Result : P45956
| Protein Information |
| Information Type | Description |
|---|---|
| Protein name | CRISPR-associated endoribonuclease Cas2 (EC 3.1.-.-) |
| NCBI Accession ID | U29579.1 |
| Organism | Escherichia coli (strain K12) |
| Left | 50872 |
| Right | 51156 |
| Strand | - |
| Nucleotide Sequence | ATGAGTATGTTGGTCGTGGTCACTGAAAATGTACCTCCGCGCTTACGAGGCAGATTAGCCATCTGGTTGTTGGAGGTACGTGCAGGGGTATATGTAGGTGATGTATCCGCAAAAATTCGTGAAATGATCTGGGAACAAATAGCTGGACTGGCGGAAGAAGGCAATGTAGTGATGGCATGGGCAACGAATACGGAAACGGGATTTGAGTTCCAGACATTTGGGTTAAACAGGCGTACCCCGGTAGATTTGGATGGTTTAAGGTTGGTGTCTTTTTTACCTGTTTGA |
| Sequence | MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAWATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPV |
| Source of smORF | Swiss-Prot |
| Function | CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids) (Pubmed:21255106, Pubmed:24920831, Pubmed:24793649). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). The Cas1-Cas2 complex is involved in CRISPR adaptation, the first stage of CRISPR immunity, being required for the addition/removal of CRISPR spacers at the leader end of the CRISPR locus (Pubmed:24920831, Pubmed:25707795, Pubmed:24793649). The Cas1-Cas2 complex introduces staggered nicks into both strands of the CRISPR array near the leader repeat and joins the 5'-ends of the repeat strands with the 3'-ends of the new spacer sequence (Pubmed:24920831). Spacer DNA integration requires supercoiled target DNA and 3'-OH ends on the inserted (spacer) DNA and probably initiates with a nucleophilic attack of the C 3'-OH end of the protospacer on the minus strand of the first repeat sequence (Pubmed:25707795). Expression of Cas1-Cas2 in a strain lacking both genes permits spacer acquisition (Pubmed:24793649, Pubmed:24920831). Cas2 not seen to bind DNA alone; the Cas1-Cas2 complex preferentially binds CRISPR-locus DNA (Pubmed:24793649). Highest binding is seen to a dual forked DNA complex with 3'-overhangs and a protospacer-adjacent motif-complement specifically positioned (Pubmed:26478180). The protospacer DNA lies across a flat surface extending from 1 Cas1 dimer, across the Cas2 dimer and contacting the other Cas1 dimer; the 23 bp-long ds section of the DNA is bracketed by 1 Tyr-22 from each of the Cas1 dimers (Pubmed:26478180, Pubmed:26503043). Cas1 cuts within the 3'-overhang, to generate a 33-nucleotide DNA that is probably incorporated into the CRISPR leader by a cut-and-paste mechanism (Pubmed:26478180). This subunit's probable nuclease activity is not required for spacer acquisition (Pubmed:24793649). {ECO:0000269|Pubmed:21255106, ECO:0000269|Pubmed:24793649, ECO:0000269|Pubmed:24920831, ECO:0000269|Pubmed:26478180}. |
| Pubmed ID | 2656660 9278503 16738553 7567469 19429622 20132443 21255106 24920831 25707795 24793649 26478180 26503043 |
| Domain | CDD:415474 |
| Functional Category | DNA-binding |
| Uniprot ID | P45956 |
| ORF Length (Amino Acid) | 94 |
++ More..
| Conservation Analysis |
No. of Species: 106
| Sr.No. | Left Position | Right Position | Strand | NCBI Accession id | Species Name |
|---|---|---|---|---|---|
| 1 | 2878569 | 2878853 | - | NC_000913.3 | Escherichia coli str. K-12 substr. MG1655 |
| 2 | 875921 | 876205 | + | NZ_CP061527.1 | Shigella dysenteriae |
| 3 | 41512 | 41805 | - | NZ_CP040428.1 | Jejubacter calystegiae |
| 4 | 3139865 | 3140158 | - | NC_017910.1 | Shimwellia blattae DSM 4481 = NBRC 105725 |
| 5 | 2637569 | 2637862 | - | NZ_CP007445.1 | Gilliamella apicola |
| 6 | 4160832 | 4161125 | - | NC_012880.1 | Musicola paradisiaca Ech703 |
| 7 | 2354372 | 2354665 | - | NZ_CP009460.1 | Dickeya fangzhongdai |
| 8 | 2292990 | 2293283 | - | NZ_CP027107.1 | Cronobacter sakazakii |
| 9 | 5188785 | 5189078 | - | NZ_CP020388.1 | Pluralibacter gergoviae |
| 10 | 421302 | 421595 | + | NZ_CP025799.1 | Dickeya zeae |
| 11 | 1143429 | 1143722 | + | NZ_CP012266.1 | Cronobacter dublinensis subsp. dublinensis LMG 23823 |
| 12 | 3852105 | 3852401 | - | NZ_CP031093.1 | Hydrocarboniclastica marina |
| 13 | 83207 | 83500 | + | NZ_CP028271.1 | Mixta intestinalis |
| 14 | 748594 | 748884 | + | NZ_CP014864.1 | Microbulbifer thermotolerans |
| 15 | 3858913 | 3859206 | + | NZ_CP057657.1 | Escherichia fergusonii |
| 16 | 449996 | 450289 | + | NZ_CP038498.1 | Pectobacterium punjabense |
| 17 | 4399370 | 4399663 | - | NZ_CP051652.1 | Pectobacterium carotovorum |
| 18 | 440768 | 441061 | + | NZ_CP034938.1 | Pectobacterium odoriferum |
| 19 | 3628391 | 3628684 | - | NZ_CP015749.1 | Pectobacterium parmentieri |
| 20 | 2215617 | 2215910 | + | NZ_CP015750.1 | Pectobacterium wasabiae CFBP 3304 |
| 21 | 3977529 | 3977822 | - | NZ_CP042220.2 | Dickeya poaceiphila |
| 22 | 2999861 | 3000154 | - | NZ_CP013940.1 | Cronobacter malonaticus LMG 23826 |
| 23 | 4225209 | 4225502 | + | NZ_CP017482.1 | Pectobacterium polaris |
| 24 | 3598658 | 3598951 | - | NC_002695.2 | Escherichia coli O157:H7 str. Sakai |
| 25 | 466761 | 467054 | + | NZ_LT615367.1 | Dickeya aquatica |
| 26 | 3224592 | 3224876 | + | NC_013716.1 | Citrobacter rodentium ICC168 |
| 27 | 894036 | 894329 | - | NZ_CP053416.1 | Salmonella bongori |
| 28 | 3078251 | 3078544 | - | NC_003197.2 | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 |
| 29 | 3752631 | 3752927 | - | NZ_CP021435.1 | Halomonas beimenensis |
| 30 | 3056277 | 3056561 | - | NZ_CP023567.1 | Erwinia pyrifoliae |
| 31 | 4501872 | 4502165 | - | NZ_CP065044.1 | Pectobacterium aroidearum |
| 32 | 2903662 | 2903946 | - | NC_013961.1 | Erwinia amylovora CFBP1430 |
| 33 | 2343674 | 2343967 | - | NZ_CP034752.1 | Jinshanibacter zhutongyuii |
| 34 | 3589698 | 3590015 | + | NC_009943.1 | Desulfococcus oleovorans Hxd3 |
| 35 | 534692 | 534985 | - | NZ_FO704551.1 | Xenorhabdus poinarii G6 |
| 36 | 533978 | 534274 | + | NZ_CP046269.1 | Vibrio spartinae |
| 37 | 2180334 | 2180618 | - | NZ_CP029185.2 | Limnobaculum parvum |
| 38 | 560616 | 560909 | - | NZ_FO704550.1 | Xenorhabdus doucetiae |
| 39 | 4274022 | 4274315 | - | NZ_CP060401.1 | Xenorhabdus nematophila |
| 40 | 135633 | 135929 | - | NZ_CP026364.1 | Proteus hauseri |
| 41 | 849541 | 849840 | + | NZ_CP048711.1 | Kineobactrum salinum |
| 42 | 1099515 | 1099808 | - | NZ_CP048812.1 | Halomonas socia |
| 43 | 1393233 | 1393529 | - | NZ_CP021358.1 | Kushneria marisflavi |
| 44 | 3646061 | 3646354 | + | NC_013892.1 | Xenorhabdus bovienii SS-2004 |
| 45 | 264261 | 264557 | + | NC_007963.1 | Chromohalobacter salexigens DSM 3043 |
| 46 | 1629991 | 1630293 | - | NZ_AP012273.1 | Thiolapillus brandeum |
| 47 | 1469650 | 1469943 | + | NZ_CP043042.1 | Marinobacter fonticola |
| 48 | 1948113 | 1948409 | + | NC_008709.1 | Psychromonas ingrahamii 37 |
| 49 | 759668 | 759967 | + | NZ_AP017372.2 | Halorhodospira halochloris |
| 50 | 4352320 | 4352625 | - | NZ_CP043046.1 | Pigmentiphaga aceris |
| 51 | 1601232 | 1601477 | - | NZ_CP007031.1 | Marichromatium purpuratum 984 |
| 52 | 2946198 | 2946497 | - | NZ_CP011835.1 | Azotobacter chroococcum |
| 53 | 1627769 | 1628092 | - | NZ_CP014476.1 | Methylomonas denitrificans |
| 54 | 1273040 | 1273348 | - | NZ_CP072426.1 | Pseudoalteromonas viridis |
| 55 | 4285975 | 4286277 | - | NC_016112.1 | Methylotuvimicrobium alcaliphilum 20Z |
| 56 | 4574644 | 4574946 | - | NZ_CP035467.1 | Methylotuvimicrobium buryatense |
| 57 | 722344 | 722643 | + | NZ_AP018724.1 | Sulfurivermis fontis |
| 58 | 479806 | 480051 | + | NC_018012.1 | Thiocystis violascens DSM 198 |
| 59 | 186307 | 186606 | - | NZ_CP068286.1 | Ralstonia syzygii subsp. celebesensis |
| 60 | 959476 | 959775 | - | NZ_CP012943.1 | Ralstonia solanacearum |
| 61 | 4030422 | 4030730 | - | NC_013960.1 | Nitrosococcus halophilus Nc 4 |
| 62 | 291502 | 291804 | - | NZ_LR134378.1 | Lautropia mirabilis |
| 63 | 4924303 | 4924548 | - | NZ_AP017928.1 | Methylocaldum marinum |
| 64 | 2156325 | 2156582 | - | NZ_CP009788.1 | Geobacter pickeringii |
| 65 | 1531190 | 1531489 | - | NC_014315.1 | Nitrosococcus watsonii C-113 |
| 66 | 2642164 | 2642457 | - | NC_010814.1 | Geobacter lovleyi SZ |
| 67 | 762462 | 762752 | - | NC_013851.1 | Allochromatium vinosum DSM 180 |
| 68 | 5267483 | 5267806 | + | NC_018025.1 | Desulfomonile tiedjei DSM 6799 |
| 69 | 1521467 | 1521772 | + | NC_002939.5 | Geobacter sulfurreducens PCA |
| 70 | 1280088 | 1280372 | - | NZ_AP014568.1 | Serpentinomonas raichei |
| 71 | 2732633 | 2732935 | - | NZ_CP060084.1 | Teredinibacter haidensis |
| 72 | 1649203 | 1649445 | - | NC_011832.1 | Methanosphaerula palustris E1-9c |
| 73 | 762436 | 762711 | + | NZ_CP039543.1 | Desulfovibrio marinus |
| 74 | 994694 | 994978 | + | NC_009483.1 | Geobacter uraniireducens Rf4 |
| 75 | 2992246 | 2992488 | + | NZ_CP029331.1 | Thauera hydrothermalis |
| 76 | 1331476 | 1331781 | - | NZ_CP026538.1 | Desulfovibrio carbinolicus |
| 77 | 976272 | 976556 | - | NZ_CP011451.1 | Nitrosomonas communis |
| 78 | 949211 | 949516 | + | NZ_LR778301.1 | Denitratisoma oestradiolicum |
| 79 | 2137306 | 2137623 | - | NZ_CP043043.1 | Gluconobacter thailandicus |
| 80 | 886318 | 886566 | - | NC_007519.1 | Desulfovibrio alaskensis G20 |
