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This gene has the annotation "phosphoserine phosphatase (serB)".
The target was selected as part of Igor's sets.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | jmc | 2001-08-24 |
| Cloned | Done | abwaight | 2001-09-10 |
| Expression tested | Done | abwaight | 2001-09-10 |
| Solubility tested | S | abwaight | 2001-09-10 |
| Purified | Done | abwaight | 2001-09-10 |
| Crystallized | Done | abwaight | 2001-09-10 |
| Diffraction quality crystals | Done | abwaight | 2001-09-10 |
| Phasing diffraction data | Done | abwaight | 2001-09-10 |
| Traceable map | Done | abwaight | 2001-09-10 |
| Crystal structure | Done | dhshin | 2002-10-29 |
| In PDB | 1F5S 1J97 1L7M 1L7N 1L7O 1L7P | dhshin | 2002-10-29 |
| Biochemical function | Done | dhshin | 2002-10-28 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP622 / MPN209 | -56.70 | 12.86 | 99.53 |
ATGGAGAAGAAGAAAAAGCTTATTTTATTTGATTTTGATAGCACATTGGTTAATAATGAGACAATTGATGAGATTGCAAG AGAGGCGGGAGTTGAGGAAGAAGTTAAAAAAATTACTAAAGAAGCAATGGAAGGGAAATTAAATTTTGAGCAATCTTTAA GAAAAAGAGTTAGTTTATTAAAAGACCTTCCAATTGAAAAGGTTGAAAAAGCTATTAAAAGAATAACACCAACAGAGGGA GCTGAAGAGACTATTAAAGAGTTAAAAAATAGAGGTTATGTTGTTGCTGTTGTTAGTGGAGGTTTTGATATTGCTGTTAA TAAAATTAAAGAAAAATTGGGATTAGATTATGCTTTTGCAAATAGATTGATTGTTAAAGATGGAAAACTAACTGGAGATG TTGAGGGAGAGGTTTTAAAAGAAAATGCTAAGGGAGAAATTTTGGAAAAGATAGCTAAAATTGAGGGAATAAATTTGGAG GATACTGTTGCTGTAGGAGATGGAGCTAATGACATAAGTATGTTTAAAAAAGCTGGTTTGAAGATAGCTTTTTGTGCTAA GCCAATTTTAAAAGAGAAGGCAGATATTTGTATAGAGAAAAGGGATTTGAGAGAGATTTTAAAGTATATTAAATAA
(212 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU33.0( 7) UCU4.7( 1) UAU14.2( 3) UGU9.4( 2) UUC0.0( 0) UCC0.0( 0) UAC0.0( 0) UGC0.0( 0) UUA47.2( 10) UCA0.0( 0) UAA4.7( 1) UGA0.0( 0) UUG33.0( 7) UCG0.0( 0) UAG0.0( 0) UGG0.0( 0) CUU9.4( 2) CCU0.0( 0) CAU0.0( 0) CGU0.0( 0) CUC0.0( 0) CCC0.0( 0) CAC0.0( 0) CGC0.0( 0) CUA4.7( 1) CCA14.2( 3) CAA4.7( 1) CGA0.0( 0) CUG0.0( 0) CCG0.0( 0) CAG0.0( 0) CGG0.0( 0) AUU75.5( 16) ACU18.9( 4) AAU42.5( 9) AGU14.2( 3) AUC0.0( 0) ACC0.0( 0) AAC0.0( 0) AGC4.7( 1) AUA28.3( 6) ACA18.9( 4) AAA108.5( 23) AGA33.0( 7) AUG14.2( 3) ACG0.0( 0) AAG47.2( 10) AGG4.7( 1) GUU66.0( 14) GCU56.6( 12) GAU51.9( 11) GGU14.2( 3) GUC0.0( 0) GCC0.0( 0) GAC9.4( 2) GGC0.0( 0) GUA4.7( 1) GCA18.9( 4) GAA51.9( 11) GGA51.9( 11) GUG0.0( 0) GCG4.7( 1) GAG75.5( 16) GGG4.7( 1)
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 |
|---|---|---|
| 1070B-R1 | 60.70 | CATATGGAGAAGAAGAAAAAGCTTATTTTATTT |
| 1070B-R2 | 61.10 | GGATCCTTATTTAATATACTTTAAAATCTCTCTCAAATCCC |
| 1070B-R10 | 63.70 | GGCGGTGGTGGCGGCATGGAGAAGAAGAAAAAGCTTATTTTATTTGA |
| 1070B-R11 | 63.00 | GTTCTTCTCCTTTGCGCCCCTATTTAATATACTTTAAAATCTCTCTCAAATCCCTTTT |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atggagaagaagaaaaagcttattttatttgattttgatagcacattggttaataatgag M E K K K K L I L F D F D S T L V N N E acaattgatgagattgcaagagaggcgggagttgaggaagaagttaaaaaaattactaaa T I D E I A R E A G V E E E V K K I T K gaagcaatggaagggaaattaaattttgagcaatctttaagaaaaagagttagtttatta E A M E G K L N F E Q S L R K R V S L L aaagaccttccaattgaaaaggttgaaaaagctattaaaagaataacaccaacagaggga K D L P I E K V E K A I K R I T P T E G gctgaagagactattaaagagttaaaaaatagaggttatgttgttgctgttgttagtgga A E E T I K E L K N R G Y V V A V V S G ggttttgatattgctgttaataaaattaaagaaaaattgggattagattatgcttttgca G F D I A V N K I K E K L G L D Y A F A aatagattgattgttaaagatggaaaactaactggagatgttgagggagaggttttaaaa N R L I V K D G K L T G D V E G E V L K gaaaatgctaagggagaaattttggaaaagatagctaaaattgagggaataaatttggag E N A K G E I L E K I A K I E G I N L E gatactgttgctgtaggagatggagctaatgacataagtatgtttaaaaaagctggtttg D T V A V G D G A N D I S M F K K A G L aagatagctttttgtgctaagccaattttaaaagagaaggcagatatttgtatagagaaa K I A F C A K P I L K E K A D I C I E K agggatttgagagagattttaaagtatattaaataa R D L R E I L K Y I K *
MEKKKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEG AEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLE DTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 211
Molecular weight: 23593.6
Theoretical pI: 7.60
Amino acid composition:
Ala (A) 17 8.1%
Arg (R) 8 3.8%
Asn (N) 9 4.3%
Asp (D) 13 6.2%
Cys (C) 2 0.9%
Gln (Q) 1 0.5%
Glu (E) 27 12.8%
Gly (G) 15 7.1%
His (H) 0 0.0%
Ile (I) 22 10.4%
Leu (L) 20 9.5%
Lys (K) 33 15.6%
Met (M) 3 1.4%
Phe (F) 7 3.3%
Pro (P) 3 1.4%
Ser (S) 5 2.4%
Thr (T) 8 3.8%
Trp (W) 0 0.0%
Tyr (Y) 3 1.4%
Val (V) 15 7.1%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 40
Total number of positively charged residues (Arg + Lys): 41
Atomic composition:
Carbon C 1055
Hydrogen H 1766
Nitrogen N 278
Oxygen O 318
Sulfur S 5
Formula: C1055H1766N278O318S5
Total number of atoms: 3422
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 4495 4327 4155 3960 3720
Abs 0.1% (=1 g/l) 0.191 0.183 0.176 0.168 0.158
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 4350 4200 4035 3840 3600
Abs 0.1% (=1 g/l) 0.184 0.178 0.171 0.163 0.153
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 28.20
This classifies the protein as stable.
Aliphatic index: 106.30
Grand average of hydropathicity (GRAVY): -0.309