Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107508
Name   oriT_893916|unnamed in_silico
Organism   Shigella sonnei strain 893916
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MW396864 (60511..60602 [+], 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_893916|unnamed
CGGGGTGTCGGGGCGCAGCCCTGACCAGGTGGTAATCGGATGGCTGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTTTCAGGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5032 GenBank   WP_000991405
Name   Relaxase_J5X09_RS00300_893916|unnamed insolico UniProt ID   A0A896Z1V0
Length   906 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 906 a.a.        Molecular weight: 104972.66 Da        Isoelectric Point: 8.2349

>WP_000991405.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPKKRRDGKSSFEDLIAYTSVRDDVPEDELRPDTEMKAEIPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCLSLESAAEEMQKAAELAHFSKDDTDPVFHYILSWPAHESPRSEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINCLPWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIDQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDKAREGIALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPAMARNGELKSCLAVHRTLAEAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
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 A0A896Z1V0


Auxiliary protein

ID   2307 GenBank   WP_001291057
Name   WP_001291057_893916|unnamed 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   5242 GenBank   WP_013307869
Name   trbC_J5X09_RS00295_893916|unnamed 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: 86950.82 Da        Isoelectric Point: 6.5117

>WP_013307869.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETFPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
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: 11815..54930

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J5X09_RS00045 (PCENFMJK_00008) 7884..8297 + 414 WP_124983997 type IV pilus biogenesis protein PilM -
J5X09_RS00050 (PCENFMJK_00009) 8329..9948 + 1620 WP_001035562 PilN family type IVB pilus formation outer membrane protein -
J5X09_RS00055 (PCENFMJK_00010) 9969..11264 + 1296 WP_000129885 type 4b pilus protein PilO2 -
J5X09_RS00060 (PCENFMJK_00011) 11254..11712 + 459 WP_000095887 type IV pilus biogenesis protein PilP -
J5X09_RS00065 (PCENFMJK_00012) 11815..13323 + 1509 WP_000880806 ATPase, T2SS/T4P/T4SS family virB11
J5X09_RS00070 (PCENFMJK_00013) 13325..14419 + 1095 WP_000697154 type II secretion system F family protein -
J5X09_RS00075 (PCENFMJK_00014) 14481..15017 + 537 WP_000111521 type 4 pilus major pilin -
J5X09_RS00080 (PCENFMJK_00015) 15062..15547 + 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
J5X09_RS00085 (PCENFMJK_00016) 15563..16189 + 627 WP_013307883 prepilin peptidase -
J5X09_RS00090 (PCENFMJK_00017) 16207..17472 + 1266 WP_013307882 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
J5X09_RS00095 17451..17777 - 327 WP_171265817 pilus assembly protein -
J5X09_RS00100 18016..18171 - 156 WP_001358489 hypothetical protein -
J5X09_RS00105 (PCENFMJK_00018) 18269..18607 + 339 WP_072106734 prepilin, shufflon protein A -
J5X09_RS00110 (PCENFMJK_00019) 18612..19001 - 390 Protein_21 phage tail protein -
J5X09_RS00115 (PCENFMJK_00020) 19065..20189 + 1125 WP_013307880 site-specific integrase -
J5X09_RS00120 (PCENFMJK_00021) 20402..21223 + 822 WP_001681675 hypothetical protein traE
J5X09_RS00125 (PCENFMJK_00022) 21325..22527 + 1203 WP_013307879 conjugal transfer protein TraF -
