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This gene has the annotation "hypothetical protein (yabB) homolog; similar to Swiss-Prot Accession Number P22186, 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 | 2001-09-10 |
| Expression tested | Done | abwaight | 2001-09-10 |
| Solubility tested | S | abwaight | 2001-09-10 |
| Purified | Done | abwaight | 2001-09-10 |
| Crystallized | Done | abwaight | 2001-09-10 |
| Diffraction quality crystals | Done | abwaight | 2001-09-10 |
| Phasing diffraction data | Done | abwaight | 2001-09-10 |
| Traceable map | Done | abwaight | 2001-09-10 |
| Crystal structure | Done | schen | 2002-10-28 |
| In PDB | 1N0E 1N0F 1N0G | schen | 2002-10-28 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP522 / MPN314 | -51.00 | 100.00 | 100.00 |
ATGCTTTTAGGAACCTTCAACATTACCCTTGATGCAAAAAACAGGATCAGTCTGCCAGCGAAGCTGCGGGCTTTCTTTGA AGGTAGCATTGTTATCAACCGTGGCTTTGAAAACTGCTTGGAAGTGCGTAAACCACAAGACTTCCAAAAGTACTTTGAGC AGTTCAACAGCTTTCCCTCCACCCAAAAAGACACTAGAACACTCAAGCGCTTAATTTTTGCCAACGCTAACTTTGTGGAT GTAGATACAGCGGGACGGGTTTTAATTCCCAACAATCTGATTAACGATGCCAAGCTAGACAAGGAAATTGTTTTAATTGG CCAGTTTGACCACTTAGAGATTTGGGACAAGAAGCTGTATGAGGACTACCTAGCCAACTCTGAGTCGTTGGAAACGGTAG CGGAAAGGATGAAAGATGTTAAGTAA
(142 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU49.3( 7) UCU7.0( 1) UAU7.0( 1) UGU0.0( 0) UUC28.2( 4) UCC7.0( 1) UAC14.1( 2) UGC7.0( 1) UUA35.2( 5) UCA0.0( 0) UAA7.0( 1) UGA0.0( 0) UUG14.1( 2) UCG7.0( 1) UAG0.0( 0) UGG7.0( 1) CUU14.1( 2) CCU0.0( 0) CAU0.0( 0) CGU14.1( 2) CUC7.0( 1) CCC14.1( 2) CAC7.0( 1) CGC7.0( 1) CUA14.1( 2) CCA14.1( 2) CAA21.1( 3) CGA0.0( 0) CUG28.2( 4) CCG0.0( 0) CAG14.1( 2) CGG14.1( 2) AUU56.3( 8) ACU7.0( 1) AAU7.0( 1) AGU7.0( 1) AUC14.1( 2) ACC21.1( 3) AAC70.4( 10) AGC14.1( 2) AUA0.0( 0) ACA14.1( 2) AAA28.2( 4) AGA7.0( 1) AUG14.1( 2) ACG7.0( 1) AAG56.3( 8) AGG14.1( 2) GUU28.2( 4) GCU14.1( 2) GAU35.2( 5) GGU7.0( 1) GUC0.0( 0) GCC21.1( 3) GAC42.3( 6) GGC14.1( 2) GUA14.1( 2) GCA7.0( 1) GAA42.3( 6) GGA14.1( 2) GUG14.1( 2) GCG21.1( 3) GAG28.2( 4) GGG0.0( 0)
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 |
|---|---|---|
| 1080B-R1 | 60.10 | CATATGCTTTTAGGAACCTTCAACATTAC |
| 1080B-R2 | 60.90 | GGATCCTTACTTAACATCTTTCATCCTTTCCG |
| 1080B-R10 | 65.30 | GGCGGTGGTGGCGGCATGCTTTTAGGAACCTTCAACATTACCC |
| 1080B-R11 | 63.40 | GTTCTTCTCCTTTGCGCCCCTACTTAACATCTTTCATCCTTTCCGCT |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgcttttaggaaccttcaacattacccttgatgcaaaaaacaggatcagtctgccagcg M L L G T F N I T L D A K N R I S L P A aagctgcgggctttctttgaaggtagcattgttatcaaccgtggctttgaaaactgcttg K L R A F F E G S I V I N R G F E N C L gaagtgcgtaaaccacaagacttccaaaagtactttgagcagttcaacagctttccctcc E V R K P Q D F Q K Y F E Q F N S F P S acccaaaaagacactagaacactcaagcgcttaatttttgccaacgctaactttgtggat T Q K D T R T L K R L I F A N A N F V D gtagatacagcgggacgggttttaattcccaacaatctgattaacgatgccaagctagac V D T A G R V L I P N N L I N D A K L D aaggaaattgttttaattggccagtttgaccacttagagatttgggacaagaagctgtat K E I V L I G Q F D H L E I W D K K L Y gaggactacctagccaactctgagtcgttggaaacggtagcggaaaggatgaaagatgtt E D Y L A N S E S L E T V A E R M K D V aagtaa K *
MLLGTFNITLDAKNRISLPAKLRAFFEGSIVINRGFENCLEVRKPQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVD VDTAGRVLIPNNLINDAKLDKEIVLIGQFDHLEIWDKKLYEDYLANSESLETVAERMKDVK
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 141
Molecular weight: 16334.7
Theoretical pI: 5.88
Amino acid composition:
Ala (A) 9 6.4%
Arg (R) 8 5.7%
Asn (N) 11 7.8%
Asp (D) 11 7.8%
Cys (C) 1 0.7%
Gln (Q) 5 3.5%
Glu (E) 10 7.1%
Gly (G) 5 3.5%
His (H) 1 0.7%
Ile (I) 10 7.1%
Leu (L) 16 11.3%
Lys (K) 12 8.5%
Met (M) 2 1.4%
Phe (F) 11 7.8%
Pro (P) 4 2.8%
Ser (S) 6 4.3%
Thr (T) 7 5.0%
Trp (W) 1 0.7%
Tyr (Y) 3 2.1%
Val (V) 8 5.7%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 21
Total number of positively charged residues (Arg + Lys): 20
Atomic composition:
Carbon C 738
Hydrogen H 1164
Nitrogen N 196
Oxygen O 216
Sulfur S 3
Formula: C738H1164N196O216S3
Total number of atoms: 2317
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 9750 9800 9695 9530 9200
Abs 0.1% (=1 g/l) 0.597 0.600 0.594 0.583 0.563
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 9750 9800 9695 9530 9200
Abs 0.1% (=1 g/l) 0.597 0.600 0.594 0.583 0.563
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 21.06
This classifies the protein as stable.
Aliphatic index: 94.75
Grand average of hydropathicity (GRAVY): -0.324