Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103855
Name   oriT_Rm41|accessoryA in_silico
Organism   Sinorhizobium meliloti strain Rm41
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021811 (68168..68222 [-], 55 nt)
oriT length   55 nt
IRs (inverted repeats)      25..30, 35..40  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 55 nt

>oriT_Rm41|accessoryA
CCCCGCCGGGGCGCAAAAGCAGAGCGTCGCAACAGCGACGTATAATTGCGCCCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2866 GenBank   WP_041169435
Name   traA_CDO27_RS34970_Rm41|accessoryA insolico UniProt ID   _
Length   1107 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1107 a.a.        Molecular weight: 123045.14 Da        Isoelectric Point: 10.0902

>WP_041169435.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMQYEREARTIDYTRKQGLLHEEFVIPADAPEWLRSMVADR
SVSSASEAFWNKVEDFEKRSDAQLAKDVTIALPIELTADQNIALVRDFVERHITSKGIVADWVYHDAPGN
PHVHLMTTLRPLTDDGFGAKKVALLGPDGKPIRNDAGKIVYELWAGSLDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIEVEPTIHIGVGATAIDRKAEQAKTQSSAGSPKLERIELQEARRSENARRIQRRPE
IVLDLITREKSVFDERDVAKILHRYIDDAALFQSLMIRVLQSPEALRLERERISFATGTRLSAKYTTRKL
IRLEAEMAKRAIWLAGRFSHGVREAVLEATFARHSRLSEEQKTAIEHVAGSERIAAVIGRAGAGKTTMMK
AAREGWEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSSWELRWNEGRNQLDAKTVFVLDEAGMVSSRQM
AHLVETVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGKVRKA
VATYTAHGRMIGLRLKDEAVDTLIADWSRDYDPAKTTLILAHLRRDVRMLNDMARAELVERGILGEGFAF
RTEDGHRNFAVGDQIVFLKNEGSLGVKNGMLGKVVEAAHNRIVAEIGEGEHRRQVAIEQRSYNNVDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHRDDLRVYYGSRSFAFAGGLTKILSRKNAKETTLDYE
KAPFYRQALRFAETRGLHIVNVARTIARDRLEWTVRQKQKLADLAHRLLAIGTKLGFGASTKPTHSQSSK
ETRPMVAGIATFPKTVEQAVADKIEADPGLKKQWEDVSSRFNLVYAQPEAAFKTVNVDAMLKDETVARST
LAKVAGQPESFGPLKGKSGLLASRVDKQDRERAERNIPALAQSLGDYLRQRSQAEQRYQAEEVVARRKLS
INIPALSPNARQTLERVRDAIDRNDLPSALEFALADKMVKAELEGFAKAVADRFGERTFLTLAAKDTNGE
TFKTITAGIGPGQKAEVQSAWSLMRAVQKLSAHERTVEAVKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(863-959)

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(684-741)


  Protein structure



No available structure.




T4CP

ID   2702 GenBank   WP_014989434
Name   traG_CDO27_RS34955_Rm41|accessoryA insolico UniProt ID   _
Length   660 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 660 a.a.        Molecular weight: 71017.95 Da        Isoelectric Point: 8.8337

>WP_014989434.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MTANKITLAVAPVVLMVLAVIGLTGIEQWMSTLGKTDAARLILGRVGIALPYVTAAAIGVIYLFASAGST
SVRVAGWGALAGSATTMLVAMAREATRLATFAGQVPDNTSITSYLDHATMVGATAAFMAGCFALRVALIG
NAAFARAEPKRIRGKRALHGEADWMKMHDAAKLFADTGGIVIGERYRVDKDSTAARSFRADDPETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMIHEHRKGAARFIRILD
PKEPETGFNALDWIGQFGGTKEEDIASVASWIMSDSGGMRGVRDDFFRASALQLLTALLADVCLSGHTGP
ENQTLRQVRANLAEPEPKLRERLQSIYDNSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYSNYA
ALVSGSTFSTDALAAGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGEVEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIAQVSRSFQAKGSSRTRSKQLAARPLIQAHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHPSGTTSEARVIQPARSATSKADPGE

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   2703 GenBank   WP_014989453
Name   t4cp2_CDO27_RS35055_Rm41|accessoryA insolico UniProt ID   _
Length   817 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 817 a.a.        Molecular weight: 91661.63 Da        Isoelectric Point: 6.3231

>WP_014989453.1 conjugal transfer protein TrbE [Sinorhizobium meliloti]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINSILSRLG
SGWMIQVEAVRIPTFDYPSEDRCHFPDTVTRAIDAERRAHFARERGHFESKHALILTYRPIESKKTALSR
YIYSDEESRKRTYADTVLFIFKNAVREIEQYFANTLSIRRMETREAVERGGVRVARYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPITYRWSSRFIF
LDAEEARQKLERTRKKWRQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIIL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPSAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYNQAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDVQEAGPALAFCPLAELATDADRAWATEWIEMLVALQGVTVTPDHRN
AISRQVGLMANAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLTLGAFQTFEIEVLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLILLDEAWLMLGHPVFRRKIQEWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSIATPKREYYIATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLQTRGVHDAATLLKA

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 73335..88076

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CDO27_RS34975 (CDO27_34980) 71599..72165 + 567 WP_014989437 conjugative transfer signal peptidase TraF -
CDO27_RS34980 (CDO27_34985) 72155..73318 + 1164 WP_014989438 conjugal transfer protein TraB -
CDO27_RS34985 (CDO27_34990) 73335..73943 + 609 WP_014989439 TraH family protein virB1
CDO27_RS34990 (CDO27_34995) 74065..74691 - 627 WP_014989440 DUF433 domain-containing protein -
CDO27_RS34995 (CDO27_35000) 74963..75679 + 717 WP_014989441 DUF6088 family protein -
CDO27_RS35000 (CDO27_35005) 75660..76769 + 1110 WP_041169408 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
CDO27_RS35005 (CDO27_35010) 76799..77017 - 219 WP_014989443 helix-turn-helix transcriptional regulator -
CDO27_RS35010 (CDO27_35015) 77222..77539 + 318 WP_014989444 transcriptional repressor TraM -
CDO27_RS35015 (CDO27_35020) 77543..78247 - 705 WP_014989445 autoinducer binding domain-containing protein -
CDO27_RS35020 (CDO27_35025) 78563..79861 - 1299 WP_014989446 IncP-type conjugal transfer protein TrbI virB10
CDO27_RS35025 (CDO27_35030) 79874..80311 - 438 WP_014989447 conjugal transfer protein TrbH -
CDO27_RS35030 (CDO27_35035) 80315..81127 - 813 WP_014989448 P-type conjugative transfer protein TrbG virB9
CDO27_RS35035 (CDO27_35040) 81145..81807 - 663 WP_014989449 conjugal transfer protein TrbF virB8
CDO27_RS35040 (CDO27_35045) 81814..82998 - 1185 WP_014989450 P-type conjugative transfer protein TrbL virB6
CDO27_RS35045 (CDO27_35050) 82992..83192 - 201 WP_014989451 entry exclusion protein TrbK -
CDO27_RS35050 (CDO27_35055) 83189..83989 - 801 WP_014989452 P-type conjugative transfer protein TrbJ virB5
CDO27_RS35055 (CDO27_35060) 83964..86417 - 2454 WP_014989453 conjugal transfer protein TrbE virb4
CDO27_RS35060 (CDO27_35065) 86428..86727 - 300 WP_014989454 conjugal transfer protein TrbD virB3
CDO27_RS35065 (CDO27_35070) 86720..87109 - 390 WP_014989455 TrbC/VirB2 family protein virB2
CDO27_RS35070 (CDO27_35075) 87099..88076 - 978 WP_014989456 P-type conjugative transfer ATPase TrbB virB11
CDO27_RS35075 (CDO27_35080) 88087..88710 - 624 WP_014989457 acyl-homoserine-lactone synthase -
CDO27_RS35080 (CDO27_35085) 89002..90285 + 1284 WP_041169395 plasmid partitioning protein RepA -
CDO27_RS35085 (CDO27_35090) 90282..91304 + 1023 WP_014989225 plasmid partitioning protein RepB -
CDO27_RS35090 (CDO27_35095) 91507..92721 + 1215 WP_014989226 plasmid replication protein RepC -

Host bacterium

ID   4295 GenBank   NZ_CP021811
Plasmid name   Rm41|accessoryA Incompatibility group   -
Plasmid size   247065 bp Coordinate of oriT [Strand]   68168..68222 [-]
Host baterium   Sinorhizobium meliloti strain Rm41

Cargo genes

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