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This gene has the annotation "glyceraldehyde-3-phosphate dehydrogenase A".
The target was selected as part of Collaborators' targets.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | dhshin | 2002-11-01 |
| Cloned | Done | dhshin | 2002-11-04 |
| Expression tested | Done | dhshin | 2002-11-04 |
| Solubility tested | S | dhshin | 2002-11-04 |
| Purified | Done | dhshin | 2002-11-04 |
| Crystallized | Done | dhshin | 2002-11-04 |
| Diffraction quality crystals | Done | dhshin | 2002-11-04 |
| Phasing diffraction data | Done | dhshin | 2002-11-04 |
| Traceable map | Done | dhshin | 2002-11-04 |
| Crystal structure | Done | dhshin | 2003-07-28 |
| In PDB | 1S7C | dhshin | 2004-01-29 |
| Biochemical function | Done | dhshin | 2003-01-23 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP411 / MPN430 | -143.00 | 48.79 | 99.70 |
ATGACTATCAAAGTAGGTATCAACGGTTTTGGCCGTATCGGTCGCATTGTTTTCCGTGCTGCTCAGAAACGTTCTGACAT CGAGATCGTTGCAATCAACGACCTGTTAGACGCTGATTACATGGCATACATGCTGAAATATGACTCCACTCACGGCCGTT TCGACGGTACCGTTGAAGTGAAAGACGGTCATCTGATCGTTAACGGTAAAAAAATCCGTGTTACCGCTGAACGTGATCCG GCTAACCTGAAATGGGACGAAGTTGGTGTTGACGTTGTCGCTGAAGCAACTGGTCTGTTCCTGACTGACGAAACTGCTCG TAAACACATCACCGCTGGTGCGAAGAAAGTGGTTATGACTGGTCCGTCTAAAGACAACACTCCGATGTTCGTTAAAGGCG CTAACTTCGACAAATATGCTGGCCAGGACATCGTTTCCAACGCTTCCTGCACCACCAACTGCCTGGCTCCGCTGGCTAAA GTTATCAACGATAACTTCGGCATCATCGAAGGTCTGATGACCACCGTTCACGCTACTACCGCTACTCAGAAAACCGTTGA TGGCCCGTCTCACAAAGACTGGCGCGGCGGCCGCGGCGCTTCCCAGAACATCATCCCGTCCTCTACCGGTGCTGCTAAAG CTGTAGGTAAAGTACTGCCAGAACTGAATGGCAAACTGACTGGTATGGCGTTCCGCGTTCCGACCCCGAACGTATCTGTA GTTGACCTGACCGTTCGTCTGGAAAAAGCTGCAACTTACGAGCAGATCAAAGCTGCCGTTAAAGCTGCTGCTGAAGGCGA AATGAAAGGCGTTCTGGGCTACACCGAAGATGACGTAGTATCTACCGATTTCAACGGCGAAGTTTGCACTTCCGTGTTCG ATGCTAAAGCTGGTATCGCTCTGAACGACAACTTCGTGAAACTGGTATCCTGGTACGACAACGAAACCGGTTACTCCAAC AAAGTTCTGGACCTGATCGCTCACATCTCCAAATAA
(332 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU3.0( 1) UCU18.1( 6) UAU6.0( 2) UGU0.0( 0) UUC30.1( 10) UCC27.1( 9) UAC18.1( 6) UGC9.0( 3) UUA3.0( 1) UCA0.0( 0) UAA3.0( 1) UGA0.0( 0) UUG0.0( 0) UCG0.0( 0) UAG0.0( 0) UGG9.0( 3) CUU0.0( 0) CCU0.0( 0) CAU3.0( 1) CGU24.1( 8) CUC0.0( 0) CCC0.0( 0) CAC15.1( 5) CGC12.0( 4) CUA0.0( 0) CCA3.0( 1) CAA0.0( 0) CGA0.0( 0) CUG57.2( 19) CCG24.1( 8) CAG15.1( 5) CGG0.0( 0) AUU3.0( 1) ACU36.1( 12) AAU3.0( 1) AGU0.0( 0) AUC57.2( 19) ACC45.2( 15) AAC51.2( 17) AGC0.0( 0) AUA0.0( 0) ACA0.0( 0) AAA78.3( 26) AGA0.0( 0) AUG24.1( 8) ACG0.0( 0) AAG3.0( 1) AGG0.0( 0) GUU63.3( 21) GCU84.3( 28) GAU21.1( 7) GGU48.2( 16) GUC3.0( 1) GCC3.0( 1) GAC54.2( 18) GGC42.2( 14) GUA24.1( 8) GCA12.0( 4) GAA39.2( 13) GGA0.0( 0) GUG12.0( 4) GCG6.0( 2) GAG6.0( 2) GGG0.0( 0)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
atgactatcaaagtaggtatcaacggttttggccgtatcggtcgcattgttttccgtgct
gctcagaaacgttctgacatcgagatcgttgcaatcaacgacctgttagacgctgattac
atggcatacatgctgaaatatgactccactcacggccgtttcgacggtaccgttgaagtg
aaagacggtcatctgatcgttaacggtaaaaaaatccgtgttaccgctgaacgtgatccg
gctaacctgaaatgggacgaagttggtgttgacgttgtcgctgaagcaactggtctgttc
ctgactgacgaaactgctcgtaaacacatcaccgctggtgcgaagaaagtggttatgact
ggtccgtctaaagacaacactccgatgttcgttaaaggcgctaacttcgacaaatatgct
ggccaggacatcgtttccaacgcttcctgcaccaccaactgcctggctccgctggctaaa
gttatcaacgataacttcggcatcatcgaaggtctgatgaccaccgttcacgctactacc
gctactcagaaaaccgttgatggcccgtctcacaaagactggcgcgGCGGCCGCggcgct
5
tcccagaacatcatcccgtcctctaccggtgctgctaaagctgtaggtaaagtactgcca
gaactgaatggcaaactgactggtatggcgttccgcgttccgaccccgaacgtatctgta
gttgacctgaccgttcgtctggaaaaagctgcaacttacgagcagatcaaagctgccgtt
aaagctgctgctgaaggcgaaatgaaaggcgttctgggctacaccgaagatgacgtagta
tctaccgatttcaacggcgaagtttgcacttccgtgttcgatgctaaagctggtatcgct
ctgaacgacaacttcgtgaaactggtatcctggtacgacaacgaaaccggttactccaac
aaagttctggacctgatcgctcacatctccaaataa
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 |
|---|---|---|
| 1291B-R1 | 60.60 | CATATGACTATCAAAGTAGGTATCAACGGTT |
| 1291B-R2 | 61.70 | GGATCCTTATTTGGAGATGTGAGCGATCA |
| 1291B-R10 | 64.40 | GGCGGTGGTGGCGGCATGACTATCAAAGTAGGTATCAACGGTTTTG |
| 1291B-R11 | 64.60 | GTTCTTCTCCTTTGCGCCCCTATTTGGAGATGTGAGCGATCAGG |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgactatcaaagtaggtatcaacggttttggccgtatcggtcgcattgttttccgtgct M T I K V G I N G F G R I G R I V F R A gctcagaaacgttctgacatcgagatcgttgcaatcaacgacctgttagacgctgattac A Q K R S D I E I V A I N D L L D A D Y atggcatacatgctgaaatatgactccactcacggccgtttcgacggtaccgttgaagtg M A Y M L K Y D S T H G R F D G T V E V aaagacggtcatctgatcgttaacggtaaaaaaatccgtgttaccgctgaacgtgatccg K D G H L I V N G K K I R V T A E R D P gctaacctgaaatgggacgaagttggtgttgacgttgtcgctgaagcaactggtctgttc A N L K W D E V G V D V V A E A T G L F ctgactgacgaaactgctcgtaaacacatcaccgctggtgcgaagaaagtggttatgact L T D E T A R K H I T A G A K K V V M T ggtccgtctaaagacaacactccgatgttcgttaaaggcgctaacttcgacaaatatgct G P S K D N T P M F V K G A N F D K Y A ggccaggacatcgtttccaacgcttcctgcaccaccaactgcctggctccgctggctaaa G Q D I V S N A S C T T N C L A P L A K gttatcaacgataacttcggcatcatcgaaggtctgatgaccaccgttcacgctactacc V I N D N F G I I E G L M T T V H A T T gctactcagaaaaccgttgatggcccgtctcacaaagactggcgcggcggccgcggcgct A T Q K T V D G P S H K D W R G G R G A tcccagaacatcatcccgtcctctaccggtgctgctaaagctgtaggtaaagtactgcca S Q N I I P S S T G A A K A V G K V L P gaactgaatggcaaactgactggtatggcgttccgcgttccgaccccgaacgtatctgta E L N G K L T G M A F R V P T P N V S V gttgacctgaccgttcgtctggaaaaagctgcaacttacgagcagatcaaagctgccgtt V D L T V R L E K A A T Y E Q I K A A V aaagctgctgctgaaggcgaaatgaaaggcgttctgggctacaccgaagatgacgtagta K A A A E G E M K G V L G Y T E D D V V tctaccgatttcaacggcgaagtttgcacttccgtgttcgatgctaaagctggtatcgct S T D F N G E V C T S V F D A K A G I A ctgaacgacaacttcgtgaaactggtatcctggtacgacaacgaaaccggttactccaac L N D N F V K L V S W Y D N E T G Y S N aaagttctggacctgatcgctcacatctccaaataa K V L D L I A H I S K *
MTIKVGINGFGRIGRIVFRAAQKRSDIEIVAINDLLDADYMAYMLKYDSTHGRFDGTVEVKDGHLIVNGKKIRVTAERDP ANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVMTGPSKDNTPMFVKGANFDKYAGQDIVSNASCTTNCLAPLAK VINDNFGIIEGLMTTVHATTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNVSV VDLTVRLEKAATYEQIKAAVKAAAEGEMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGIALNDNFVKLVSWYDNETGYSN KVLDLIAHISK
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 331
Molecular weight: 35532.4
Theoretical pI: 6.61
Amino acid composition:
Ala (A) 35 10.6%
Arg (R) 12 3.6%
Asn (N) 18 5.4%
Asp (D) 25 7.6%
Cys (C) 3 0.9%
Gln (Q) 5 1.5%
Glu (E) 15 4.5%
Gly (G) 30 9.1%
His (H) 6 1.8%
Ile (I) 20 6.0%
Leu (L) 20 6.0%
Lys (K) 27 8.2%
Met (M) 8 2.4%
Phe (F) 11 3.3%
Pro (P) 9 2.7%
Ser (S) 15 4.5%
Thr (T) 27 8.2%
Trp (W) 3 0.9%
Tyr (Y) 8 2.4%
Val (V) 34 10.3%
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): 39
Atomic composition:
Carbon C 1568
Hydrogen H 2516
Nitrogen N 432
Oxygen O 485
Sulfur S 11
Formula: C1568H2516N432O485S11
Total number of atoms: 5012
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 27945 28127 27860 27430 26520
Abs 0.1% (=1 g/l) 0.786 0.792 0.784 0.772 0.746
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 27800 28000 27740 27310 26400
Abs 0.1% (=1 g/l) 0.782 0.788 0.781 0.769 0.743
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 20.66
This classifies the protein as stable.
Aliphatic index: 87.49
Grand average of hydropathicity (GRAVY): -0.133