|
|
This gene has the annotation "hypothetical protein".
The target was selected as part of JMC's second set.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | jmc | 2002-02-25 |
| Cloned | Done | blgold | 2002-08-28 |
| Expression tested | Done | r_kim | 2002-12-30 |
| Solubility tested | S | r_kim | 2003-12-01 |
| Purified | Done | dhshin | 2004-03-12 |
| Crystallized | Done | dhshin | 2004-03-12 |
| Diffraction quality crystals | Done | dhshin | 2004-06-14 |
| Native diffraction data | Done | dhshin | 2004-06-14 |
| Phasing diffraction data | Done | dhshin | 2004-08-25 |
| Traceable map | Done | dhshin | 2004-08-25 |
| Crystal structure | Done | dhshin | 2004-10-04 |
| In PDB | 2HEK | dhshin | 2006-08-16 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP165 / MPN677 | -58.10 | 27.19 | 86.25 |
TTGATTAAGGAGTTTTCAGATCCCCTTTACGGTTTCGTAAGAGTAGGGGAGGCGGGTTTAAGGCTCATAGATTCCTTTCC TTTTCAGAGGCTCAGGTACGTAAAACAGCTCGGACTCGCTTACTTAGTATTTCCATCCGCCCAGCACACCCGTTTTGAGC ACTCACTCGGGGTTTACCACATAACGGAGAGGATATGCGAAAGCCTGAAAGTAAAGGAAAAGGAACTCGTTAAACTCGCA GGACTCCTTCACGATCTCGGACATCCACCCTTTTCCCACACCACGGAAGTGCTACTTCCTCGGGAAAGAAGCCACGAGGA CTTTACGGAAAGGGTAATAAAAGAAACGGAGATTTACGAAATATTGAAGCAGGACTACTCCCACGAAGATATAGAAAGAC TCGTGAGGATTACCCTTGGGAAACCTGAGGACGAGGAAGAAAAACTCCTCAGCGAGATAATCACCGGGGAGTTCGGCTCC GACAGGATGGACTACCTCAGGAGGGACGCCTACTTTTGCGGGGTATCTTACGGCTTTTTTGATTACGACAGACTAATAAG CACTCTCAGAGTCTATGAGAACAAAGTAGTGGTAGATGAAAGTGGACTGAGAGCCTTAGAGAACTTCCTTATCTCCCGTT ACTTTATGTATGTTCAGGTTTACTTCCACAAGGTCGTGAGGATACTTAGCATACACCTCGTTGAGTTCCTGAAGAAGCTC ATCTCCCAGGAGGACTTTACGGATATAAACAACTTTCTAAGGTTAAACGACGCTTTTGTAATATCCGAACTCTTCAAAAG GAAAGCATTCAGAGAGGATTTTGAGAGGATATTCCAGAGGAAGCACTTCAAAACGCTCCTTTCCACGGAGAATTACGAGA AATTCTCAGAAACGAAGGAAAGACTTTTAGAAAAATTCCCGCAGGAAAAAGTGAGATTTGACGAGGTGGAGAAAGAAGTT TACGGGGGGAATATATACGTTCTCAGTTCAGAAGGACTAAAGAAAGCTCACGAACTCTCCCCGCTCATTGCTTCCCTCAA ACCCATAAAACTTTATAGAATTTACGTAGACAGGCAGTTATGGGAGAAAGCCCGTTCAGAATTAAAACTCTCTTGA
(372 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU43.0( 16) UCU5.4( 2) UAU8.1( 3) UGU0.0( 0) UUC29.6( 11) UCC29.6( 11) UAC43.0( 16) UGC5.4( 2) UUA18.8( 7) UCA13.4( 5) UAA0.0( 0) UGA2.7( 1) UUG5.4( 2) UCG0.0( 0) UAG0.0( 0) UGG2.7( 1) CUU24.2( 9) CCU8.1( 3) CAU2.7( 1) CGU8.1( 3) CUC61.8( 23) CCC8.1( 3) CAC29.6( 11) CGC0.0( 0) CUA10.8( 4) CCA5.4( 2) CAA0.0( 0) CGA0.0( 0) CUG8.1( 3) CCG5.4( 2) CAG24.2( 9) CGG2.7( 1) AUU13.4( 5) ACU2.7( 1) AAU5.4( 2) AGU5.4( 2) AUC8.1( 3) ACC10.8( 4) AAC13.4( 5) AGC13.4( 5) AUA40.3( 15) ACA0.0( 0) AAA51.1( 19) AGA26.9( 10) AUG5.4( 2) ACG21.5( 8) AAG26.9( 10) AGG40.3( 15) GUU18.8( 7) GCU10.8( 4) GAU21.5( 8) GGU5.4( 2) GUC5.4( 2) GCC10.8( 4) GAC29.6( 11) GGC5.4( 2) GUA29.6( 11) GCA5.4( 2) GAA59.1( 22) GGA13.4( 5) GUG16.1( 6) GCG2.7( 1) GAG56.5( 21) GGG18.8( 7)
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 |
|---|---|---|
| 1275B-R1 | 61.70 | CATATGATTAAGGAGTTTTCAGATCCCC |
| 1275B-R2 | 62.20 | GGATCCTTAAGAGAGTTTTAATTCTGAACGGGC |
| 1275B-R10 | 63.40 | GGCGGTGGTGGCGGCATGATTAAGGAGTTTTCAGATCCCCTT |
| 1275B-R11 | 63.80 | GTTCTTCTCCTTTGCGCCCCTAAGAGAGTTTTAATTCTGAACGGGCTT |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
