Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100015 |
| Name | oriT_R100  |
| Organism | Shigella flexneri 2b |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | AP000342 (50353..50902 [-], 550 nt) |
| oriT length | 550 nt |
| IRs (inverted repeats) | 243..255, 257..269 (TATTTAATAATTC..GAATTATTAAATA) 311..318, 321..328 (GCAAAAAC..GTTTTTGC) |
| Location of nic site | 337..338 |
| Conserved sequence flanking the nic site |
GTAGTGTGT|GG |
| Note | _ |
oriT sequence
Download Length: 550 nt
TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAACGAACTTTTCACTATAAATATGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTATAAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCGTGAAAATTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTCTCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCAATCTGCCTGATGTTTATAAATGGGATCTGCGAAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTAAGAATGATATC
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Guja KE et al. (2015) Completing the specificity swap: Single-stranded DNA recognition by F and R100 TraI relaxase domains. Plasmid. 80:1-7. [PMID:25841886]
Relaxosome
This oriT is a component of a relaxosome.
| Relaxosome name | RelaxosomeR100  |
| oriT | oriT_R100 |
| Relaxase | TraI_R100 (MOBF) |
| Auxiliary protein | TraM_R100 , TraY_R100 |
Reference
[1] Guja KE et al. (2015) Completing the specificity swap: Single-stranded DNA recognition by F and R100 TraI relaxase domains. Plasmid. 80:1-7. [PMID:25841886]
[2] Joyce J W Wong et al. (2012) Relaxosome function and conjugation regulation in F-like plasmids - a structural biology perspective. Molecular microbiology. 85(4):602-17. [PMID:22788760]
Relaxase
| ID | 14 | GenBank | BAA78885 |
| Name | TraI_R100 |
UniProt ID | Q9WTB0 |
| Length | 1756 a.a. | PDB ID | |
| Note | relaxase | ||
Relaxase protein sequence
Download Length: 1756 a.a. Molecular weight: 191683.22 Da Isoelectric Point: 5.6912
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Reference
[1] Guja KE et al. (2015) Completing the specificity swap: Single-stranded DNA recognition by F and R100 TraI relaxase domains. Plasmid. 80:1-7. [PMID:25841886]
[2] Joyce J W Wong et al. (2012) Relaxosome function and conjugation regulation in F-like plasmids - a structural biology perspective. Molecular microbiology. 85(4):602-17. [PMID:22788760]
Auxiliary protein
| ID | 21 | GenBank | NP_052944 |
| Name | TraM_R100 |
UniProt ID | _ |
| Length | 127 a.a. | PDB ID | _ |
| Note | TraM of plasmid R100, responsible for initiation of conjugal transfer and conjugal-DNA metabolism | ||
Auxiliary protein sequence
Download Length: 127 a.a. Molecular weight: 14508.47 Da Isoelectric Point: 4.7116
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Reference
[1] Paterson ES et al. (1999) Genetic analysis of the mobilization and leading regions of the IncN plasmids pKM101 and pCU1. J Bacteriol. 181(8):2572-83. [PMID:10198024]
| ID | 22 | GenBank | NP_052946 |
| Name | TraY_R100 |
UniProt ID | Q7AK74 |
| Length | 75 a.a. | PDB ID | _ |
| Note | _ | ||
Auxiliary protein sequence
Download Length: 75 a.a. Molecular weight: 8541.74 Da Isoelectric Point: 8.6796
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q7AK74 |
Reference
[1] Joyce J W Wong et al. (2012) Relaxosome function and conjugation regulation in F-like plasmids - a structural biology perspective. Molecular microbiology. 85(4):602-17. [PMID:22788760]
T4CP
| ID | 14 | GenBank | BAA78884 |
| Name | TraD_R100 |
UniProt ID | Q7AK62 |
| Length | 738 a.a. | PDB ID | _ |
| Note | Type IV Secretion System Coupling Protein | ||
T4CP protein sequence
Download Length: 738 a.a. Molecular weight: 83900.57 Da Isoelectric Point: 5.1644
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q7AK62 |
Reference
[1] Joyce J W Wong et al. (2012) Relaxosome function and conjugation regulation in F-like plasmids - a structural biology perspective. Molecular microbiology. 85(4):602-17. [PMID:22788760]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 49965..78466
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_54 | 45293..45868 | + | 576 | BAA78839 | - | - |
| Locus_55 | 45937..46371 | + | 435 | BAA78840 | plasmid SOS inhibition protein | - |
| Locus_56 | 46368..47087 | + | 720 | BAA78841 | plasmid SOS inhibition protein | - |
| Locus_57 | 47309..47521 | + | 213 | BAA78842 | modulator of Hok protein | - |
| Locus_58 | 47367..47525 | + | 159 | BAA78843 | post-segregation killing protein | - |
| Locus_59 | 47763..48140 | - | 378 | BAA78844 | - | - |
| Locus_60 | 48440..48736 | + | 297 | BAA78845 | - | - |
| Locus_61 | 48847..49668 | + | 822 | BAA78846 | - | - |
| Locus_62 | 49965..50474 | - | 510 | BAA78847 | - | virB1 |
| Locus_63 | 50890..51273 | + | 384 | BAA78848 | - | - |
| Locus_64 | 51467..52138 | + | 672 | BAA78849 | positive rugulator of tra operon | - |
| Locus_65 | 52275..52502 | + | 228 | BAA78850 | component of oriT-specific nickase | - |
| Locus_66 | 52535..52894 | + | 360 | BAA78851 | prepropilin | - |
| Locus_67 | 52909..53220 | + | 312 | BAA78852 | - | traL |
| Locus_68 | 53242..53808 | + | 567 | BAA78853 | - | traE |
| Locus_69 | 53795..54523 | + | 729 | BAA78854 | - | traK |
| Locus_70 | 54523..55974 | + | 1452 | BAA78855 | - | traB |
| Locus_71 | 55943..56530 | + | 588 | BAA78856 | - | - |
| Locus_72 | 56469..56837 | + | 369 | BAA78857 | - | - |
| Locus_73 | 56834..57349 | + | 516 | BAA78858 | - | traV |
| Locus_74 | 57484..57705 | + | 222 | BAA78859 | - | - |
| Locus_75 | 57698..58111 | + | 414 | BAA78860 | - | - |
| Locus_76 | 58104..58577 | + | 474 | BAA78861 | - | - |
| Locus_77 | 58657..58875 | + | 219 | BAA78862 | - | - |
| Locus_78 | 58903..59250 | + | 348 | BAA78863 | - | - |
| Locus_79 | 59376..62006 | + | 2631 | BAA78864 | - | virb4 |
| Locus_80 | 62003..62389 | + | 387 | BAA78865 | - | - |
| Locus_81 | 62386..63018 | + | 633 | BAA78866 | - | traW |
| Locus_82 | 63015..64007 | + | 993 | BAA78867 | - | traU |
| Locus_83 | 64031..64342 | + | 312 | BAA78868 | - | - |
| Locus_84 | 64351..64989 | + | 639 | BAA78869 | - | trbC |
| Locus_85 | 64986..65888 | + | 903 | BAA78870 | - | traN |
| Locus_86 | 65901..66836 | + | 936 | BAA78871 | - | traN |
| Locus_87 | 66860..67120 | + | 261 | BAA78872 | - | - |
| Locus_88 | 67095..67856 | + | 762 | BAA78873 | - | traF |
| Locus_89 | 67870..68214 | + | 345 | BAA78874 | - | - |
| Locus_90 | 68333..68617 | + | 285 | BAA78875 | possible cleavage protein of preproplin | - |
| Locus_91 | 68604..69149 | + | 546 | BAA78876 | - | traF |
| Locus_92 | 69079..69426 | + | 348 | BAA78877 | - | - |
| Locus_93 | 69374..69799 | + | 426 | BAA78878 | - | - |
| Locus_94 | 69777..71159 | + | 1383 | BAA78879 | - | traH |
| Locus_95 | 71156..73978 | + | 2823 | BAA78880 | - | traG |
| Locus_96 | 74000..74479 | + | 480 | BAA78881 | possible surface exclusion protein | - |
| Locus_97 | 74528..75259 | + | 732 | BAA78882 | surface exclusion protein | - |
| Locus_98 | 75417..76199 | + | 783 | BAA78883 | - | - |
| Locus_99 | 76250..78466 | + | 2217 | BAA78884 | - | virb4 |
Host bacterium
| ID | 14 | GenBank | AP000342 |
| Plasmid name | R100 | Incompatibility group | IncFII |
| Plasmid size | 94281 bp | Coordinate of oriT [Strand] | 50353..50902 [-] |
| Host baterium | Shigella flexneri 2b |
Cargo genes
| Drug resistance gene | resistance to sulfonamide and streptomycin |
| Virulence gene | - |
| Metal resistance gene | merR, merT, merP, merA, merD, merE |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |