Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116454
Name   oriT_pNIID-071400-001-1 in_silico
Organism   Clostridium tetani strain NIID-071400-001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP026824 (24568..24771 [-], 204 nt)
oriT length   204 nt
IRs (inverted repeats)      125..130, 143..148  (AAATCC..GGATTT)
 66..72, 83..89  (ACCCCCC..GGGGGGT)
Location of nic site      135..136
Conserved sequence flanking the
  nic site    		  TTTGGTTACA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 204 nt

>oriT_pNIID-071400-001-1
AAGCGGAAGTCGCAGGTGTGGACTGATCTTGCTGGCTGGTGTGGCAATAGCCACGCCAGCACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATACGCCTTTTTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10514 GenBank   WP_000398284
Name   mobT_R9A53_RS13890_pNIID-071400-001-1 insolico UniProt ID   A0A3P3PY43
Length   401 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 401 a.a.        Molecular weight: 47398.10 Da        Isoelectric Point: 6.5091

>WP_000398284.1 MULTISPECIES: MobT family relaxase [Bacteria]
MEGFLLNEQTWLQHLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLWEALERFNPDAP
LEMLFDYVRIRFPTTDVQQVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKK

  Protein domains


Predicted by InterproScan.

Helix-turn-helix (HTH_3)

(15-53)

Replication initiation factor (Rep_trans)

(169-373)

Rolling Circle replication initiation protein N-terminal domain (Rol_Rep_N)

(73-161)


  Protein structure


Source ID Structure
AlphaFold DB A0A3P3PY43


Auxiliary protein

ID   6175 GenBank   WP_001291561
Name   WP_001291561_pNIID-071400-001-1 insolico UniProt ID   A0A3P3Q021
Length   405 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 405 a.a.        Molecular weight: 47021.92 Da        Isoelectric Point: 9.7978

>WP_001291561.1 MULTISPECIES: tyrosine-type recombinase/integrase [Bacteria]
MSEKRRDNKGRILKTGESQRKDGRYLYKYIDSFGEPQFVYSWKLVATDRVPAGKRDCISLREKIAELQKD
IHDGIDVVGKKMTLCQLYAKQNAQRPKVRKNTETGRKYLMDILKKDKLGVRSIDSIKPSDAKEWAIRMSE
NGYAYQTINNYKRSLKASFYIAIQDDCVRKNPFDFQLKAVLDDDTVPKTVLTEEQEEKLLAFAKADKTYS
KNYDEILILLKTGLRISEFGGLTLPDLDFENRLVNIDHQLLRDTEIGYYIETPKTKSGERQVPMVEEAYQ
AFKRVLANRKNDKRVEIDGYSDFLFLNRKNYPKVASDYNGMMKGLVKKYNKYNEDKLPHITPHSLRHTFC
TNYANAGMNPKALQYIMGHANIAMTLNYYAHATFDSAMAEMKRLNKEKQQERLVA

  Protein domains


Predicted by InterproScan.

Phage integrase family (Phage_integrase)

(190-383)

DNA binding domain of tn916 integrase (Integrase_DNA)

(1-71)


  Protein structure


Source ID Structure
AlphaFold DB A0A3P3Q021


T4CP

ID   12279 GenBank   WP_000813488
Name   tcpA_R9A53_RS13900_pNIID-071400-001-1 insolico UniProt ID   _
Length   461 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 461 a.a.        Molecular weight: 53370.27 Da        Isoelectric Point: 9.0687

>WP_000813488.1 MULTISPECIES: FtsK/SpoIIIE domain-containing protein [Bacteria]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD

  Protein domains


Predicted by InterproScan.

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(217-301)

  Protein structure



No available structure.



ID   12280 GenBank   WP_035142135
Name   t4cp2_R9A53_RS14395_pNIID-071400-001-1 insolico UniProt ID   _
Length   776 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 776 a.a.        Molecular weight: 89803.17 Da        Isoelectric Point: 7.4131

>WP_035142135.1 type IV secretion system DNA-binding domain-containing protein [Clostridium tetani]
MKSIKISKYFEFINPEYVYLKITPDKSIRNYNSSSIAKSIAHTYKSISQRIRKEQKKIFFETNFKISYII
DIYSNDVEFYFIVPNPFVKIITEKILEVWPNVTIKESNRVRAYSSSAISYQLKYKKEDALSLAVDKKTNE
PLNSILSVIDILDEGDRVTIVYNFLPRNKLGWTKQYNDTMKKIKEHKPLERQKLALEYIVKSVISLLIHL
IDSISEVLNDFAGGNNKNNENLLEAVITSLSNEKDISIATKKKKDMDILDTQIAILSSSNDEIRQTSNVL
SVCQAYRVLDQDNELLYSRVNNISNFKLDDYKLKGIETNTISTDEAQNFIQLPGRRLLSTFNINHINTTE
IQVPHDLQKGFFYLGEVKYKGIKTKAFLEDEYNIGNLPLVLIGSQGSGKTTYIKNIAKYCNKNKEGLFIL
DFIKNCEMSSDISKIIPEDDLVILNLSKEDDMQGLGYNEINITEDMTTFERLNLANLQSQQAMALIDSIS
IGDALSSRMRRFFNAAANVVFSQNYSSIKSVIECLESHIKRDMYINNLSDELKAMLEDEINTLKELDEYS
KASKGHPKIELIGTRESKIEHILDRVNMLREDFKLKYMYNKPTKNNINLVELMEEGKTVIIQMKESDFPT
KMIKNTLVTYWISKIWLTSQLRGSLHEKPLRCNVIVDEIFQAPTCMKTLEYILPQCRKFGCKFIFSTQYI
RQLDDIFDTLEASGSSYMLLKGCMEDDFNHLKSKLYNFEYEDLRDMKQWHSLNLVYYSKGYSSFISKLPS
PINDKQ

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15466..26876

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R9A53_RS13815 (N071400001_p10110) 10653..10856 - 204 WP_000814511 excisionase -
R9A53_RS13820 10840..11091 + 252 WP_001845478 hypothetical protein -
R9A53_RS13825 (N071400001_p10120) 11317..11547 - 231 WP_000857133 helix-turn-helix domain-containing protein -
R9A53_RS13830 (N071400001_p10130) 11544..11966 - 423 WP_000804885 sigma-70 family RNA polymerase sigma factor -
R9A53_RS13835 (N071400001_p10140) 12471..12824 + 354 WP_001227347 helix-turn-helix transcriptional regulator -
R9A53_RS13840 12884..13051 - 168 WP_000336323 cysteine-rich KTR domain-containing protein -
R9A53_RS13845 (N071400001_p10150) 13170..15089 - 1920 WP_317739008 tetracycline resistance ribosomal protection protein Tet(M) -
R9A53_RS13850 15105..15221 - 117 WP_001814923 tetracycline resistance determinant leader peptide -
R9A53_RS13855 (N071400001_p10160) 15466..16398 - 933 WP_001224318 conjugal transfer protein orf13
R9A53_RS13860 (N071400001_p10170) 16395..17396 - 1002 WP_000769868 lysozyme family protein orf14
R9A53_RS13865 (N071400001_p10180) 17393..19570 - 2178 WP_000804748 CD3337/EF1877 family mobilome membrane protein orf15
R9A53_RS13870 (N071400001_p10190) 19573..22020 - 2448 WP_000331160 ATP-binding protein virb4
R9A53_RS13875 22004..22396 - 393 WP_000723888 conjugal transfer protein orf17a
R9A53_RS13880 (N071400001_p10200) 22485..22982 - 498 WP_000342539 antirestriction protein ArdA -
R9A53_RS13885 (N071400001_p10210) 23099..23320 - 222 WP_001009056 hypothetical protein orf19
R9A53_RS13890 (N071400001_p10220) 23363..24568 - 1206 WP_000398284 MobT family relaxase -
R9A53_RS13895 24591..24743 - 153 WP_000879507 hypothetical protein -
R9A53_RS13900 (N071400001_p10230) 24746..26131 - 1386 WP_000813488 FtsK/SpoIIIE domain-containing protein virb4
R9A53_RS13905 (N071400001_p10240) 26160..26546 - 387 WP_000985015 YdcP family protein orf23
R9A53_RS13910 (N071400001_p10250) 26562..26876 - 315 WP_000420682 YdcP family protein orf23
R9A53_RS13915 (N071400001_p10260) 27211..28281 - 1071 WP_317739009 ABC transporter permease -
R9A53_RS13920 (N071400001_p10280) 29356..30042 - 687 WP_035141379 N-acetylmuramoyl-L-alanine amidase -
R9A53_RS13925 (N071400001_p10290) 30415..30714 - 300 WP_035141380 hypothetical protein -
R9A53_RS13930 (N071400001_p10300) 31039..31257 - 219 WP_035141381 DUF2922 domain-containing protein -
R9A53_RS13935 (N071400001_p10310) 31281..31502 - 222 WP_035109232 DUF1659 domain-containing protein -
R9A53_RS13940 (N071400001_p10320) 31591..31770 - 180 WP_035111455 YvrJ family protein -

Host bacterium

ID   16887 GenBank   NZ_AP026824
Plasmid name   pNIID-071400-001-1 Incompatibility group   -
Plasmid size   112887 bp Coordinate of oriT [Strand]   24568..24771 [-]
Host baterium   Clostridium tetani strain NIID-071400-001

Cargo genes

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