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This gene has the annotation "putative DNA-binding protein".
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 | r_kim | 2003-02-11 |
| Expression tested | Done | r_kim | 2003-02-11 |
| Solubility tested | S | r_kim | 2003-02-11 |
| Purified | Done | dewemmer | 2003-06-09 |
| Crystallized | Done | dhshin | 2003-09-12 |
| Diffraction quality crystals | Done | dhshin | 2003-11-12 |
| Native diffraction data | Done | dhshin | 2003-11-12 |
| Phasing diffraction data | Done | dhshin | 2003-11-12 |
| Traceable map | Done | dhshin | 2003-11-12 |
| Crystal structure | Done | dhshin | 2003-12-02 |
| NMR characterization | Done | dewemmer | 2003-06-09 |
| HSQC | Done | dewemmer | 2003-06-09 |
| In PDB | 1S7O | dhshin | 2005-01-19 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP417 / MPN424 | -21.15 | 27.36 | 93.81 |
ATGAACATTATGGAAATTGAAAAAACAAACAGGATGAATGCCCTTTTTGAATTTTATGCAGCTTTGCTAACAGATAAACA AATGAATTATATTGAACTGTATTATGCCGATGATTATAGCTTAGCTGAGATTGCTGATGAATTTGGTGTCAGTCGTCAGG CTGTCTATGATAATATTAAGCGTACGGAAAAAATTTTAGAGACTTATGAGATGAAACTTCATATGTATTCGGATTATGTT GTTCGAAGTGAAATCTTTGACGACATGATTGCTCACTACCCTCATGATGAGTATTTGCAAGAAAAAATTTCCATTCTAAC CAGTATTGACAATAGAGAGTAA
(114 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU35.1( 4) UCU0.0( 0) UAU87.7( 10) UGU0.0( 0) UUC0.0( 0) UCC8.8( 1) UAC8.8( 1) UGC0.0( 0) UUA17.5( 2) UCA0.0( 0) UAA8.8( 1) UGA0.0( 0) UUG17.5( 2) UCG8.8( 1) UAG0.0( 0) UGG0.0( 0) CUU17.5( 2) CCU8.8( 1) CAU17.5( 2) CGU17.5( 2) CUC0.0( 0) CCC0.0( 0) CAC8.8( 1) CGC0.0( 0) CUA17.5( 2) CCA0.0( 0) CAA17.5( 2) CGA8.8( 1) CUG8.8( 1) CCG0.0( 0) CAG8.8( 1) CGG0.0( 0) AUU87.7( 10) ACU8.8( 1) AAU35.1( 4) AGU26.3( 3) AUC8.8( 1) ACC8.8( 1) AAC17.5( 2) AGC8.8( 1) AUA0.0( 0) ACA17.5( 2) AAA43.9( 5) AGA8.8( 1) AUG61.4( 7) ACG8.8( 1) AAG8.8( 1) AGG8.8( 1) GUU17.5( 2) GCU43.9( 5) GAU61.4( 7) GGU8.8( 1) GUC17.5( 2) GCC17.5( 2) GAC26.3( 3) GGC0.0( 0) GUA0.0( 0) GCA8.8( 1) GAA70.2( 8) GGA0.0( 0) GUG0.0( 0) GCG0.0( 0) GAG43.9( 5) GGG0.0( 0)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
atgaacattatggaaattgaaaaaacaaacaggatgaatgccctttttgaattttatgca
gctttgctaacagataaacaaatgaattatattgaactgtattatgccgatgattatagc
ttagctgagattgctgatgaatttggtgtcagtcgtcaggctgtctatgataatattaag
cgtacggaaaaaattttagagacttatgagatgaaacttCATATGtattcggattatgtt
1
gttcgaagtgaaatctttgacgacatgattgctcactaccctcatgatgagtatttgcaa
gaaaaaatttccattctaaccagtattgacaatagagagtaa
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 |
|---|---|---|
| 1325B-R1 | 60.80 | CATATGAACATTATGGAAATTGAAAAAACA |
| 1325B-R2 | 62.30 | GGATCCTTACTCTCTATTGTCAATACTGGTTAGAATGG |
| 1325B-R10 | 63.30 | GGCGGTGGTGGCGGCATGAACATTATGGAAATTGAAAAAACAAAC |
| 1325B-R11 | 63.50 | GTTCTTCTCCTTTGCGCCCCTACTCTCTATTGTCAATACTGGTTAGAATGGAA |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgaacattatggaaattgaaaaaacaaacaggatgaatgccctttttgaattttatgca M N I M E I E K T N R M N A L F E F Y A gctttgctaacagataaacaaatgaattatattgaactgtattatgccgatgattatagc A L L T D K Q M N Y I E L Y Y A D D Y S ttagctgagattgctgatgaatttggtgtcagtcgtcaggctgtctatgataatattaag L A E I A D E F G V S R Q A V Y D N I K cgtacggaaaaaattttagagacttatgagatgaaacttcatatgtattcggattatgtt R T E K I L E T Y E M K L H M Y S D Y V gttcgaagtgaaatctttgacgacatgattgctcactaccctcatgatgagtatttgcaa V R S E I F D D M I A H Y P H D E Y L Q gaaaaaatttccattctaaccagtattgacaatagagagtaa E K I S I L T S I D N R E *
MNIMEIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYV VRSEIFDDMIAHYPHDEYLQEKISILTSIDNRE
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 113
Molecular weight: 13590.3
Theoretical pI: 4.52
Amino acid composition:
Ala (A) 8 7.1%
Arg (R) 5 4.4%
Asn (N) 6 5.3%
Asp (D) 10 8.8%
Cys (C) 0 0.0%
Gln (Q) 3 2.7%
Glu (E) 13 11.5%
Gly (G) 1 0.9%
His (H) 3 2.7%
Ile (I) 11 9.7%
Leu (L) 9 8.0%
Lys (K) 6 5.3%
Met (M) 7 6.2%
Phe (F) 4 3.5%
Pro (P) 1 0.9%
Ser (S) 6 5.3%
Thr (T) 5 4.4%
Trp (W) 0 0.0%
Tyr (Y) 11 9.7%
Val (V) 4 3.5%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 23
Total number of positively charged residues (Arg + Lys): 11
Atomic composition:
Carbon C 607
Hydrogen H 925
Nitrogen N 149
Oxygen O 191
Sulfur S 7
Formula: C607H925N149O191S7
Total number of atoms: 1879
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 .
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 15950 15400 14795 14080 13200
Abs 0.1% (=1 g/l) 1.174 1.133 1.089 1.036 0.971
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 64.02
This classifies the protein as unstable.
Aliphatic index: 86.37
Grand average of hydropathicity (GRAVY): -0.466