| 81 | 1134216 | 1134476 | + | NC_007498.2 | Syntrophotalea carbinolica DSM 2380 |
| 82 | 1147943 | 1148203 | + | NZ_AP021884.1 | Sulfuriferula plumbiphila |
| 83 | 1571985 | 1572227 | + | NZ_CP021455.1 | Comamonas serinivorans |
| 84 | 273199 | 273495 | - | NZ_CP014671.1 | Immundisolibacter cernigliae |
| 85 | 2444154 | 2444435 | - | NZ_CP061202.1 | Rhodobacter capsulatus |
| 86 | 52614 | 52946 | + | NZ_CP044115.1 | Roseomonas mucosa |
| 87 | 3392914 | 3393213 | + | NZ_CP045508.1 | Desulfolutivibrio sulfoxidireducens |
| 88 | 2523141 | 2523437 | - | NC_008609.1 | Pelobacter propionicus DSM 2379 |
| 89 | 435251 | 435550 | + | NZ_CP022423.1 | Vitreoscilla filiformis |
| 90 | 3307336 | 3307623 | - | NZ_CP020470.1 | Rhodobacter blasticus |
| 91 | 2430805 | 2431092 | + | NZ_CP015421.1 | Rhodovulum sulfidophilum |
| 92 | 12237 | 12527 | + | NZ_CP035514.1 | Haematobacter massiliensis |
| 93 | 4281148 | 4281402 | + | NZ_CP017707.1 | Chromobacterium vaccinii |
| 94 | 2386959 | 2387270 | - | NC_017059.1 | Pararhodospirillum photometricum DSM 122 |
| 95 | 610406 | 610693 | + | NC_007955.1 | Methanococcoides burtonii DSM 6242 |
| 96 | 2038321 | 2038605 | + | NZ_CP015093.1 | Salipiger abyssi |
| 97 | 36591 | 36860 | + | NZ_CP012664.1 | Defluviimonas alba |
| 98 | 3031802 | 3032056 | + | NZ_CP029495.1 | Chromobacterium phragmitis |
| 99 | 1562573 | 1562860 | - | NZ_CP003182.2 | Granulibacter bethesdensis CGDNIH4 |
| 100 | 1573458 | 1573751 | - | NC_007796.1 | Methanospirillum hungatei JF-1 |
| 101 | 1669290 | 1669586 | - | NC_015676.1 | Methanosalsum zhilinae DSM 4017 |
| 102 | 3464612 | 3464908 | - | NZ_HG322949.1 | Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628 |
| 103 | 1104491 | 1104784 | + | NZ_CP021255.1 | Desulfobulbus oralis |
| 104 | 200012 | 200305 | - | NC_017584.1 | Rhodospirillum rubrum F11 |
| 105 | 4881954 | 4882244 | + | NZ_CP039690.1 | Phreatobacter stygius |
| 106 | 5494368 | 5494646 | - | NC_011894.1 | Methylobacterium nodulans ORS 2060 |
| 107 | 2108071 | 2108376 | + | NZ_CP009530.1 | Methanosarcina barkeri 227 |
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| Neighborhood Conservation Analysis |
* Arrows marked in Genome Diagram shows ORFs; Multiple PFAMs can be mapped to a single ORF.
* 'Small ORF' represents the entry/query analyzed.
* Image generated using 'gggenes'(R-Package).
Neighborhood Representative Chosen(Species): NC_000913.3
| Sr.No. | Domain | Co-occurrence Frequency | No. of species in which domain occurs with smORF | Median distance b/w smORF and domain bearing ORFs | Orientation relative to smORF | PFAM Information |
|---|---|---|---|---|---|---|
| 1 | PF08798.13 | 0.92 | 97 | 934.5 | same-strand | CRISPR associated protein |
| 2 | PF09704.12 | 0.89 | 94 | 1610 | same-strand | CRISPR-associated protein (Cas Cas5) |
| 3 | PF09344.12 | 0.85 | 90 | 2338 | same-strand | CT1975-like protein |
| 4 | PF09485.12 | 0.7 | 74 | 3418 | same-strand | CRISPR-associated protein Cse2 (CRISPR cse2) |
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