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This gene has the annotation "fibrillarin-like pre-rRNA processing protein".
The target was selected as part of pre-BSGC set.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | jmc | 2003-09-26 |
| Cloned | Done | dhshin | 2003-10-01 |
| Expression tested | Done | dhshin | 2003-10-01 |
| Solubility tested | S | dhshin | 2003-10-01 |
| Purified | Done | dhshin | 2003-10-01 |
| Crystallized | Done | dhshin | 2003-10-01 |
| Diffraction quality crystals | Done | dhshin | 2003-10-01 |
| Native diffraction data | Done | dhshin | 2003-10-01 |
| Phasing diffraction data | Done | dhshin | 2003-10-01 |
| Traceable map | Done | dhshin | 2003-10-01 |
| Crystal structure | Done | dhshin | 2003-10-01 |
| In PDB | 1G8A | dhshin | 2003-12-15 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP474 / MPN362 | -6.30 | 14.74 | 41.85 |
ATGGTTGAGGTAAAAAAGCATAAGTTTCCTGGTGTTTACACAGTTATTGACGATGATGGAAGCGAGAGGATAGCAACTAA AAACCTAGTCCCAGGACAGAGGGTTTACGGGGAGAGGGTTATAAAGTGGGAAGGAGAGGAGTACAGGATTTGGAACCCTA ACCGTTCAAAGCTTGGTGCAGCGATAATGAATGGGCTCAAAAACTTCCCGATAAAACCAGGAAAGAGCGTTCTTTACTTG GGAATTGCTAGCGGTACCACGGCTTCTCACGTTAGTGACATAGTTGGATGGGAGGGGAAGATATTTGGAATTGAATTTTC TCCAAGGGTTCTTAGGGAGCTCGTCCCTATAGTTGAGGAGAGGAGGAACATAGTCCCAATCCTTGGGGATGCAACTAAGC CGGAAGAATACAGGGCTTTGGTACCTAAGGTTGACGTTATATTTGAGGATGTAGCCCAGCCAACGCAGGCTAAGATACTC ATTGACAATGCTGAAGTATACCTAAAGAGGGGTGGTTACGGGATGATAGCCGTTAAGAGCAGGAGCATTGACGTTACAAA GGAGCCAGAGCAGGTGTTCAGGGAGGTTGAGAGGGAGCTGAGCGAATACTTTGAGGTTATAGAGAGGCTTAACTTGGAAC CCTACGAGAAGGATCACGCACTCTTTGTGGTTAGAAAAACTTGA
(228 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU26.3( 6) UCU8.8( 2) UAU0.0( 0) UGU0.0( 0) UUC8.8( 2) UCC0.0( 0) UAC39.5( 9) UGC0.0( 0) UUA0.0( 0) UCA4.4( 1) UAA0.0( 0) UGA4.4( 1) UUG13.2( 3) UCG0.0( 0) UAG0.0( 0) UGG13.2( 3) CUU21.9( 5) CCU17.5( 4) CAU4.4( 1) CGU4.4( 1) CUC17.5( 4) CCC4.4( 1) CAC8.8( 2) CGC0.0( 0) CUA8.8( 2) CCA26.3( 6) CAA0.0( 0) CGA0.0( 0) CUG4.4( 1) CCG8.8( 2) CAG17.5( 4) CGG0.0( 0) AUU26.3( 6) ACU13.2( 3) AAU8.8( 2) AGU4.4( 1) AUC4.4( 1) ACC4.4( 1) AAC26.3( 6) AGC26.3( 6) AUA52.6( 12) ACA8.8( 2) AAA21.9( 5) AGA4.4( 1) AUG13.2( 3) ACG8.8( 2) AAG57.0( 13) AGG61.4( 14) GUU74.6( 17) GCU21.9( 5) GAU21.9( 5) GGU21.9( 5) GUC13.2( 3) GCC8.8( 2) GAC21.9( 5) GGC0.0( 0) GUA17.5( 4) GCA17.5( 4) GAA30.7( 7) GGA30.7( 7) GUG8.8( 2) GCG4.4( 1) GAG78.9( 18) GGG21.9( 5)
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 |
|---|---|---|
| 1386B-R10 | 64.50 | GGCGGTGGTGGCGGCATGGTTGAGGTAAAAAAGCATAAGTTTCC |
| 1386B-R11 | 63.00 | GTTCTTCTCCTTTGCGCCCCTAAGTTTTTCTAACCACAAAGAGTGCG |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atggttgaggtaaaaaagcataagtttcctggtgtttacacagttattgacgatgatgga M V E V K K H K F P G V Y T V I D D D G agcgagaggatagcaactaaaaacctagtcccaggacagagggtttacggggagagggtt S E R I A T K N L V P G Q R V Y G E R V ataaagtgggaaggagaggagtacaggatttggaaccctaaccgttcaaagcttggtgca I K W E G E E Y R I W N P N R S K L G A gcgataatgaatgggctcaaaaacttcccgataaaaccaggaaagagcgttctttacttg A I M N G L K N F P I K P G K S V L Y L ggaattgctagcggtaccacggcttctcacgttagtgacatagttggatgggaggggaag G I A S G T T A S H V S D I V G W E G K atatttggaattgaattttctccaagggttcttagggagctcgtccctatagttgaggag I F G I E F S P R V L R E L V P I V E E aggaggaacatagtcccaatccttggggatgcaactaagccggaagaatacagggctttg R R N I V P I L G D A T K P E E Y R A L gtacctaaggttgacgttatatttgaggatgtagcccagccaacgcaggctaagatactc V P K V D V I F E D V A Q P T Q A K I L attgacaatgctgaagtatacctaaagaggggtggttacgggatgatagccgttaagagc I D N A E V Y L K R G G Y G M I A V K S aggagcattgacgttacaaaggagccagagcaggtgttcagggaggttgagagggagctg R S I D V T K E P E Q V F R E V E R E L agcgaatactttgaggttatagagaggcttaacttggaaccctacgagaaggatcacgca S E Y F E V I E R L N L E P Y E K D H A ctctttgtggttagaaaaacttga L F V V R K T *
MVEVKKHKFPGVYTVIDDDGSERIATKNLVPGQRVYGERVIKWEGEEYRIWNPNRSKLGAAIMNGLKNFPIKPGKSVLYL GIASGTTASHVSDIVGWEGKIFGIEFSPRVLRELVPIVEERRNIVPILGDATKPEEYRALVPKVDVIFEDVAQPTQAKIL IDNAEVYLKRGGYGMIAVKSRSIDVTKEPEQVFREVERELSEYFEVIERLNLEPYEKDHALFVVRKT
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 227
Molecular weight: 25827.7
Theoretical pI: 6.38
Amino acid composition:
Ala (A) 12 5.3%
Arg (R) 16 7.0%
Asn (N) 8 3.5%
Asp (D) 10 4.4%
Cys (C) 0 0.0%
Gln (Q) 4 1.8%
Glu (E) 25 11.0%
Gly (G) 17 7.5%
His (H) 3 1.3%
Ile (I) 19 8.4%
Leu (L) 15 6.6%
Lys (K) 18 7.9%
Met (M) 3 1.3%
Phe (F) 8 3.5%
Pro (P) 13 5.7%
Ser (S) 10 4.4%
Thr (T) 8 3.5%
Trp (W) 3 1.3%
Tyr (Y) 9 4.0%
Val (V) 26 11.5%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 35
Total number of positively charged residues (Arg + Lys): 34
Atomic composition:
Carbon C 1171
Hydrogen H 1862
Nitrogen N 314
Oxygen O 337
Sulfur S 3
Formula: C1171H1862N314O337S3
Total number of atoms: 3687
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 29250 29400 29085 28590 27600
Abs 0.1% (=1 g/l) 1.133 1.138 1.126 1.107 1.069
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 32.52
This classifies the protein as stable.
Aliphatic index: 96.92
Grand average of hydropathicity (GRAVY): -0.311