Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100038 |
| Name | oriTB_pSKU146  |
| Organism | Spiroplasma kunkelii CR2-3x |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_006400 ( 1160..1334 [+], 175 nt) |
| oriT length | 175 nt |
| IRs (inverted repeats) | IR1: 16..26, 30..40 (CAAGATATTTT..AAAATGACTTG) IR2: 42..48, 56..62 (TGCACAA..TTGAGCA) IR3: 107..112, 113..117 (AGGGAT..ATCCT) IR4: 124..130, 135..141 (ATTATTT..AAATGAT) IR5: 146..153, 161..169 (GTGAAATT..AATTTGAAC) |
| Location of nic site | 118..119 |
| Conserved sequence flanking the nic site |
TATCCTG|A |
| Note | putative oriT region; oriTB |
oriT sequence
Download Length: 175 nt
>oriTB_pSKU146
TATGAACTTCCCCACCAAGATATTTTGATAAAATGACTTGTTGCACAAAATGACATTGAGCACTACCAAACTGAACGGGAGTTAAAAATGGAAAATGGTAATCTTAAGGGATATCCTGACTTAATTATTTACAAAAATGATGATAGTGAAATTTATATAGAATTTGAACGAACAC
TATGAACTTCCCCACCAAGATATTTTGATAAAATGACTTGTTGCACAAAATGACATTGAGCACTACCAAACTGAACGGGAGTTAAAAATGGAAAATGGTAATCTTAAGGGATATCCTGACTTAATTATTTACAAAAATGATGATAGTGAAATTTATATAGAATTTGAACGAACAC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Davis RE et al. (2005) Cryptic plasmid pSKU146 from the wall-less plant pathogen Spiroplasma kunkelii encodes an adhesin and components of a type IV translocation-related conjugation system. Plasmid. 53(2):179-90. [PMID:15737404]
T4CP
| ID | 36 | GenBank | YP_138235 |
| Name | Mob_pSKU146 |
UniProt ID | Q5VCB6 |
| Length | 504 a.a. | PDB ID | _ |
| Note | contains VirD4 domain; similar to Mob protein of Streptococcus mutans accession number NP_114056, conjugative coupling factor of Vibrio cholerae GenBank Accession Number AAL59680 | ||
T4CP protein sequence
Download Length: 504 a.a. Molecular weight: 58267.14 Da Isoelectric Point: 9.5909
>YP_138235.1 Mob (plasmid) [Spiroplasma kunkelii CR2-3x]
MLKKIINWRDKNISNKIIYWFIFIFVVPFILLCFINCASAIIIMFLKYHTLDFKNFHIAYVDKYSWIISL
VLFVIGFLFFLWFYVCHKIDNMDSPKIKQQKSSKASDKEFKTLQLKMLALNNKYGIPKTNLSQHTILVGT
TGSGKTTTLMFLVKQLTQLFKQTTIIIDGKGDIDLINKVKQQDPNAFIWEIGGTTEYNPFATKDSVVLSD
KIMSLFTFSEPHYEALVNDYVLILTETLINKNVELTLENIIKYFDIKELKQLISKKDNNYEYLEKLNEDD
ILGMRSRLNVYRQQLKTNIGINNKLLELITKHKTILFSINSLMYPKLAGSVGKIIIQDLKELTTLKPVNQ
KINIVLDEFNVFASETIINLINKSRSFNYQCFLSFQTINDLKTNNMNLTDTIFGNVNSIVCHNIKDPNTT
EYVASVFGTQETEKLTRQLDFKNNTADMGSVRSVDEFVVHPNDLKTLKIGECYFKTTLPSGKLFIKKIKI
NPTYLDGVFQKLNK
MLKKIINWRDKNISNKIIYWFIFIFVVPFILLCFINCASAIIIMFLKYHTLDFKNFHIAYVDKYSWIISL
VLFVIGFLFFLWFYVCHKIDNMDSPKIKQQKSSKASDKEFKTLQLKMLALNNKYGIPKTNLSQHTILVGT
TGSGKTTTLMFLVKQLTQLFKQTTIIIDGKGDIDLINKVKQQDPNAFIWEIGGTTEYNPFATKDSVVLSD
KIMSLFTFSEPHYEALVNDYVLILTETLINKNVELTLENIIKYFDIKELKQLISKKDNNYEYLEKLNEDD
ILGMRSRLNVYRQQLKTNIGINNKLLELITKHKTILFSINSLMYPKLAGSVGKIIIQDLKELTTLKPVNQ
KINIVLDEFNVFASETIINLINKSRSFNYQCFLSFQTINDLKTNNMNLTDTIFGNVNSIVCHNIKDPNTT
EYVASVFGTQETEKLTRQLDFKNNTADMGSVRSVDEFVVHPNDLKTLKIGECYFKTTLPSGKLFIKKIKI
NPTYLDGVFQKLNK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q5VCB6 |
Reference
[1] Davis RE et al. (2005) Cryptic plasmid pSKU146 from the wall-less plant pathogen Spiroplasma kunkelii encodes an adhesin and components of a type IV translocation-related conjugation system. Plasmid. 53(2):179-90. [PMID:15737404]
Host bacterium
| ID | 36 | GenBank | NC_006400 |
| Plasmid name | pSKU146 | Incompatibility group | IncP1 |
| Plasmid size | 14615 bp | Coordinate of oriT [Strand] | 377..551 [+]; 1160..1334 [+] |
| Host baterium | Spiroplasma kunkelii CR2-3x |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | Plasmid pSKU146 harbors genes encoding putative proteins similar to known bacterial virulence factors and conjugative elements including Mob family proteins, origins of plasmid transfer, Vir domains, ICEF ORF-like proteins,and the ScARP1 adhesin of S. citri, implicating a role of pSKU146-encoded genes in conjugal cell-to-cell ommunication and pathogenesis. |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |