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This gene has the annotation "ribosome binding factor A; similar to Swiss-Prot Accession Number P32731, from E. coli".
The target was selected as part of Igor's sets.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | igrigoriev | 2001-08-24 |
| Cloned | Done | abwaight | 2001-08-24 |
| Expression tested | Done | abwaight | 2001-11-12 |
| Solubility tested | S | abwaight | 2001-11-12 |
| Purified | Done | dewemmer | 2002-10-10 |
| NMR characterization | Done | dewemmer | 2002-10-10 |
| HSQC | Done | dewemmer | 2002-10-10 |
| NMR structure | Done | jmc | 2003-06-09 |
| In PDB | 1PA4 | jmc | 2003-06-09 |
| Suggested work stop | 13685 13941 13941 | jmc | 2002-08-26 |
| Override suggest work stop | Remote homolog sequence was deposited. Since homology was low, and NMR data collection was far along we decided it was worthwhile to continue and complete the structure. In the end the structural homology was correct, although the alignment was poor, in the correct structure based alignment the level of sequence idenity was very low. | dewemmer | 2003-09-22 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP675 / MPN156 | -25.40 | 100.00 | 100.00 |
ATGGCTAGTTACAAAAAGGAACGTCTGGAAAACGACATTATTCGTTTAATTAACCGCACTGTTATTCACGAAATCTACAA CGAAACGGTCAAAACCGGTCATGTAACCCACGTGAAACTATCGGATGATTTACTCCATGTAACAGTTTACCTAGACTGTT ATAACCGTGAGCAAATTGACCGCGTGGTGGGTGCCTTTAACCAGGCCAAAGGGGTGTTTAGCCGCGTGTTAGCACACAAT TTGTACTTAGCCAAAGCCGTGCAAATCCATTTTGTCAAGGACAAAGCAATTGATAACGCAATGCGCATTGAGTCTATCAT CAACTCCCTTAAAAAATCAAAGCCTAATTAA
(117 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU25.6( 3) UCU8.5( 1) UAU8.5( 1) UGU8.5( 1) UUC0.0( 0) UCC8.5( 1) UAC34.2( 4) UGC0.0( 0) UUA34.2( 4) UCA8.5( 1) UAA8.5( 1) UGA0.0( 0) UUG8.5( 1) UCG8.5( 1) UAG0.0( 0) UGG0.0( 0) CUU8.5( 1) CCU8.5( 1) CAU25.6( 3) CGU25.6( 3) CUC8.5( 1) CCC0.0( 0) CAC25.6( 3) CGC34.2( 4) CUA17.1( 2) CCA0.0( 0) CAA17.1( 2) CGA0.0( 0) CUG8.5( 1) CCG0.0( 0) CAG8.5( 1) CGG0.0( 0) AUU59.8( 7) ACU8.5( 1) AAU17.1( 2) AGU8.5( 1) AUC34.2( 4) ACC17.1( 2) AAC59.8( 7) AGC8.5( 1) AUA0.0( 0) ACA8.5( 1) AAA68.4( 8) AGA0.0( 0) AUG17.1( 2) ACG8.5( 1) AAG25.6( 3) AGG0.0( 0) GUU17.1( 2) GCU8.5( 1) GAU25.6( 3) GGU17.1( 2) GUC17.1( 2) GCC34.2( 4) GAC34.2( 4) GGC0.0( 0) GUA17.1( 2) GCA25.6( 3) GAA34.2( 4) GGA0.0( 0) GUG51.3( 6) GCG0.0( 0) GAG17.1( 2) GGG8.5( 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 |
|---|---|---|
| 1100B-R1 | 60.90 | CATATGGCTAGTTACAAAAAGGAACGTC |
| 1100B-R2 | 60.70 | GGATCCTTAATTAGGCTTTGATTTTTTAAGGGA |
| 1100B-R10 | 63.80 | GGCGGTGGTGGCGGCATGGCTAGTTACAAAAAGGAACGTCTG |
| 1100B-R11 | 63.70 | GTTCTTCTCCTTTGCGCCCCTAATTAGGCTTTGATTTTTTAAGGGAGTTG |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atggctagttacaaaaaggaacgtctggaaaacgacattattcgtttaattaaccgcact M A S Y K K E R L E N D I I R L I N R T gttattcacgaaatctacaacgaaacggtcaaaaccggtcatgtaacccacgtgaaacta V I H E I Y N E T V K T G H V T H V K L tcggatgatttactccatgtaacagtttacctagactgttataaccgtgagcaaattgac S D D L L H V T V Y L D C Y N R E Q I D cgcgtggtgggtgcctttaaccaggccaaaggggtgtttagccgcgtgttagcacacaat R V V G A F N Q A K G V F S R V L A H N ttgtacttagccaaagccgtgcaaatccattttgtcaaggacaaagcaattgataacgca L Y L A K A V Q I H F V K D K A I D N A atgcgcattgagtctatcatcaactcccttaaaaaatcaaagcctaattaa M R I E S I I N S L K K S K P N *
MASYKKERLENDIIRLINRTVIHEIYNETVKTGHVTHVKLSDDLLHVTVYLDCYNREQIDRVVGAFNQAKGVFSRVLAHN LYLAKAVQIHFVKDKAIDNAMRIESIINSLKKSKPN
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 116
Molecular weight: 13389.5
Theoretical pI: 9.41
Amino acid composition:
Ala (A) 8 6.9%
Arg (R) 7 6.0%
Asn (N) 9 7.8%
Asp (D) 7 6.0%
Cys (C) 1 0.9%
Gln (Q) 3 2.6%
Glu (E) 6 5.2%
Gly (G) 3 2.6%
His (H) 6 5.2%
Ile (I) 11 9.5%
Leu (L) 10 8.6%
Lys (K) 11 9.5%
Met (M) 2 1.7%
Phe (F) 3 2.6%
Pro (P) 1 0.9%
Ser (S) 6 5.2%
Thr (T) 5 4.3%
Trp (W) 0 0.0%
Tyr (Y) 5 4.3%
Val (V) 12 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): 13
Total number of positively charged residues (Arg + Lys): 18
Atomic composition:
Carbon C 597
Hydrogen H 970
Nitrogen N 172
Oxygen O 171
Sulfur S 3
Formula: C597H970N172O171S3
Total number of atoms: 1913
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 7250 7000 6725 6400 6000
Abs 0.1% (=1 g/l) 0.541 0.523 0.502 0.478 0.448
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 7250 7000 6725 6400 6000
Abs 0.1% (=1 g/l) 0.541 0.523 0.502 0.478 0.448
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 13.37
This classifies the protein as stable.
Aliphatic index: 107.50
Grand average of hydropathicity (GRAVY): -0.273