J5X09_RS00130 (PCENFMJK_00023) 22631..23089 + 459 WP_001170111 DotD/TraH family lipoprotein -
J5X09_RS00135 (PCENFMJK_00024) 23086..23922 + 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
J5X09_RS00140 (PCENFMJK_00025) 23906..25054 + 1149 WP_013307876 plasmid transfer ATPase TraJ virB11
J5X09_RS00145 (PCENFMJK_00026) 25051..25341 + 291 WP_000817801 IcmT/TraK family protein traK
J5X09_RS00150 (PCENFMJK_00027) 25573..26154 + 582 WP_025750394 hypothetical protein -
J5X09_RS00155 (PCENFMJK_00028) 26508..30569 + 4062 WP_013307874 LPD7 domain-containing protein -
J5X09_RS00160 (PCENFMJK_00029) 30586..30936 + 351 WP_001056367 hypothetical protein traL
J5X09_RS00165 (PCENFMJK_00030) 30948..31643 + 696 WP_001681668 DotI/IcmL family type IV secretion protein traM
J5X09_RS00170 (PCENFMJK_00031) 31654..32628 + 975 WP_000547383 DotH/IcmK family type IV secretion protein traN
J5X09_RS00175 (PCENFMJK_00032) 32632..33969 + 1338 WP_013307873 conjugal transfer protein TraO traO
J5X09_RS00180 (PCENFMJK_00033) 33966..34679 + 714 WP_000787003 conjugal transfer protein TraP traP
J5X09_RS00185 (PCENFMJK_00034) 34676..35206 + 531 WP_000987023 conjugal transfer protein TraQ traQ
J5X09_RS00190 (PCENFMJK_00035) 35253..35651 + 399 WP_000088812 DUF6750 family protein traR
J5X09_RS00505 (PCENFMJK_00036) 35708..35959 + 252 WP_001277573 hypothetical protein -
J5X09_RS00200 (PCENFMJK_00037) 36066..36692 + 627 WP_000785703 hypothetical protein traT
J5X09_RS00205 (PCENFMJK_00038) 36987..40031 + 3045 WP_001024766 conjugal transfer protein traU
J5X09_RS00210 (PCENFMJK_00039) 40031..40651 + 621 WP_000286854 hypothetical protein traV
J5X09_RS00215 (PCENFMJK_00040) 40609..41814 + 1206 WP_001189548 conjugal transfer protein TraW traW
J5X09_RS00220 (PCENFMJK_00041) 41811..42380 + 570 WP_000650752 conjugal transfer protein TraX -
J5X09_RS00225 (PCENFMJK_00042) 42455..44620 + 2166 WP_000691808 DotA/TraY family protein traY
J5X09_RS00230 (PCENFMJK_00043) 44708..45361 + 654 WP_001401768 plasmid IncI1-type surface exclusion protein ExcA -
J5X09_RS00240 (PCENFMJK_00045) 46295..47998 + 1704 WP_243747282 TnsA endonuclease N-terminal domain-containing protein -
J5X09_RS00245 (PCENFMJK_00046) 48136..48288 - 153 WP_001302699 Hok/Gef family protein -
J5X09_RS00250 (PCENFMJK_00047) 48618..48860 + 243 WP_000650923 hypothetical protein -
J5X09_RS00255 (PCENFMJK_00048) 49151..49519 + 369 WP_001345852 hypothetical protein -
J5X09_RS00260 (PCENFMJK_00049) 49523..49738 + 216 WP_000266543 hypothetical protein -
J5X09_RS00265 (PCENFMJK_00051) 49936..50559 - 624 WP_001155247 helix-turn-helix domain-containing protein -
J5X09_RS00270 (PCENFMJK_00052) 50718..51185 + 468 WP_000598962 thermonuclease family protein -
J5X09_RS00275 (PCENFMJK_00053) 51335..51511 + 177 WP_001054907 hypothetical protein -
J5X09_RS00510 51574..51669 - 96 WP_001363141 DinQ-like type I toxin DqlB -
J5X09_RS00285 (PCENFMJK_00054) 52466..53809 + 1344 WP_032253916 hypothetical protein trbA
J5X09_RS00290 (PCENFMJK_00055) 53806..54930 + 1125 WP_000152382 DsbC family protein trbB
J5X09_RS00295 (PCENFMJK_00056) 54911..57211 + 2301 WP_013307869 F-type conjugative transfer protein TrbC -

Host bacterium

ID   7943 GenBank   NZ_MW396864
Plasmid name   893916|unnamed Incompatibility group   IncB/O/K/Z
Plasmid size   86816 bp Coordinate of oriT [Strand]   60511..60602 [+]
Host baterium   Shigella sonnei strain 893916

Cargo genes

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