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This gene has the annotation "Type I restriction-modification enzyme, S subunit".
The target was selected as part of JMC's third set.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | jmc | 2002-11-07 |
| Cloned | Done | blgold | 2004-03-12 |
| Expression tested | Done | blgold | 2004-03-12 |
| Solubility tested | S | r_kim | 2004-06-04 |
| Purified | Done | r_kim | 2004-06-04 |
| Crystallized | Done | dhshin | 2004-06-09 |
| Diffraction quality crystals | Done | dhshin | 2004-06-16 |
| Native diffraction data | Done | dhshin | 2004-06-16 |
| Phasing diffraction data | Done | dhshin | 2004-06-16 |
| Traceable map | Done | dhshin | 2004-08-05 |
| Crystal structure | Done | dhshin | 2004-08-25 |
| In PDB | 1YF2 | dhshin | 2004-12-30 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP066 / MPN089 | -39.40 | 15.22 | 78.82 |
| MP204 / MPN638 | -42.22 | 17.60 | 96.24 |
| MP227 / MPN615 | -32.00 | 20.31 | 60.24 |
| MP335 / MPN507 | -44.00 | 17.86 | 92.24 |
| MP471 / MPN365 | -33.22 | 19.70 | 62.12 |
| MP493 / MPN343 | -31.30 | 18.94 | 62.12 |
| MP545 / MPN290 | -17.30 | 18.55 | 29.18 |
| MP546 / MPN289 | -18.00 | 11.96 | 49.18 |
| MP550 / MPN285 | -30.70 | 18.36 | 60.24 |
| MP630 / MPN201 | -30.70 | 19.92 | 60.24 |
ATGTTCTATAAAGAAGAGAATTTTAAAAAAACAGAGATTGGAGAGATTCCAGAGGATTGGGAGATTGTTGAGCTAAAGGA TGTTTGTAAAAAAATAAAAGCAGGAGGAACACCAAAAACCAGTGTAGAAGAATATTATAAAAATGGGACTATTCCATTTG TTAAAATTGAAGATATAACCAATTCAAATAAATATTTAACCAATACAAAAATAAAAATAACTGAAGAAGGTTTAAATAAT TCCAATGCGTGGATAGTTCCGAAAAATTCTGTATTATTTGCTATGTATGGAAGTATTGGAGAAACAGCAATAAATAAAAT AGAAGTAGCCACAAATCAAGCAATTTTAGGGATAATACCAAAAGATAATATTTTAGAAAGTGAATTTTTGTATTATATTT TAGCTAAAAATAAAAATTATTACTCTAAGTTAGGAATGCAAACAACACAGAAAAATTTGAATGCTCAAATAGTAAAAAGT TTTAAAATCCCTCTCCCTCCATTAGAAGAGCAAAAACAAATAGCTAAAATTTTAACTAAAATTGATGAAGGTATTGAGAT TATTGAGAAATCAATTAATAAATTGGAGAGGATTAAAAAGGGTTTAATGCATAAATTATTAACTAAGGGAATAGGGCATA GTAGATTTAAAAAATCTGAGATTGGGGAGATTCCAGAGGATTGGGAAGTTTTTGAGATTAAAGATATATTTGAAGTAAAA ACGGGAACTACCCCATCAACTAAAAAATCAGAATATTGGGAAAATGGAGAAATAAATTGGATAACACCATTGGATTTAAG CAGGTTAAATGAAAAAATCTATATTGGAAGTAGTGAAAGAAAAGTAACAAAAATAGCATTAGAAAAGTGTAACTTAAATT TAATTCCAAAAGGTTCAATTATTATATCAACAAGAGCACCAGTTGGGTATGTTGCAGTTTTAACTGTAGAATCTACATTT AATCAAGGTTGCAAGGGATTATTCCAAAAAAATAACGATTCGGTTAATACTGAATTTTATGCTTATTATTTAAAGTTTAA AAAAAATTTACTTGAAAATCTAAGTGGGGGAAGCACTTTTAAAGAATTATCAAAATCTATGCTTGAAAACTTTAAAATCC CTCTCCCTCCTTTAGAAGAGCAAAAACAAATAGCTAAAATATTAAGTTCAGTAGATAAAAGCATAGAATTGAAAAAACAA AAGAAAGAAAAACTACAAAGAATGAAAAAGAAAATTATGGAGTTATTATTAACTGGAAAAGTTAGAGTAAAAACTTAG
