Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104203
Name   oriT_JAM7|unnamed in_silico
Organism   Methylophaga frappieri
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_017858 (39213..39312 [+], 100 nt)
oriT length   100 nt
IRs (inverted repeats)      24..31, 35..42  (TAATCGGC..GCCGATTA)
Location of nic site      61..62
Conserved sequence flanking the
  nic site    		  TCCTGCCCGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 100 nt

>oriT_JAM7|unnamed
GAATAAGGGGAAGTGAAGTTAGGTAATCGGCTCCGCCGATTAGCTAACTTCACCTATCCTGCCCGCCTTACGGCGTTCATAACACCAAGGTAAGTGTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3085 GenBank   WP_041367303
Name   Relaxase_Q7C_RS13160_JAM7|unnamed insolico UniProt ID   _
Length   762 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 762 a.a.        Molecular weight: 83874.22 Da        Isoelectric Point: 10.6401

>WP_041367303.1 TraI/MobA(P) family conjugative relaxase [Methylophaga frappieri]
MIAKHVPMRSLKKSDFAGLVKYITDEQSKTERLGLVNATNCEADTMQAVIGEVLATQQANTRAKGDKTYH
LIVSFPAGEKPEDGVLKAVEERICAGLGYADHQRVSAVHHDTDNVHIHIAINKIHPTRNTMHEPYQAYRT
LGGLCDALEDEYGLQKDNHQGRKSVSQGRASDMERHAGIESLVSWIKRECLEEIRTAKTWEELHQVMGDN
GLEIRQRANGFVIESEDGTQVKASTVARDLSKPKLEARLGAFEETEAQAERKAKRRYDKRPTRFKVNTTE
LYARYQEEQKNLTAARKVEWDNARGRKDRRIEAAKRSNRLRRSAIKLMGGDRLSKKLLYAQAHKALKDEI
QSINKEHKRERQELYEQYKRRAWADWLKQQALDGDKKALEALRAREQAKGLQGDTIKGEGGAKPGHAPVT
DNITKKGTIIFRTASSAVRDDGDKLQVSKAATGDAVTEALRMAMERYGNRITVNGSPQFKAQVIHAAATS
NLPITFADAGLERRRQQLLQQENSHDRRNEQARRGNERGRADRRGTGRPGRGAADDAGRGRGAADSRAAA
ASRTGGGQRGRGPSAGTGSAAAGRRNDAGNGGRHVLNKPHVTGIGGEPPSFAKNRLRALSSLGVVRFARG
GEVLLPGNVPGELEHQGAKPDNQLRWGVSGSGGIAADKASAADKYIAEREAKRLKGFDIPKHSRYTNQDG
AVTYGGTRNVQGQSLALLNRGDEVLVLPIDKATAQRMKRVRIGEAVTVTPQGSLKRSRGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(419-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)


  Protein structure



No available structure.




Auxiliary protein

ID   1336 GenBank   WP_014708279
Name   WP_014708279_JAM7|unnamed insolico UniProt ID   I1YLS0
Length   123 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13743.80 Da        Isoelectric Point: 9.4637

>WP_014708279.1 conjugal transfer transcriptional regulator TraJ [Methylophaga frappieri]
MSEEKKSGKKRSHHLRVPVFDDEKDAIEAQAARAGMSVARYLREVGQGYQIKGVVDYEQVRELARINGDL
GRLGGLLKLWLTDDVRTAQFGQSTILAVLSKIEATQEEMGKVMTKVVMPRSEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB I1YLS0


T4CP

ID   2986 GenBank   WP_008929955
Name   t4cp2_Q7C_RS13015_JAM7|unnamed insolico UniProt ID   _
Length   845 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 845 a.a.        Molecular weight: 94119.90 Da        Isoelectric Point: 6.3398

>WP_008929955.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Gammaproteobacteria]
MIQAISFAIAVCGAALLLILFARIRAVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVCKNGAFMASWL
YKGDDNASSTDEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERNVSAFPDPVSAAIDEERRQLF
EGLGAMYEGYFVLTLTWFPPLLAQRKFVELMFDDDAEVVGKKARTKGLINQFKREISGIENRLTTAVKLT
RLRGQKIVNEDGSRVTHDDFLSWLQFCVTGVSHPVQLPNNPMYMDAYIGGQEMWGGVVPKVGRKFIQVVS
IEGFPLESHPGILSALAELPVEYRWSSRFIFMDQHESVKHLDKFRKKWKQKVRGFFDQVFNTNSGNVDQD
ALTMVQDAESAIAEVNSGLVAVGYYTSVVVLMDESRDRLEQSARQVEKSINRLGFAARTETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTIWTGTAEAPCPMYPPLSPALMHCVTSGSTPFRLNLHVRDLGH
TFMFGPTGAGKSTHLALIAAQLRRYAGMSIFAFDKGMSMYPLTKAVGGLHFSVGADDDRLSFCPLQYLET
KSDRAWAMEWIDTILALNGVNSTPAQRNEIAHAIVSMHESGARTLSEFSLTIQDESIREAIRQYTVDGSM
GHLLDADEDGLSLTDFTTFEIEELMNLGEKFALPVLLYLFRRIERSLKGQPAVIILDEAWLMLGHPAFRE
KIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMGLNARQIE
ILATAVPKRQYYYVSENGRRLYDLALGPLALSFVGASDKESVAAIKQLEAKFGEQWVHEWLAGRGLKLDN
YLEAA

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(221-431)

TraG P-loop domain (P-loop_TraG)

(617-747)

  Protein structure



No available structure.



ID   2987 GenBank   WP_014708277
Name   t4cp2_Q7C_RS13155_JAM7|unnamed insolico UniProt ID   _
Length   635 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 635 a.a.        Molecular weight: 69935.85 Da        Isoelectric Point: 7.5772

>WP_014708277.1 type IV secretory system conjugative DNA transfer family protein [Methylophaga frappieri]
MKPKINNAVGPQVRDRKPKKQRLLPALGAVSVLGGLQAATQFFAYTFNYQDNLGGHINHVYAPWSILSWA
SDWYSIYPDEFMRSGSIGMVVTTVGLLGVAIAKVVTSNSSKASEYLHGSARWAEKKDIQAAGLLPRERTA
LEVVTGKDAPTSTGVYVGGWEDKDGKFYYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPQSTVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSNGGVCWNPLDEIRIGTEYEVGDVQNLATLIVDPDGKGMDSHWQ
KTSYALLVGVILHALYKAKNEGTPASLPVVDAMLADPERDTGELWMEMATYGHVDGQNHPAVGSAARDMM
DRPEEEGGSVLSTAKSYLALYRDPVVARNVSKSEFRIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVLTN
MIIRLLADEMSFEKGRPVAHYKHRLLAMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDLNQLKSRET
GYGPDETITSNCHVQNAYPPNRIETAEHLSRLTGQTTVVKEQITTSGRRTSAMLGQVSRTIQEVQRPLLT
PDECLRMPGPTKNAAGDIEKAGDMVIYVAGYPAVYGKQPLYFKDPVFQARASVDAPKLSDKLRIVAEPEG
EGVTI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(121-620)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 6278..15945

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Q7C_RS12970 (Q7C_2703) 1419..1853 - 435 WP_008929947 antirestriction protein -
Q7C_RS12975 (Q7C_2704) 1975..2271 - 297 WP_014708245 hypothetical protein -
Q7C_RS13730 2358..2663 - 306 WP_041367294 hypothetical protein -
Q7C_RS12985 (Q7C_2705) 4021..5151 - 1131 WP_008929949 plasmid replication initiator TrfA -
Q7C_RS12990 (Q7C_2706) 5197..5544 - 348 WP_008929950 single-stranded DNA-binding protein -
Q7C_RS12995 (Q7C_2707) 5643..6026 + 384 WP_008929951 transcriptional regulator -
Q7C_RS13000 (Q7C_2708) 6278..7237 + 960 WP_008929952 P-type conjugative transfer ATPase TrbB virB11
Q7C_RS13005 (Q7C_2709) 7264..7689 + 426 WP_014708247 IncP-type conjugal transfer pilin TrbC virB2
Q7C_RS13010 (Q7C_2710) 7692..8003 + 312 WP_008929954 conjugal transfer protein TrbD virB3
Q7C_RS13015 (Q7C_2711) 8003..10540 + 2538 WP_008929955 VirB4 family type IV secretion/conjugal transfer ATPase virb4
Q7C_RS13020 (Q7C_2712) 10540..11322 + 783 WP_014708250 conjugal transfer protein TrbF virB8
Q7C_RS13025 (Q7C_2713) 11340..12245 + 906 WP_014708251 P-type conjugative transfer protein TrbG virB9
Q7C_RS13030 12248..12721 + 474 WP_008929958 conjugal transfer protein TrbH -
Q7C_RS13035 (Q7C_2715) 12725..14152 + 1428 WP_008929959 TrbI/VirB10 family protein virB10
Q7C_RS13040 (Q7C_2716) 14180..14941 + 762 WP_014708253 P-type conjugative transfer protein TrbJ virB5
Q7C_RS13045 (Q7C_2717) 14951..15178 + 228 WP_008929961 entry exclusion lipoprotein TrbK -
Q7C_RS13050 (Q7C_2718) 15190..15945 + 756 WP_014708255 sulfate transporter CysZ virB6
Q7C_RS13055 (Q7C_2719) 16261..18309 + 2049 WP_014708256 TonB-dependent receptor -
Q7C_RS13060 (Q7C_2720) 18371..18574 - 204 WP_014708257 (2Fe-2S)-binding protein -
Q7C_RS13065 (Q7C_2721) 18862..20172 + 1311 Protein_21 type IV secretion system protein -
Q7C_RS13070 20192..20671 + 480 WP_041367297 hypothetical protein -

Host bacterium

ID   4642 GenBank   NC_017858
Plasmid name   JAM7|unnamed Incompatibility group   -
Plasmid size   47825 bp Coordinate of oriT [Strand]   39213..39312 [+]
Host baterium   Methylophaga frappieri

Cargo genes

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