Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200444 |
| Name | oriT_ICEMlSymR88b  |
| Organism | Mesorhizobium loti R88b |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | CP033367 (133586..133646 [+], 61 nt) |
| oriT length | 61 nt |
| IRs (inverted repeats) | 27..33, 37..43 (CCGCCTC..GAGGCGG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 61 nt
>oriT_ICEMlSymR88b
AAAACGATGTGCAGACAAAGGCTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCCTTA
AAAACGATGTGCAGACAAAGGCTTCGCCGCCTCATGGAGGCGGTGCCTTTATCTTGCCTTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 17041 | GenBank | QKD05593 |
| Name | t4cp2_EB235_32295_ICEMlSymR88b |
UniProt ID | _ |
| Length | 816 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 816 a.a. Molecular weight: 90272.73 Da Isoelectric Point: 5.9576
>QKD05593.1 conjugal transfer protein TrbE [Mesorhizobium loti R88b]
MLNLSEYRGRADRLADHLPWAALVAPGIVLNKDGSVQRTLRFRGPDLESSTEAELLGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMARFRDETDRVLDLLSGFMPEVRPLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLDKTEATKTLTRLRR
QWFAKRKSIVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHVGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVTLTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNNRQIELIARATPKRHYYLQSRCGNRLFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGARGLDWGAELLQQFPQPTKEQSS
MLNLSEYRGRADRLADHLPWAALVAPGIVLNKDGSVQRTLRFRGPDLESSTEAELLGICARANNALRRLG
SGWTLFFEAERIEALGYPSSRFPDAASWLVDEERRAAFEGKVAHFESRYHLTLLSMPPPDAQARAESALV
DSHHSEGERDWRQEMARFRDETDRVLDLLSGFMPEVRPLDDAETLTYLHDTISTRRHPVAVPETPMYLDG
ILVDVPLTGGLEPMLGEQHLRTLTILGFPNLTRPGILDALNHQDFAYRWMTRFIPLDKTEATKTLTRLRR
QWFAKRKSIVAILREVVSNEPVPLVDSDADNKALDADEALQALGGDHVGFGYLTATVTVWDEDRQAAAEK
LRAVERIINGLGFTTIRESVNAVEAWLGSLPGHVYANVRQPLVHTLNLAHLMPLSSVWAGPAANEHLAEV
TGREAPPLLIAETSGSTPFRLSSHVEDVGHMLIVGPTGAGKSVLLALIALQFRRYAGAQVYVFDKGNSAR
AATLAMGGEHHVLGSDGALAFQPLRNIGDQGRRSWAAEWIAGLIAHENVTLTPEVKEAIWSALNSLATAP
AQERTLTGLSVLLQSNALKSALMPYTLDGPFGRLLDADDDRLALSDVQCFETEELMHSQSAVLPVLTYLF
HRLEERFDGRPTLLMLDEAWVYLDNPLFAARIREWLKVLRKKNVSVIFATQSLADIAGSAIAPAIIESCP
QRIFLPNDRAVEPQARTAYERFGLNNRQIELIARATPKRHYYLQSRCGNRLFELGLGPIALALCGASGPA
AQSLIDRVLSEHGQDSFVFRFLGARGLDWGAELLQQFPQPTKEQSS
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 17042 | GenBank | QKD05598 |
| Name | t4cp2_EB235_32320_ICEMlSymR88b |
UniProt ID | _ |
| Length | 676 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 676 a.a. Molecular weight: 75089.54 Da Isoelectric Point: 6.6518
>QKD05598.1 conjugal transfer protein TraG [Mesorhizobium loti R88b]
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGTSGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAATREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGAANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DDLSRPADDDSEAMADKRVMDRISTVAGAYGINEGRGDDKDIVPGF
MTPTKLLIGQIAIVFAIVLLGVWAATQWCAHMLAFQEQLGAPWFVAAGWPIYEPWKLLEWWFQFDAYAPE
VFDKAGMLAGTSGFMGCAAAIAGSLWRARQRGLVTTYGSSRWAATREIEKAGLFQPAGVFLGKLKDRYLR
HDGPEHVMAFAPTRSGKGVGLVVPTLLSWSGSAVIHDIKGENWQLSSGWRSRFSHCLLFNPTDPRSARYN
PLLEVRKGSDEIRDVQNIADILVDPEGALERRNHWEKTSHSLLVGAILHVLYAEEEKTLARVATFLSDPQ
RSFAATLRRMMTTNHLGAANKPQVHPVVASAAREVLNKSENERSGVLSTAMSFLGLYRDPTVAAVTSDCD
WRIADLMDAEWPMSLYLVVPPSDISRTKPLVRLILNQIGRRLTERLEGDPKKSRKHQLLMMLDEFPALGR
LDFFETALAFMAGYGIRAYLIAQSLNQISKAYGDNNAILDNCHLRIAFSSNDERTAKRISDALGTATELR
SMRNYAGHRLAPWLSHVMVSRQETARPLLTPGEVMQLPPADELVLVSGLPPIRAKKLRYYEDHNFTERVL
PSPVLRDGPYADCPMSRPDDWTGQVRGVDRRLASDDESAGAALADEGGVQQQRHPGLPEEHTAVTQEPDQ
DDLSRPADDDSEAMADKRVMDRISTVAGAYGINEGRGDDKDIVPGF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 17043 | GenBank | QKD05622 |
| Name | t4cp2_EB235_32480_ICEMlSymR88b |
UniProt ID | _ |
| Length | 581 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 581 a.a. Molecular weight: 64292.71 Da Isoelectric Point: 8.2057
>QKD05622.1 type IV secretion system protein VirD4 [Mesorhizobium loti R88b]
MSSTKTTSPNIAISIACSLALGFCAASLYATFRHGGSGEALMAFDVRAFWFETPFYLGFATPVFYQGAAI
VLSTSAVVLLIQQVVLRRKLEHHGTARWARVDEMRRTGYLRRYRGVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKAAGHEVFKFAPLDSERRTNCYNPL
LDLIALHPQQQFTEARRLAANLITAKGEGAEGFVAGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQIVSILQRSLPRQDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPNYISKAIGEYTFEAKSISYSQSRAFDRNI
QNSFQGAPLLRPEQVRLLNDEYEIVLIKGLPPLQLRKVRYFSDRILKRIFESQTGALPEPAPLTEAEEGF
SAESRLDEPLRGLAQDFDDTV
MSSTKTTSPNIAISIACSLALGFCAASLYATFRHGGSGEALMAFDVRAFWFETPFYLGFATPVFYQGAAI
VLSTSAVVLLIQQVVLRRKLEHHGTARWARVDEMRRTGYLRRYRGVTGPVFGKTSGPFWPGYYLTNGEQP
HSLIVAPTRAGKGVGIVIPTLLTFKGSVIALDVKGELFELTSRARKAAGHEVFKFAPLDSERRTNCYNPL
LDLIALHPQQQFTEARRLAANLITAKGEGAEGFVAGARDIFVAGILACIERGTPTIGAVYDLFAQPGEKF
KLFAQLAMETRNKEAQRIFDDMAGNDTKILTSYTSVLGDGGLNLWADPAVKAATSRSDFSVYDLRRRRTC
IYLCVGPNDLEVIAPLIRLFFQQIVSILQRSLPRQDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMLIIQSLSALTGAYGEAGKQNFLSNTGLQVFMATADDETPNYISKAIGEYTFEAKSISYSQSRAFDRNI
QNSFQGAPLLRPEQVRLLNDEYEIVLIKGLPPLQLRKVRYFSDRILKRIFESQTGALPEPAPLTEAEEGF
SAESRLDEPLRGLAQDFDDTV
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 6575937..6584994
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EB235_32250 | 6572308..6572847 | + | 540 | QKD05584 | hemerythrin domain-containing protein | - |
| EB235_32255 | 6572851..6573606 | - | 756 | QKD05585 | Crp/Fnr family transcriptional regulator | - |
| EB235_32260 | 6573764..6575113 | + | 1350 | QKD05586 | oxygen-independent coproporphyrinogen III oxidase | - |
| EB235_32265 | 6575652..6575924 | - | 273 | QKD05587 | DUF2274 domain-containing protein | - |
| EB235_32270 | 6575937..6577151 | - | 1215 | QKD05588 | TrbI/VirB10 family protein | virB10 |
| EB235_32275 | 6577163..6578191 | - | 1029 | QKD05589 | P-type conjugative transfer protein TrbG | virB9 |
| EB235_32280 | 6578188..6578913 | - | 726 | QKD05590 | conjugal transfer protein TrbF | virB8 |
| EB235_32285 | 6578914..6580236 | - | 1323 | QKD05591 | P-type conjugative transfer protein TrbL | virB6 |
| EB235_32290 | 6580268..6580993 | - | 726 | QKD05592 | P-type conjugative transfer protein TrbJ | virB5 |
| EB235_32295 | 6580990..6583440 | - | 2451 | QKD05593 | conjugal transfer protein TrbE | virb4 |
| EB235_32300 | 6583434..6583706 | - | 273 | QKD05594 | conjugal transfer protein | virB3 |
| EB235_32305 | 6583706..6584014 | - | 309 | QKD05595 | conjugal transfer protein TrbC | virB2 |
| EB235_32310 | 6584026..6584994 | - | 969 | QKD05596 | P-type conjugative transfer ATPase TrbB | virB11 |
| EB235_32315 | 6584991..6585404 | - | 414 | QKD05597 | CopG family transcriptional regulator | - |
| EB235_32320 | 6585523..6587553 | - | 2031 | QKD05598 | conjugal transfer protein TraG | - |
| EB235_32325 | 6587713..6587920 | + | 208 | Protein_6404 | XRE family transcriptional regulator | - |
| EB235_32330 | 6588215..6588604 | - | 390 | QKD05599 | hypothetical protein | - |
| EB235_32335 | 6588815..6589582 | + | 768 | QKD05600 | ZinT family metal-binding protein | - |
Region 2: 6605998..6615421
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| EB235_32390 | 6601602..6601729 | + | 128 | Protein_6417 | IS630 family transposase | - |
| EB235_32395 | 6601729..6602353 | + | 625 | Protein_6418 | ISKra4 family transposase | - |
| EB235_32400 | 6603335..6605875 | + | 2541 | QKD06717 | two-component system VirA-like sensor kinase | - |
| EB235_32405 | 6605998..6607038 | - | 1041 | QKD05608 | P-type DNA transfer ATPase VirB11 | virB11 |
| EB235_32410 | 6607022..6608161 | - | 1140 | QKD05609 | type IV secretion system protein VirB10 | virB10 |
| EB235_32415 | 6608158..6609039 | - | 882 | QKD05610 | type IV secretion system protein VirB9 | virB9 |
| EB235_32420 | 6609036..6609749 | - | 714 | QKD05611 | type IV secretion system protein VirB8 | virB8 |
| EB235_32425 | 6609746..6609904 | - | 159 | QKD05612 | type IV secretion system lipoprotein VirB7 | - |
| EB235_32430 | 6609931..6610818 | - | 888 | QKD05613 | type IV secretion system protein | virB6 |
| EB235_32435 | 6610876..6611550 | - | 675 | QKD05614 | type IV secretion system protein VirB5 | - |
| EB235_32440 | 6611564..6613933 | - | 2370 | QKD05615 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| EB235_32445 | 6613933..6614259 | - | 327 | QKD05616 | type IV secretion system protein VirB3 | virB3 |
| EB235_32450 | 6614259..6614624 | - | 366 | QKD05617 | pilin major subunit VirB2 | virB2 |
| EB235_32455 | 6614639..6615421 | - | 783 | QKD05618 | type IV secretion system lytic transglycosylase VirB1 | virB1 |
| EB235_32460 | 6616726..6617451 | + | 726 | QKD05619 | response regulator | - |
| EB235_32465 | 6617427..6617771 | - | 345 | QKD05620 | transposase domain-containing protein | - |
| EB235_32470 | 6617710..6617805 | - | 96 | Protein_6433 | hypothetical protein | - |
Host bacterium
| ID | 395 | Element type | ICE (Integrative and conjugative element) |
| Element name | ICEMlSymR88b | GenBank | CP033367 |
| Element size | 7207166 bp | Coordinate of oriT [Strand] | 133586..133646 [+] |
| Host bacterium | Mesorhizobium loti R88b | Coordinate of element | 6552772..7054589 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | gmd |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | fixS, fixI, fixH, fixG, fixP, fixQ, fixO, fixN, nodM, nodD, nolL, nodB, eB234_29755, nodJ, nodI, nodC, nodA, nodS, mlr6097, nifU, nifX, nifN, nifE, nifK, nifD, nifH, nifQ, mLTONO_5203, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, nolK, noeL, nodZ |
| Anti-CRISPR | AcrIIC1 |