC -
MCP55_RS00260 41988..42332 + 345 WP_000999874 hypothetical protein -
MCP55_RS00265 42443..42763 - 321 WP_000211833 protein CcgAII -
MCP55_RS00270 42818..42997 - 180 WP_000214483 protein CcgAI -
MCP55_RS00275 43829..44338 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   4502 GenBank   NZ_MT745953
Plasmid name   |unnamed Incompatibility group   IncN
Plasmid size   51531 bp Coordinate of oriT [Strand]   39928..40028 [+]
Host baterium   Citrobacter freundii

Cargo genes

Drug resistance gene   tet(X4)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -