Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115710
Name   oriT_pCCH060_77 in_silico
Organism   Shigella flexneri strain CCH060
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099867 (43281..43369 [+], 89 nt)
oriT length   89 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 89 nt

>oriT_pCCH060_77
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10060 GenBank   WP_024260454
Name   nikB_NIU13_RS25685_pCCH060_77 insolico UniProt ID   A0A5F0RK03
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103933.39 Da        Isoelectric Point: 7.3474

>WP_024260454.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A5F0RK03


Auxiliary protein

ID   5923 GenBank   WP_001283947
Name   WP_001283947_pCCH060_77 insolico UniProt ID   A0A142CMC2
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12613.57 Da        Isoelectric Point: 10.7463

>WP_001283947.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A142CMC2


T4CP

ID   11744 GenBank   WP_001289262
Name   trbC_NIU13_RS25680_pCCH060_77 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86896.00 Da        Isoelectric Point: 6.7712

>WP_001289262.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKKSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1203..37903

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NIU13_RS25485 (NIU13_25350) 740..1192 + 453 WP_001247337 type IV pilus biogenesis protein PilP -
NIU13_RS25490 (NIU13_25355) 1203..2756 + 1554 WP_000362206 GspE/PulE family protein virB11
NIU13_RS25495 (NIU13_25360) 2769..3854 + 1086 WP_001208802 type II secretion system F family protein -
NIU13_RS25500 (NIU13_25365) 3871..4485 + 615 WP_000908227 type 4 pilus major pilin -
NIU13_RS25505 (NIU13_25370) 4495..5055 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
NIU13_RS25510 (NIU13_25375) 5040..5696 + 657 WP_001193549 A24 family peptidase -
NIU13_RS25515 (NIU13_25380) 5696..6985 + 1290 Protein_7 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NIU13_RS25520 (NIU13_25385) 7384..8538 + 1155 WP_001139956 tyrosine-type recombinase/integrase -
NIU13_RS25525 (NIU13_25390) 8689..9513 + 825 WP_001238932 conjugal transfer protein TraE traE
NIU13_RS25530 (NIU13_25395) 9599..10801 + 1203 WP_000976357 conjugal transfer protein TraF -
NIU13_RS25535 (NIU13_25400) 10860..11444 + 585 WP_000977522 histidine phosphatase family protein -
NIU13_RS25540 (NIU13_25405) 11839..12297 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NIU13_RS25545 (NIU13_25410) 12294..13112 + 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
NIU13_RS25550 (NIU13_25415) 13109..14257 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
NIU13_RS25555 (NIU13_25420) 14254..14544 + 291 WP_001314267 hypothetical protein traK
NIU13_RS25560 (NIU13_25425) 14559..15110 + 552 WP_000014586 phospholipase D family protein -
NIU13_RS25565 (NIU13_25430) 15200..18964 + 3765 WP_001141540 LPD7 domain-containing protein -
NIU13_RS25570 (NIU13_25435) 18982..19329 + 348 WP_001055900 conjugal transfer protein traL
NIU13_RS25575 (NIU13_25440) 19326..20018 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NIU13_RS25580 (NIU13_25445) 20029..21012 + 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
NIU13_RS25585 (NIU13_25450) 21015..22304 + 1290 WP_001271994 conjugal transfer protein TraO traO
NIU13_RS25590 (NIU13_25455) 22304..23008 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
NIU13_RS25595 (NIU13_25460) 23008..23535 + 528 WP_001055569 conjugal transfer protein TraQ traQ
NIU13_RS25600 (NIU13_25465) 23586..23990 + 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
NIU13_RS25605 (NIU13_25470) 24054..24242 + 189 WP_001277253 putative conjugal transfer protein TraS -
NIU13_RS25610 (NIU13_25475) 24226..25026 + 801 WP_001164784 IncI1-type conjugal transfer protein TraT traT
NIU13_RS25615 (NIU13_25480) 25116..28160 + 3045 WP_001024789 IncI1-type conjugal transfer protein TraU traU
NIU13_RS25620 (NIU13_25485) 28160..28774 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
NIU13_RS25625 (NIU13_25490) 28741..29943 + 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
NIU13_RS25630 (NIU13_25495) 29972..30556 + 585 WP_001037983 IncI1-type conjugal transfer protein TraX -
NIU13_RS25635 (NIU13_25500) 30653..32821 + 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
NIU13_RS25640 (NIU13_25505) 32897..33511 + 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
NIU13_RS25645 (NIU13_25510) 33609..33818 + 210 WP_001140543 hemolysin expression modulator Hha -
NIU13_RS25650 (NIU13_25515) 33936..34178 + 243 WP_000504400 hypothetical protein -
NIU13_RS25655 34243..34338 - 96 WP_000609148 DinQ-like type I toxin DqlB -
NIU13_RS25660 (NIU13_25525) 34839..35090 + 252 WP_001291964 hypothetical protein -
NIU13_RS25665 (NIU13_25530) 35162..35314 - 153 WP_001331364 Hok/Gef family protein -
NIU13_RS25670 (NIU13_25535) 35606..36814 + 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
NIU13_RS25675 (NIU13_25540) 36833..37903 + 1071 WP_000151589 IncI1-type conjugal transfer protein TrbB trbB
NIU13_RS25680 (NIU13_25545) 37896..40187 + 2292 WP_001289262 F-type conjugative transfer protein TrbC -

Host bacterium

ID   16143 GenBank   NZ_CP099867
Plasmid name   pCCH060_77 Incompatibility group   IncI1
Plasmid size   77769 bp Coordinate of oriT [Strand]   43281..43369 [+]
Host baterium   Shigella flexneri strain CCH060

Cargo genes

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