Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200030 |
| Name | oriT_Tn5397  |
| Organism | Clostridium difficile 630 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | AM180355 (587811..588025 [+], 215 nt) |
| oriT length | 215 nt |
| IRs (inverted repeats) | 61..76, 80..95 (ACTTAACCCCCCGTAT..ACAGGGGGGTACAAAT) 125..134, 139..148 ( AAATCCTTTG.. CAAGGGATTT) |
| Location of nic site | 135..136 |
| Conserved sequence flanking the nic site |
TGG|T |
| Note | blastn alignment with the oriT_Tn916 |
oriT sequence
Download Length: 215 nt
>oriT_Tn5397
AAGCGGAAGTCGCAGGTGTGGACTAATCTTGCTGGCTGGTGTGGCGACAGCCACGCCAGCACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGGCAAAAAAATAGTAGAAAATCCTTTGGTTACAAGGGATTTAGAAAATTTCGGTGTATGTCAAATGAGCTTTAAAAGTTGACATACGCCTTTTTGATTGGAGGAATTT
AAGCGGAAGTCGCAGGTGTGGACTAATCTTGCTGGCTGGTGTGGCGACAGCCACGCCAGCACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGGCAAAAAAATAGTAGAAAATCCTTTGGTTACAAGGGATTTAGAAAATTTCGGTGTATGTCAAATGAGCTTTAAAAGTTGACATACGCCTTTTTGATTGGAGGAATTT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 244 | GenBank | CAJ67329 |
| Name | CTn3-Orf20_Tn5397 |
UniProt ID | Q188U0 |
| Length | 402 a.a. | PDB ID | |
| Note | _ | ||
Relaxase protein sequence
Download Length: 402 a.a. Molecular weight: 47304.05 Da Isoelectric Point: 6.9549
>CAJ67329.1 putative replication initiation factor Tn5397,CTn3-Orf20 [Clostridioides difficile 630]
MIGGISLNEQTWVQHLKEKRLSYGLSQNRLAIATGITRQYLSDIETGKVKPSDELQLALLETLERFNPDA
PLEMLFDYVRIRFPTTDVQHVVEDVLRLKLSYMLHEDYGFYSYTEHYALGNIFVLCSHELDKGVLVELKG
RGCRQFESYLLAQQRSWYEFFMDALVASGVMKRLDLAINDKTGILNIPILTEKCRQEECISVFRSFKSYR
SGELVRKDEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDL
LAYDNPEHTAFKIINRYIRFVDKDDSKARSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQ
VAPTLKVAITLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITNKK
MIGGISLNEQTWVQHLKEKRLSYGLSQNRLAIATGITRQYLSDIETGKVKPSDELQLALLETLERFNPDA
PLEMLFDYVRIRFPTTDVQHVVEDVLRLKLSYMLHEDYGFYSYTEHYALGNIFVLCSHELDKGVLVELKG
RGCRQFESYLLAQQRSWYEFFMDALVASGVMKRLDLAINDKTGILNIPILTEKCRQEECISVFRSFKSYR
SGELVRKDEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDL
LAYDNPEHTAFKIINRYIRFVDKDDSKARSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQ
VAPTLKVAITLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITNKK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q188U0 |
T4CP
| ID | 244 | GenBank | CAJ67327 |
| Name | CTn3-Orf21_Tn5397 |
UniProt ID | Q188U2 |
| Length | 461 a.a. | PDB ID | _ |
| Note | putative cell-division FtsK/SpoIIIE-family protein Tn5397, CTn3-Orf21 | ||
T4CP protein sequence
Download Length: 461 a.a. Molecular weight: 53440.27 Da Isoelectric Point: 8.2601
>CAJ67327.1 putative cell-division FtsK/SpoIIIE-family protein Tn5397, CTn3-Orf21 [Clostridioides difficile 630]
MKQRGKRIRPSDKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDLDLLQVDKIDIPYLVISFSVAIL
VCLLGAFIFRRYKYDMFKQLQHRQKLAKMILENKWYESEQVKTDGFFKDSTSRTKEKITYFPKMYYRLKD
GLISIRVEIMLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIANRLSIDEVQAKDGKLRL
MTNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTNSKLTILDPKNADLADLGSVMGNVYYRKDDML
SCIDRFYDEMMKRSEVMKKMENYKTGENYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVLNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKQIKGRGYVDVGTSV
ISEFYTPLVPKGHDFLEEIKRLSHSKQDTQATCEAEVAGVD
MKQRGKRIRPSDKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDLDLLQVDKIDIPYLVISFSVAIL
VCLLGAFIFRRYKYDMFKQLQHRQKLAKMILENKWYESEQVKTDGFFKDSTSRTKEKITYFPKMYYRLKD
GLISIRVEIMLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIANRLSIDEVQAKDGKLRL
MTNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTNSKLTILDPKNADLADLGSVMGNVYYRKDDML
SCIDRFYDEMMKRSEVMKKMENYKTGENYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVLNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKQIKGRGYVDVGTSV
ISEFYTPLVPKGHDFLEEIKRLSHSKQDTQATCEAEVAGVD
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q188U2 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 585695..599749
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CD630_04910 (CD0491) | 581655..582062 | + | 408 | CAJ67320 | PTS system, mannose/fructose/sorbose IIA component | - |
| CD630_04920 (CD0492) | 582091..582564 | + | 474 | CAJ67321 | PTS system, mannose/fructose/sorbose IIB component | - |
| CD630_04930 (CD0493) | 582611..583369 | + | 759 | CAJ67322 | PTS system, mannose/fructose/sorbose IIC component | - |
| CD630_04940 (CD0494) | 583393..584232 | + | 840 | CAJ67323 | PTS system, mannose/fructose/sorbose IID component | - |
| CD630_04960 (CD0496) | 585695..586009 | + | 315 | CAJ67325 | putative conjugative transposon protein DUF961 family Tn5397, CTn3-Orf23 | orf23 |
| CD630_04970 (CD0497) | 586031..586417 | + | 387 | CAJ67326 | putative conjugative transposon protein DUF961 family Tn5397, CTn3-Orf22 | orf23 |
| CD630_04980 (CD0498) | 586451..587836 | + | 1386 | CAJ67327 | putative cell-division FtsK/SpoIIIE-family protein Tn5397, CTn3-Orf21 | virb4 |
| CD630_04981 (CD0498A) | 587839..587991 | + | 153 | CAJ67328 | putative conjugative transposon protein Tn5397,CTn3-Orf20.1 | - |
| CD630_04990 (CD0499) | 588010..589218 | + | 1209 | CAJ67329 | putative replication initiation factor Tn5397,CTn3-Orf20 | - |
| CD630_04991 (CD0499A) | 589261..589482 | + | 222 | CAJ67330 | putative conjugative transposon protein Tn5397,CTn3-Orf19 | orf19 |
| CD630_05000 (CD0500) | 589599..590096 | + | 498 | CAJ67331 | putative antirestriction protein Tn5397,CTn3-Orf18 | - |
| CD630_05010 (CD0501) | 590184..590576 | + | 393 | CAJ67332 | putative conjugative transposon protein Tn5397,CTn3-Orf17 | orf17a |
| CD630_05020 (CD0502) | 590560..593007 | + | 2448 | CAJ67333 | putative ATPase Tn5397, CTn3-Orf16 | virb4 |
| CD630_05030 (CD0503) | 593007..595175 | + | 2169 | CAJ67334 | putative membrane protein Tn5397, CTn3-Orf15 | orf15 |
| CD630_05040 (CD0504) | 595172..598820 | + | 3649 | Protein_529 | Fragment of putative conjugative transposon protein Tn5397, CTn3-Orf14 | - |
| CD630_05060 (CD0506) | 596830..598659 | + | 1830 | CAJ67336 | Reverse transcriptase/maturase/endonuclease,Group II intron | - |
| CD630_05070 (CD0507) | 598817..599749 | + | 933 | CAJ67337 | putative conjugative transposon protein Tn5397,CTn3-Orf13 | orf13 |
| CD630_05071 (CD0507A) | 599962..600018 | + | 57 | Protein_532 | Fragment of Tet(M) leader peptide Tn5397,CTn3-orf12 (C-terminal region) | - |
| CD630_05080 (CD0508) | 600034..601953 | + | 1920 | CAJ67339 | Tetracycline resistance protein Tn5397 | - |
| CD630_05081 (CD0508A) | 602049..602243 | + | 195 | CAJ67340 | putative conjugative transposon protein Tn5397,CTn3-Orf6 | - |
| CD630_05090 (CD0509) | 602302..602655 | - | 354 | CAJ67341 | Transcriptional regulator, HTH-type Tn5397,CTn3-Orf9 | - |
| CD630_05091 (CD0509A) | 602866..602931 | + | 66 | CAJ67342 | putative conjugative transposon protein Tn5397,CTn3-Orf10 | - |
| CD630_05100 (CD0510) | 603157..603582 | + | 426 | CAJ67343 | putative RNA polymerase sigma factor Tn5397,CTn3-Orf7 | - |
| CD630_05101 (CD0510A) | 603579..603809 | + | 231 | CAJ67344 | putative conjugative transposon protein Tn5397,CTn3-Orf8 | - |
| CD630_05102 (CD0510B) | 603931..604068 | - | 138 | Protein_539 | Fragment of putative conjugative transposon protein Tn5397, CTn3-Orf5 (C-terminal region) | - |