(426 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU30.5( 13) UCU11.7( 5) UAU32.9( 14) UGU4.7( 2) UUC4.7( 2) UCC2.3( 1) UAC2.3( 1) UGC2.3( 1) UUA63.4( 27) UCA18.8( 8) UAA0.0( 0) UGA0.0( 0) UUG11.7( 5) UCG2.3( 1) UAG2.3( 1) UGG11.7( 5) CUU4.7( 2) CCU11.7( 5) CAU4.7( 2) CGU0.0( 0) CUC4.7( 2) CCC0.0( 0) CAC0.0( 0) CGC0.0( 0) CUA7.0( 3) CCA23.5( 10) CAA25.8( 11) CGA0.0( 0) CUG0.0( 0) CCG2.3( 1) CAG2.3( 1) CGG0.0( 0) AUU56.3( 24) ACU25.8( 11) AAU61.0( 26) AGU21.1( 9) AUC7.0( 3) ACC9.4( 4) AAC7.0( 3) AGC7.0( 3) AUA46.9( 20) ACA25.8( 11) AAA126.8( 54) AGA11.7( 5) AUG16.4( 7) ACG2.3( 1) AAG21.1( 9) AGG4.7( 2) GUU23.5( 10) GCU14.1( 6) GAU23.5( 10) GGU11.7( 5) GUC0.0( 0) GCC2.3( 1) GAC0.0( 0) GGC0.0( 0) GUA21.1( 9) GCA14.1( 6) GAA65.7( 28) GGA30.5( 13) GUG0.0( 0) GCG2.3( 1) GAG37.6( 16) GGG14.1( 6)
Note: These were generated using Hisao's algorithm, and do not take into account possible mispriming, self-complementarity, or requirements for mutations anywhere in the sequences. The -R1 primers are for the N-terminal end, and begin with an NdeI restriction site (CATATG). The -R2 primers are for the C-terminal end, and begin with a BamHI site (GGATCC) if the target has no other BamHI sites. If the target does have a BamHI site, the -R2 primer wil begin with a BglII site (AGATCT), unless the target has no BglII sites. If the target has both sites, the design program gives up and doesn't prepend a restriction site to the -R2 primer!
Predicted Tm was obtained using the Tm determination tool at the Virtual Genome Center.
| Primer ID | Predicted Tm | sequence |
|---|---|---|
| 1322B-R1 | 60.00 | CATATGTTCTATAAAGAAGAGAATTTTAAAAAAACA |
| 1322B-R2 | 61.00 | GGATCCTTAAGTTTTTACTCTAACTTTTCCAGTTAATAATAACTC |
| 1322B-R10 | 63.20 | GGCGGTGGTGGCGGCATGTTCTATAAAGAAGAGAATTTTAAAAAAACAGAGA |
| 1322B-R11 | 63.30 | GTTCTTCTCCTTTGCGCCCCTAAGTTTTTACTCTAACTTTTCCAGTTAATAATAACTCC |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgttctataaagaagagaattttaaaaaaacagagattggagagattccagaggattgg M F Y K E E N F K K T E I G E I P E D W gagattgttgagctaaaggatgtttgtaaaaaaataaaagcaggaggaacaccaaaaacc E I V E L K D V C K K I K A G G T P K T agtgtagaagaatattataaaaatgggactattccatttgttaaaattgaagatataacc S V E E Y Y K N G T I P F V K I E D I T aattcaaataaatatttaaccaatacaaaaataaaaataactgaagaaggtttaaataat N S N K Y L T N T K I K I T E E G L N N tccaatgcgtggatagttccgaaaaattctgtattatttgctatgtatggaagtattgga S N A W I V P K N S V L F A M Y G S I G gaaacagcaataaataaaatagaagtagccacaaatcaagcaattttagggataatacca E T A I N K I E V A T N Q A I L G I I P aaagataatattttagaaagtgaatttttgtattatattttagctaaaaataaaaattat K D N I L E S E F L Y Y I L A K N K N Y tactctaagttaggaatgcaaacaacacagaaaaatttgaatgctcaaatagtaaaaagt Y S K L G M Q T T Q K N L N A Q I V K S tttaaaatccctctccctccattagaagagcaaaaacaaatagctaaaattttaactaaa F K I P L P P L E E Q K Q I A K I L T K attgatgaaggtattgagattattgagaaatcaattaataaattggagaggattaaaaag I D E G I E I I E K S I N K L E R I K K ggtttaatgcataaattattaactaagggaatagggcatagtagatttaaaaaatctgag G L M H K L L T K G I G H S R F K K S E attggggagattccagaggattgggaagtttttgagattaaagatatatttgaagtaaaa I G E I P E D W E V F E I K D I F E V K acgggaactaccccatcaactaaaaaatcagaatattgggaaaatggagaaataaattgg T G T T P S T K K S E Y W E N G E I N W ataacaccattggatttaagcaggttaaatgaaaaaatctatattggaagtagtgaaaga I T P L D L S R L N E K I Y I G S S E R aaagtaacaaaaatagcattagaaaagtgtaacttaaatttaattccaaaaggttcaatt K V T K I A L E K C N L N L I P K G S I attatatcaacaagagcaccagttgggtatgttgcagttttaactgtagaatctacattt I I S T R A P V G Y V A V L T V E S T F aatcaaggttgcaagggattattccaaaaaaataacgattcggttaatactgaattttat N Q G C K G L F Q K N N D S V N T E F Y gcttattatttaaagtttaaaaaaaatttacttgaaaatctaagtgggggaagcactttt A Y Y L K F K K N L L E N L S G G S T F aaagaattatcaaaatctatgcttgaaaactttaaaatccctctccctcctttagaagag K E L S K S M L E N F K I P L P P L E E caaaaacaaatagctaaaatattaagttcagtagataaaagcatagaattgaaaaaacaa Q K Q I A K I L S S V D K S I E L K K Q aagaaagaaaaactacaaagaatgaaaaagaaaattatggagttattattaactggaaaa K K E K L Q R M K K K I M E L L L T G K gttagagtaaaaacttag V R V K T *
MFYKEENFKKTEIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNSNKYLTNTKIKITEEGLNN SNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIPKDNILESEFLYYILAKNKNYYSKLGMQTTQKNLNAQIVKS FKIPLPPLEEQKQIAKILTKIDEGIEIIEKSINKLERIKKGLMHKLLTKGIGHSRFKKSEIGEIPEDWEVFEIKDIFEVK TGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAPVGYVAVLTVESTF NQGCKGLFQKNNDSVNTEFYAYYLKFKKNLLENLSGGSTFKELSKSMLENFKIPLPPLEEQKQIAKILSSVDKSIELKKQ KKEKLQRMKKKIMELLLTGKVRVKT
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 425
Molecular weight: 48567.6
Theoretical pI: 9.30
Amino acid composition:
Ala (A) 14 3.3%
Arg (R) 7 1.6%
Asn (N) 29 6.8%
Asp (D) 10 2.4%
Cys (C) 3 0.7%
Gln (Q) 12 2.8%
Glu (E) 44 10.4%
Gly (G) 24 5.6%
His (H) 2 0.5%
Ile (I) 47 11.1%
Leu (L) 39 9.2%
Lys (K) 63 14.8%
Met (M) 7 1.6%
Phe (F) 15 3.5%
Pro (P) 16 3.8%
Ser (S) 27 6.4%
Thr (T) 27 6.4%
Trp (W) 5 1.2%
Tyr (Y) 15 3.5%
Val (V) 19 4.5%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 54
Total number of positively charged residues (Arg + Lys): 70
Atomic composition:
Carbon C 2207
Hydrogen H 3577
Nitrogen N 559
Oxygen O 644
Sulfur S 10
Formula: C2207H3577N559O644S10
Total number of atoms: 6997
Extinction coefficients:
Conditions: 6.0 M guanidium hydrochloride
0.02 M phosphate buffer
pH 6.5
Extinction coefficients are in units of M-1 cm-1 .
The first table lists values computed assuming ALL Cys
residues appear as half cystines, whereas the second table
assumes that NONE do.
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 48895 49127 48595 47770 46120
Abs 0.1% (=1 g/l) 1.007 1.012 1.001 0.984 0.950
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 48750 49000 48475 47650 46000
Abs 0.1% (=1 g/l) 1.004 1.009 0.998 0.981 0.947
Estimated half-life:
The N-terminal of the sequence considered is M (Met).
The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).
Instability index:
The instability index (II) is computed to be 33.56
This classifies the protein as stable.
Aliphatic index: 95.18
Grand average of hydropathicity (GRAVY): -0.443