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This gene has the annotation "peptide chain release factor RF-1".
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 | 2001-08-24 |
| Expression tested | Done | abwaight | 2001-08-24 |
| Solubility tested | S | abwaight | 2001-08-24 |
| Purified | Done | abwaight | 2001-08-24 |
| Crystallized | Done | abwaight | 2001-08-24 |
| Diffraction quality crystals | Done | abwaight | 2001-08-24 |
| Phasing diffraction data | Done | abwaight | 2001-08-24 |
| Traceable map | Done | abwaight | 2001-08-24 |
| Crystal structure | Done | dhshin | 2003-07-28 |
| In PDB | 1RQ0 | dhshin | 2003-12-15 |
| Biochemical function | Done | dhshin | 2003-01-23 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP475 / MPN361 | -113.00 | 45.78 | 97.08 |
GTGAAAGAAAAGAAAAAAGAGATCGAAAAGCTCCTCGCCAGGCCAGATCTGACTCCCGAACAGATGAAGAACTACGGGAT GGAATACGCAAAGATAGAAGAAATAGAGAACATCACAAACAGAATAAAAGAAACTCAAGAGTTCATCGAACTTTTGAGAG AAGAAGGAGAAAATGAACTGGAGATAGAAAAGTACGAGAAAGAACTTGACCAGCTCTATCAAGAACTGCTCTTTCTTCTT TCTCCAGAAGCGAGCGATAAAGCAATCGTAGAAATCAGACCAGGCACGGGTGGAGAAGAAGCCGCTCTCTTCGCGCGGGA TCTGTTCAGAATGTACACCAGGTACGCAGAAAGAAAAGGCTGGAACCTCGAAGTCGCTGAAATCCACGAAACGGATCTCG GTGGAATAAGGGAAGTGGTCTTCTTTGTGAAGGGAAAGAACGCTTACGGTATTTTGAAGTACGAAAGCGGTGTCCATAGA GTCCAGAGAGTTCCTGTTACAGAGTCTGGAGGGAGAATCCATACGTCCACCGCTACCGTTGCCGTTCTTCCAGAGATTGA AGAAAAGGATATAGAAATCAGGCCGGAAGACTTGAAGATAGAAACTTTCAGGGCATCGGGACACGGTGGACAGTACGTCA ACAAGACCGAATCCGCTGTGAGGATCACACATCTTCCAACGGGAATAGTGGTCTCGTGTCAGAACGAAAGATCTCAGTAT CAGAACAAACAAACCGCTCTGAGGATCCTCAGAGCAAGACTCTACCAGCTACAGAAGGAACAGAAAGAAAGGGAGATCTC GCAGAAGAGAAAATCACAGATAGGAACTGGTGAGAGAAGCGAAAAAATCAGAACTTACAACTTCCCCCAGAACAGAGTTA CGGATCATAGAATAAACTACACTTCTTATAGACTGCAGGAGATCCTCGATGGAGACCTGGACGAAATCATATCGAAGCTT ATAGAACACGACATAGAAAACAACCTAGAGGAAGTTTTAGGAATTGGAGCCTCAGTCGAAGAAAAGTAA
(343 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU5.8( 2) UCU11.7( 4) UAU8.7( 3) UGU2.9( 1) UUC17.5( 6) UCC5.8( 2) UAC32.1( 11) UGC0.0( 0) UUA2.9( 1) UCA5.8( 2) UAA2.9( 1) UGA0.0( 0) UUG8.7( 3) UCG11.7( 4) UAG0.0( 0) UGG2.9( 1) CUU20.4( 7) CCU2.9( 1) CAU11.7( 4) CGU0.0( 0) CUC29.2( 10) CCC5.8( 2) CAC8.7( 3) CGC0.0( 0) CUA5.8( 2) CCA14.6( 5) CAA8.7( 3) CGA0.0( 0) CUG20.4( 7) CCG2.9( 1) CAG40.8( 14) CGG2.9( 1) AUU8.7( 3) ACU17.5( 6) AAU2.9( 1) AGU0.0( 0) AUC40.8( 14) ACC14.6( 5) AAC37.9( 13) AGC8.7( 3) AUA37.9( 13) ACA8.7( 3) AAA32.1( 11) AGA49.6( 17) AUG8.7( 3) ACG14.6( 5) AAG43.7( 15) AGG23.3( 8) GUU17.5( 6) GCU17.5( 6) GAU20.4( 7) GGU17.5( 6) GUC20.4( 7) GCC11.7( 4) GAC14.6( 5) GGC5.8( 2) GUA2.9( 1) GCA14.6( 5) GAA119.5( 41) GGA35.0( 12) GUG14.6( 5) GCG5.8( 2) GAG32.1( 11) GGG5.8( 2)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
gtgaaagaaaagaaaaaagagatcgaaaagctcctcgccaggccAGATCTgactcccgaa
4
cagatgaagaactacgggatggaatacgcaaagatagaagaaatagagaacatcacaaac
agaataaaagaaactcaagagttcatcgaacttttgagagaagaaggagaaaatgaactg
gagatagaaaagtacgagaaagaacttgaccagctctatcaagaactgctctttcttctt
tctccagaagcgagcgataaagcaatcgtagaaatcagaccaggcacgggtggagaagaa
gccgctctcttcgcgcgggatctgttcagaatgtacaccaggtacgcagaaagaaaaggc
tggaacctcgaagtcgctgaaatccacgaaacggatctcggtggaataagggaagtggtc
ttctttgtgaagggaaagaacgcttacggtattttgaagtacgaaagcggtgtccataga
gtccagagagttcctgttacagagtctggagggagaatccatacgtccaccgctaccgtt
gccgttcttccagagattgaagaaaaggatatagaaatcaggccggaagacttgaagata
gaaactttcagggcatcgggacacggtggacagtacgtcaacaagaccgaatccgctgtg
aggatcacacatcttccaacgggaatagtggtctcgtgtcagaacgaaAGATCTcagtat
4
cagaacaaacaaaccgctctgaGGATCCtcagagcaagactctaccagctacagaaggaa
2
cagaaagaaagggAGATCTcgcagaagagaaaatcacagataggaactggtgagagaagc
4
gaaaaaatcagaacttacaacttcccccagaacagagttacggatcatagaataaactac