ttgattaaggagttttcagatcccctttacggtttcgtaagagtaggggaggcgggttta L I K E F S D P L Y G F V R V G E A G L aggctcatagattcctttccttttcagaggctcaggtacgtaaaacagctcggactcgct R L I D S F P F Q R L R Y V K Q L G L A tacttagtatttccatccgcccagcacacccgttttgagcactcactcggggtttaccac Y L V F P S A Q H T R F E H S L G V Y H ataacggagaggatatgcgaaagcctgaaagtaaaggaaaaggaactcgttaaactcgca I T E R I C E S L K V K E K E L V K L A ggactccttcacgatctcggacatccacccttttcccacaccacggaagtgctacttcct G L L H D L G H P P F S H T T E V L L P cgggaaagaagccacgaggactttacggaaagggtaataaaagaaacggagatttacgaa R E R S H E D F T E R V I K E T E I Y E atattgaagcaggactactcccacgaagatatagaaagactcgtgaggattacccttggg I L K Q D Y S H E D I E R L V R I T L G aaacctgaggacgaggaagaaaaactcctcagcgagataatcaccggggagttcggctcc K P E D E E E K L L S E I I T G E F G S gacaggatggactacctcaggagggacgcctacttttgcggggtatcttacggctttttt D R M D Y L R R D A Y F C G V S Y G F F gattacgacagactaataagcactctcagagtctatgagaacaaagtagtggtagatgaa D Y D R L I S T L R V Y E N K V V V D E agtggactgagagccttagagaacttccttatctcccgttactttatgtatgttcaggtt S G L R A L E N F L I S R Y F M Y V Q V tacttccacaaggtcgtgaggatacttagcatacacctcgttgagttcctgaagaagctc Y F H K V V R I L S I H L V E F L K K L atctcccaggaggactttacggatataaacaactttctaaggttaaacgacgcttttgta I S Q E D F T D I N N F L R L N D A F V atatccgaactcttcaaaaggaaagcattcagagaggattttgagaggatattccagagg I S E L F K R K A F R E D F E R I F Q R aagcacttcaaaacgctcctttccacggagaattacgagaaattctcagaaacgaaggaa K H F K T L L S T E N Y E K F S E T K E agacttttagaaaaattcccgcaggaaaaagtgagatttgacgaggtggagaaagaagtt R L L E K F P Q E K V R F D E V E K E V tacggggggaatatatacgttctcagttcagaaggactaaagaaagctcacgaactctcc Y G G N I Y V L S S E G L K K A H E L S ccgctcattgcttccctcaaacccataaaactttatagaatttacgtagacaggcagtta P L I A S L K P I K L Y R I Y V D R Q L tgggagaaagcccgttcagaattaaaactctcttga W E K A R S E L K L S *
MIKEFSDPLYGFVRVGEAGLRLIDSFPFQRLRYVKQLGLAYLVFPSAQHTRFEHSLGVYHITERICESLKVKEKELVKLA GLLHDLGHPPFSHTTEVLLPRERSHEDFTERVIKETEIYEILKQDYSHEDIERLVRITLGKPEDEEEKLLSEIITGEFGS DRMDYLRRDAYFCGVSYGFFDYDRLISTLRVYENKVVVDESGLRALENFLISRYFMYVQVYFHKVVRILSIHLVEFLKKL ISQEDFTDINNFLRLNDAFVISELFKRKAFREDFERIFQRKHFKTLLSTENYEKFSETKERLLEKFPQEKVRFDEVEKEV YGGNIYVLSSEGLKKAHELSPLIASLKPIKLYRIYVDRQLWEKARSELKLS
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 371
Molecular weight: 44116.7
Theoretical pI: 6.35
Amino acid composition:
Ala (A) 11 3.0%
Arg (R) 29 7.8%
Asn (N) 7 1.9%
Asp (D) 19 5.1%
Cys (C) 2 0.5%
Gln (Q) 9 2.4%
Glu (E) 43 11.6%
Gly (G) 16 4.3%
His (H) 12 3.2%
Ile (I) 23 6.2%
Leu (L) 47 12.7%
Lys (K) 29 7.8%
Met (M) 3 0.8%
Phe (F) 27 7.3%
Pro (P) 10 2.7%
Ser (S) 25 6.7%
Thr (T) 13 3.5%
Trp (W) 1 0.3%
Tyr (Y) 19 5.1%
Val (V) 26 7.0%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 62
Total number of positively charged residues (Arg + Lys): 58
Atomic composition:
Carbon C 2022
Hydrogen H 3146
Nitrogen N 528
Oxygen O 569
Sulfur S 5
Formula: C2022H3146N528O569S5
Total number of atoms: 6270
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 33095 32327 31335 30130 28520
Abs 0.1% (=1 g/l) 0.750 0.733 0.710 0.683 0.646
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 32950 32200 31215 30010 28400
Abs 0.1% (=1 g/l) 0.747 0.730 0.708 0.680 0.644
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 36.92
This classifies the protein as stable.
Aliphatic index: 96.87
Grand average of hydropathicity (GRAVY): -0.363