Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107841
Name   oriT_pNDM-CWH001 in_silico
Organism   Citrobacter freundii strain CWH001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM008471 (14159..14259 [-], 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_pNDM-CWH001
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5263 GenBank   WP_012561166
Name   mobF_CQW88_RS00755_pNDM-CWH001 insolico UniProt ID   D7RU03
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120141.30 Da        Isoelectric Point: 6.5229

>WP_012561166.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
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 D7RU03


Auxiliary protein

ID   2413 GenBank   WP_000706094
Name   WP_000706094_pNDM-CWH001 insolico UniProt ID   B6UZ32
Length   96 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 96 a.a.        Molecular weight: 10829.54 Da        Isoelectric Point: 8.5040

>WP_000706094.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MKIVADRLSDVNRKLDYLFDRASDADFGPLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIA
EPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB B6UZ32


T4CP

ID   5508 GenBank   WP_021740568
Name   t4cp2_CQW88_RS00750_pNDM-CWH001 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: 57738.89 Da        Isoelectric Point: 9.6550

>WP_021740568.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacteriaceae]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVILWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
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: 39200..49525

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CQW88_RS00850 (CQW88_26370) 34427..35083 - 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
CQW88_RS00855 (CQW88_26375) 35478..36109 + 632 Protein_42 transposase -
CQW88_RS00860 (CQW88_26380) 36163..36867 - 705 WP_001067855 IS6-like element IS26 family transposase -
CQW88_RS28100 37084..37371 - 288 Protein_44 DUF6710 family protein -
CQW88_RS00875 (CQW88_26395) 37638..37817 + 180 Protein_45 helix-turn-helix domain-containing protein -
CQW88_RS00880 (CQW88_26400) 37882..38586 + 705 WP_001067855 IS6-like element IS26 family transposase -
CQW88_RS00890 (CQW88_26410) 38667..39200 - 534 WP_000792636 phospholipase D family protein -
CQW88_RS00895 (CQW88_26415) 39200..40195 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
CQW88_RS00900 (CQW88_26420) 40237..41397 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
CQW88_RS00905 (CQW88_26425) 41397..42281 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
CQW88_RS00910 (CQW88_26430) 42292..42990 - 699 WP_000646594 type IV secretion system protein virB8
CQW88_RS00915 (CQW88_26435) 42980..43126 - 147 WP_001257173 conjugal transfer protein TraN -
CQW88_RS00920 (CQW88_26440) 43209..44249 - 1041 WP_001749958 type IV secretion system protein virB6
CQW88_RS00925 (CQW88_26445) 44265..44492 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
CQW88_RS00930 (CQW88_26450) 44500..45213 - 714 WP_001749960 type IV secretion system protein virB5
CQW88_RS00935 (CQW88_26455) 45231..47831 - 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
CQW88_RS00940 (CQW88_26460) 47831..48148 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
CQW88_RS00945 (CQW88_26465) 48198..48491 - 294 WP_001749962 hypothetical protein virB2
CQW88_RS00950 (CQW88_26470) 48501..48782 - 282 WP_000440698 transcriptional repressor KorA -
CQW88_RS00955 (CQW88_26475) 48791..49525 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
CQW88_RS00960 (CQW88_26480) 49589..49939 + 351 WP_024129965 H-NS family nucleoid-associated regulatory protein -
CQW88_RS00965 (CQW88_26485) 49955..50299 + 345 WP_001749964 hypothetical protein -
CQW88_RS00970 (CQW88_26490) 50296..50610 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
CQW88_RS00975 (CQW88_26495) 50646..50957 + 312 WP_001452736 hypothetical protein -
CQW88_RS00980 (CQW88_26500) 51007..51654 + 648 WP_015344958 restriction endonuclease -
CQW88_RS00985 (CQW88_26505) 51659..51865 + 207 WP_001749967 hypothetical protein -
CQW88_RS00990 (CQW88_26510) 51876..52148 - 273 Protein_67 IS1 family transposase -
CQW88_RS00995 (CQW88_26515) 52247..53680 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   8276 GenBank   NZ_CM008471
Plasmid name   pNDM-CWH001 Incompatibility group   IncN
Plasmid size   59399 bp Coordinate of oriT [Strand]   14159..14259 [-]
Host baterium   Citrobacter freundii strain CWH001

Cargo genes

Drug resistance gene   blaNDM-1, qnrS1, dfrA14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -