Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113544
Name   oriT_2015C-3566|unnamed1 in_silico
Organism   Shigella sonnei strain 2015C-3566
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP022458 (50178..50269 [+], 92 nt)
oriT length   92 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 92 nt

>oriT_2015C-3566|unnamed1
CGGGGTGTCGGGGCTAAGCCCTGACCAGGTGGTAATCGTATAGCCGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTTTCAGGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8680 GenBank   WP_000991407
Name   Relaxase_B9128_RS27130_2015C-3566|unnamed1 insolico UniProt ID   A0A142CND5
Length   906 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 906 a.a.        Molecular weight: 104908.50 Da        Isoelectric Point: 8.2690

>WP_000991407.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPKKRRDGKSSFEDLIAYTSVRDDVPEDELRPDTEVKGEVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCLSLESAAEEMQKAADLAHFSKDDTDPVFHYILSWPAHESPRSEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINCLPWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGIALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVEAPGRYDPEAINVDIRPEKVAETE
SLKQYASRHFAERLPAMARNGELKSCLAVHRTLAEAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVVPGERFRGHSIGSQPVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
GLIQCRSLIEEMIADGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAAADIFERVKPECRYNPELAASDEVEPGFRRDPEIRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNVDRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLNLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure


Source ID Structure
AlphaFold DB A0A142CND5


Auxiliary protein

ID   5069 GenBank   WP_001291057
Name   WP_001291057_2015C-3566|unnamed1 insolico UniProt ID   A0A142CND4
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12596.69 Da        Isoelectric Point: 10.7335

>WP_001291057.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSEKKTRSGSEKRQKNVLIAVRFSPEEAEIVKEKAEKNGLTVSTLIRKTVLGKQINARIDEDFLKELMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITELANTLRRNLMGR

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF6290) (DUF6290)

(19-66)


  Protein structure


Source ID Structure
AlphaFold DB A0A142CND4


T4CP

ID   10038 GenBank   WP_000077653
Name   trbC_B9128_RS27125_2015C-3566|unnamed1 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 86872.69 Da        Isoelectric Point: 6.5117

>WP_000077653.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNIIGLCLAGSIITALIWPLALPVCLLFTLVTSVIFTLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETSPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFVTQQSMLLARDLGYRLE
GTDAQTLEVKKYKGSFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMTAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGVMGESWVDGNQITIQMESKIDVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYISVEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTAKPSRKRRKNRTEPYRIIDTFQRQLATAQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
VCYITLNRPEEEHSGPEDIPSVKVILNTLLPLEILLPVAENNKSQTINNDHPQKSCGAQPTTDEKY

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(439-528)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 8574..44597

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
B9128_RS26910 (B9128_26965) 4766..5224 + 459 WP_000095885 type IV pilus biogenesis protein PilP -
B9128_RS26915 (B9128_26970) 5328..6835 + 1508 Protein_5 ATPase, T2SS/T4P/T4SS family -
B9128_RS26920 (B9128_26975) 6837..7931 + 1095 WP_000697158 type II secretion system F family protein -
B9128_RS26925 (B9128_26980) 7993..8529 + 537 WP_000111534 type 4 pilus major pilin -
B9128_RS26930 (B9128_26985) 8574..9059 + 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
B9128_RS26935 (B9128_26990) 9075..9701 + 627 WP_000939245 prepilin peptidase -
B9128_RS26940 (B9128_26995) 9719..11080 + 1362 WP_001168171 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
B9128_RS28235 11194..11388 + 195 Protein_11 integrase -
B9128_RS26950 (B9128_27005) 11553..12374 + 822 WP_000845373 hypothetical protein traE
B9128_RS26955 (B9128_27010) 12476..13678 + 1203 WP_000979993 conjugal transfer protein TraF -
B9128_RS26960 (B9128_27015) 13782..14239 + 458 Protein_14 DotD/TraH family lipoprotein -
B9128_RS26965 (B9128_27020) 14236..15072 + 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
B9128_RS26970 (B9128_27025) 15056..16204 + 1149 WP_000775210 plasmid transfer ATPase TraJ virB11
B9128_RS26975 (B9128_27030) 16201..16491 + 291 WP_000817801 IcmT/TraK family protein traK
B9128_RS26980 (B9128_27035) 16555..20616 + 4062 WP_000842453 LPD7 domain-containing protein -
B9128_RS26985 (B9128_27040) 20633..20983 + 351 WP_001056367 hypothetical protein traL
B9128_RS26990 (B9128_27045) 20995..21690 + 696 WP_001287545 DotI/IcmL family type IV secretion protein traM
B9128_RS26995 (B9128_27050) 21701..22675 + 975 WP_000547385 DotH/IcmK family type IV secretion protein traN
B9128_RS27645 22679..24015 + 1337 Protein_22 conjugal transfer protein TraO -
B9128_RS27010 (B9128_27065) 24012..24725 + 714 WP_000787003 conjugal transfer protein TraP traP
B9128_RS27015 (B9128_27070) 24722..25252 + 531 WP_000987021 conjugal transfer protein TraQ traQ
B9128_RS27020 (B9128_27075) 25299..25697 + 399 WP_000088813 DUF6750 family protein traR
B9128_RS28355 (B9128_27080) 25721..26005 + 285 WP_001353683 hypothetical protein -
B9128_RS27030 (B9128_27085) 26112..26738 + 627 WP_000785708 hypothetical protein traT
B9128_RS27040 (B9128_27095) 27033..30077 + 3045 WP_001024767 hypothetical protein traU
B9128_RS27045 (B9128_27100) 30077..30697 + 621 WP_000286854 hypothetical protein traV
B9128_RS27050 (B9128_27105) 30655..31860 + 1206 WP_001189548 conjugal transfer protein TraW traW
B9128_RS27055 (B9128_27110) 31857..32426 + 570 WP_000650752 conjugal transfer protein TraX -
B9128_RS27060 (B9128_27115) 32501..34666 + 2166 WP_000691808 DotA/TraY family protein traY
B9128_RS27065 (B9128_27120) 34754..35407 + 654 WP_001402874 plasmid IncI1-type surface exclusion protein ExcA -
B9128_RS27070 (B9128_27125) 35681..37267 + 1587 WP_000004560 TnsA endonuclease N-terminal domain-containing protein -
B9128_RS27075 (B9128_27130) 37405..37557 - 153 WP_001302699 Hok/Gef family protein -
B9128_RS27080 (B9128_27135) 37887..38129 + 243 WP_001363144 hypothetical protein -
B9128_RS27085 (B9128_27140) 38226..38417 + 192 WP_000751583 hypothetical protein -
B9128_RS27090 (B9128_27145) 38429..38797 + 369 WP_001363143 hypothetical protein -
B9128_RS27095 (B9128_27150) 38801..39016 + 216 WP_000266543 hypothetical protein -
B9128_RS27650 (B9128_27160) 39214..39837 - 624 WP_001155250 helix-turn-helix domain-containing protein -
B9128_RS27105 (B9128_27165) 39997..40464 + 468 WP_000598962 thermonuclease family protein -
B9128_RS28245 40614..40790 + 177 WP_001054907 hypothetical protein -
B9128_RS28360 40853..40948 - 96 WP_001363141 DinQ-like type I toxin DqlB -
B9128_RS28365 41537..41632 - 96 WP_001363141 DinQ-like type I toxin DqlB -
B9128_RS27655 41685..41831 - 147 WP_001346191 hypothetical protein -
B9128_RS27115 (B9128_27175) 42169..43476 + 1308 WP_021528768 IncI1-type conjugal transfer protein TrbA trbA
B9128_RS27120 (B9128_27180) 43473..44597 + 1125 WP_000152384 DsbC family protein trbB
B9128_RS27125 (B9128_27185) 44578..46878 + 2301 WP_000077653 F-type conjugative transfer protein TrbC -

Host bacterium

ID   13979 GenBank   NZ_CP022458
Plasmid name   2015C-3566|unnamed1 Incompatibility group   -
Plasmid size   55820 bp Coordinate of oriT [Strand]   50178..50269 [+]
Host baterium   Shigella sonnei strain 2015C-3566

Cargo genes

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