acttcttatagactgcaggagatcctcgatggagacctggacgaaatcatatcgaagctt
atagaacacgacatagaaaacaacctagaggaagttttaggaattggagcctcagtcgaa
gaaaagtaa
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 |
|---|---|---|
| 1073B-R1 | 60.90 | CATATGAAAGAAAAGAAAAAAGAGATCGAA |
| 1073B-R2 | 62.20 | TTACTTTTCTTCGACTGAGGCTCC |
| 1073B-R10 | 63.40 | GGCGGTGGTGGCGGCATGAAAGAAAAGAAAAAAGAGATCGAAAAG |
| 1073B-R11 | 63.60 | GTTCTTCTCCTTTGCGCCCCTACTTTTCTTCGACTGAGGCTCCA |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
gtgaaagaaaagaaaaaagagatcgaaaagctcctcgccaggccagatctgactcccgaa V K E K K K E I E K L L A R P D L T P E cagatgaagaactacgggatggaatacgcaaagatagaagaaatagagaacatcacaaac Q M K N Y G M E Y A K I E E I E N I T N agaataaaagaaactcaagagttcatcgaacttttgagagaagaaggagaaaatgaactg R I K E T Q E F I E L L R E E G E N E L gagatagaaaagtacgagaaagaacttgaccagctctatcaagaactgctctttcttctt E I E K Y E K E L D Q L Y Q E L L F L L tctccagaagcgagcgataaagcaatcgtagaaatcagaccaggcacgggtggagaagaa S P E A S D K A I V E I R P G T G G E E gccgctctcttcgcgcgggatctgttcagaatgtacaccaggtacgcagaaagaaaaggc A A L F A R D L F R M Y T R Y A E R K G tggaacctcgaagtcgctgaaatccacgaaacggatctcggtggaataagggaagtggtc W N L E V A E I H E T D L G G I R E V V ttctttgtgaagggaaagaacgcttacggtattttgaagtacgaaagcggtgtccataga F F V K G K N A Y G I L K Y E S G V H R gtccagagagttcctgttacagagtctggagggagaatccatacgtccaccgctaccgtt V Q R V P V T E S G G R I H T S T A T V gccgttcttccagagattgaagaaaaggatatagaaatcaggccggaagacttgaagata A V L P E I E E K D I E I R P E D L K I gaaactttcagggcatcgggacacggtggacagtacgtcaacaagaccgaatccgctgtg E T F R A S G H G G Q Y V N K T E S A V aggatcacacatcttccaacgggaatagtggtctcgtgtcagaacgaaagatctcagtat R I T H L P T G I V V S C Q N E R S Q Y cagaacaaacaaaccgctctgaggatcctcagagcaagactctaccagctacagaaggaa Q N K Q T A L R I L R A R L Y Q L Q K E cagaaagaaagggagatctcgcagaagagaaaatcacagataggaactggtgagagaagc Q K E R E I S Q K R K S Q I G T G E R S gaaaaaatcagaacttacaacttcccccagaacagagttacggatcatagaataaactac E K I R T Y N F P Q N R V T D H R I N Y acttcttatagactgcaggagatcctcgatggagacctggacgaaatcatatcgaagctt T S Y R L Q E I L D G D L D E I I S K L atagaacacgacatagaaaacaacctagaggaagttttaggaattggagcctcagtcgaa I E H D I E N N L E E V L G I G A S V E gaaaagtaa E K *
MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLL SPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHR VQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQY QNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKL IEHDIENNLEEVLGIGASVEEK
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 342
Molecular weight: 39656.8
Theoretical pI: 5.35
Amino acid composition:
Ala (A) 17 5.0%
Arg (R) 26 7.6%
Asn (N) 14 4.1%
Asp (D) 12 3.5%
Cys (C) 1 0.3%
Gln (Q) 17 5.0%
Glu (E) 52 15.2%
Gly (G) 22 6.4%
His (H) 7 2.0%
Ile (I) 30 8.8%
Leu (L) 30 8.8%
Lys (K) 26 7.6%
Met (M) 4 1.2%
Phe (F) 8 2.3%
Pro (P) 9 2.6%
Ser (S) 15 4.4%
Thr (T) 19 5.6%
Trp (W) 1 0.3%
Tyr (Y) 14 4.1%
Val (V) 18 5.3%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 64
Total number of positively charged residues (Arg + Lys): 52
Atomic composition:
Carbon C 1746
Hydrogen H 2812
Nitrogen N 492
Oxygen O 550
Sulfur S 5
Formula: C1746H2812N492O550S5
Total number of atoms: 5605
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 25700 25200 24490 23610 22400
Abs 0.1% (=1 g/l) 0.648 0.635 0.618 0.595 0.565
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 25700 25200 24490 23610 22400
Abs 0.1% (=1 g/l) 0.648 0.635 0.618 0.595 0.565
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 57.38
This classifies the protein as unstable.
Aliphatic index: 88.65
Grand average of hydropathicity (GRAVY): -0.740