| CD630_05103 (CD0510C) | 604190..604330 | + | 141 | CCA62796 | putative conjugative transposon protein Tn5397,CTn3-Orf4 | - |
Region 2: 3897502..3910292
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CD630_33280 (CD3328) | 3892914..3893153 | - | 240 | CAJ70225 | putative conjugative transposon protein Tn916-like, CTn6-Orf4 | - |
| CD630_33290 (CD3329) | 3893150..3893572 | - | 423 | CAJ70226 | putative RNA polymerase sigma factor Tn916-like,CTn6-Orf5 | - |
| CD630_33300 (CD3330) | 3894170..3894526 | + | 357 | CAJ70227 | Transcriptional regulator, HTH-type Tn916-like,CTn6-Orf6 | - |
| CD630_33310 (CD3331) | 3894559..3895254 | - | 696 | CAJ70228 | putative conjugative transposon protein Tn916-like, CTn6-Orf7 | - |
| CD630_33320 (CD3332) | 3895434..3896003 | + | 570 | CAJ70229 | Transcriptional regulator, TetR family; Tn916-like, CTn6-Orf8 | - |
| CD630_33330 (CD3333) | 3896015..3896260 | + | 246 | CAJ70230 | putative conjugative transposon protein Tn916-like, CTn6-Orf9 | - |
| CD630_33331 (CD3333A) | 3896491..3896733 | + | 243 | CAJ70231 | putative conjugative transposon protein Tn916-like, CTn6-Orf10 | - |
| CD630_33340 (CD3334) | 3896730..3897200 | + | 471 | CAJ70232 | putative transcriptional regulator Tn916-like,CTn6-Orf11 | - |
| CD630_33350 (CD3335) | 3897502..3898410 | - | 909 | CAJ70233 | putative conjugative transposon protein Tn916-like, CTn6-Orf12 | orf13 |
| CD630_33360 (CD3336) | 3898427..3899431 | - | 1005 | CAJ70234 | putative cell wall hydrolase Tn916-like,CTn6-Orf13 | orf14 |
| CD630_33370 (CD3337) | 3899428..3901809 | - | 2382 | CAJ70235 | putative membrane protein Tn916-like,CTn6-Orf14 | orf15 |
| CD630_33380 (CD3338) | 3901806..3904259 | - | 2454 | CAJ70236 | putative ATPase Tn916-like, CTn6-Orf15 | virb4 |
| CD630_33390 (CD3339) | 3904243..3904635 | - | 393 | CAJ70237 | putative conjugative transposon protein Tn916-like, CTn6-Orf16 | orf17a |
| CD630_33400 (CD3340) | 3904725..3905222 | - | 498 | CAJ70238 | putative antirestriction protein Tn916-like,CTn6-Orf17 | - |
| CD630_33410 (CD3341) | 3905328..3905732 | - | 405 | Protein_3532 | Fragment of putative conjugative transposon protein Tn916-like, CTn6-Orf18 (N-terminal region) | - |
| CD630_33420 (CD3342) | 3905806..3906312 | - | 507 | CAJ70240 | putative conjugative transposon protein Tn916-like, CTn6-Orf19 | - |
| CD630_33421 (CD3342A) | 3906498..3906719 | - | 222 | CAJ70241 | putative conjugative transposon protein Tn916-like, CTn6-Orf20 | orf19 |
| CD630_33430 (CD3343) | 3906771..3907751 | - | 981 | CAJ70242 | putative replication initiation factor Tn916-like, CTn6-Orf21 | - |
| CD630_33440 (CD3344) | 3908146..3909543 | - | 1398 | CAJ70243 | putative cell-division FtsK/SpoIIIE-family protein Tn916-like, CTn6-Orf22 | virb4 |
| CD630_33450 (CD3345) | 3909579..3909956 | - | 378 | CAJ70244 | putative conjugative transposon protein Tn916-like, CTn6-Orf23 | orf23 |
| CD630_33460 (CD3346) | 3909978..3910292 | - | 315 | CAJ70245 | putative conjugative transposon protein DUF961 family Tn916-like, CTn6-Orf24 | orf23 |
| CD630_33470 (CD3347) | 3910549..3911223 | + | 675 | CAJ70246 | putative membrane protein | - |
| CD630_33480 (CD3348) | 3911224..3912117 | + | 894 | CAJ70247 | conserved hypothetical protein | - |
| CD630_33490 (CD3349) | 3912316..3914301 | - | 1986 | CAJ70248 | Exosporium glycoprotein BclA3 | - |
Host bacterium
| ID | 35 | Element type | |
| Element name | Tn5397 | GenBank | AM180355 |
| Element size | 4290252 bp | Coordinate of oriT [Strand] | 587811..588025 [+] |
| Host bacterium | Clostridium difficile 630 | Coordinate of element | 585384..606040 |
Cargo genes
| Drug resistance gene | tet(M) |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |