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This gene has the annotation "phosphotransacetylase".
The target was selected as part of JMC's third set.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | jmc | 2002-11-07 |
| Cloned | Done | r_kim | 2003-01-26 |
| Expression tested | Done | r_kim | 2003-01-26 |
| Solubility tested | S | r_kim | 2003-01-26 |
| Purified | Done | dhshin | 2003-07-14 |
| Crystallized | Done | dhshin | 2003-07-14 |
| Diffraction quality crystals | Done | dhshin | 2003-07-14 |
| Native diffraction data | Done | dhshin | 2003-07-14 |
| Phasing diffraction data | Done | dhshin | 2004-03-16 |
| Traceable map | Done | dhshin | 2004-03-16 |
| Crystal structure | Done | dhshin | 2004-09-13 |
| In PDB | 1TD9 1XCO | dhshin | 2004-09-13 |
| Suggested work stop | 0 0 20202 20202 20202 20202 20202 20202 21464 21464 21464 21464 21464 21464 22551 22551 22551 22551 22551 22551 22551 22551 23332 23332 23332 23332 23332 23332 53758 53758 53758 53758 | dallen | 2004-03-15 |
| Override suggest work stop | Traceable map obtained | dhshin | 2004-03-16 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP296 / MPN546 | -37.52 | 16.26 | 89.47 |
| MP413 / MPN428 | -76.70 | 40.50 | 99.38 |
GTGGCAGATTTATTTTCAACAGTGCAAGAAAAAGTAGCTGGAAAAGACGTTAAAATTGTATTTCCTGAAGGCTTAGACGA GCGTATTTTAGAAGCGGTCAGCAAGCTTGCAGGAAACAAAGTGCTGAATCCGATTGTGATCGGCAATGAAAATGAGATCC AAGCAAAAGCAAAAGAATTGAACCTTACGCTGGGCGGCGTTAAGATTTATGATCCTCATACATATGAAGGCATGGAAGAC CTTGTACAAGCATTCGTAGAACGCCGCAAAGGCAAAGCGACTGAAGAACAGGCTCGTAAAGCATTATTAGACGAGAACTA CTTCGGTACAATGCTGGTGTATAAAGGACTTGCAGACGGACTTGTAAGCGGAGCTGCTCACTCAACTGCTGACACTGTCC GCCCGGCTCTTCAAATCATCAAAACAAAAGAAGGCGTGAAAAAGACTTCAGGCGTGTTCATCATGGCTCGCGGAGAAGAG CAATACGTATTCGCAGATTGCGCGATCAACATTGCACCTGACAGCCAAGATCTTGCCGAGATTGCGATCGAAAGTGCCAA TACGGCAAAAATGTTCGACATTGAGCCTCGCGTGGCAATGCTCAGCTTCTCTACAAAAGGCTCAGCAAAATCTGATGAAA CAGAAAAAGTAGCGGATGCAGTGAAAATCGCGAAAGAAAAAGCGCCTGAACTGACACTTGACGGCGAATTCCAATTTGAT GCTGCATTTGTTCCATCTGTAGCTGAGAAAAAAGCGCCGGATTCCGAGATCAAAGGGGACGCTAACGTATTCGTATTCCC AAGTCTTGAAGCAGGAAACATCGGCTATAAAATCGCTCAGCGTTTGGGCAACTTTGAAGCGGTAGGACCAATCCTGCAAG GTTTAAATATGCCTGTAAACGACCTTTCAAGAGGATGTAACGCTGAAGATGTTTACAATCTCGCATTAATTACAGCGGCG CAAGCACTGTAA
(324 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU15.4( 5) UCU9.3( 3) UAU12.3( 4) UGU3.1( 1) UUC27.8( 9) UCC3.1( 1) UAC9.3( 3) UGC3.1( 1) UUA21.6( 7) UCA15.4( 5) UAA3.1( 1) UGA0.0( 0) UUG6.2( 2) UCG0.0( 0) UAG0.0( 0) UGG0.0( 0) CUU30.9( 10) CCU18.5( 6) CAU3.1( 1) CGU9.3( 3) CUC6.2( 2) CCC0.0( 0) CAC3.1( 1) CGC15.4( 5) CUA0.0( 0) CCA9.3( 3) CAA27.8( 9) CGA0.0( 0) CUG18.5( 6) CCG9.3( 3) CAG6.2( 2) CGG0.0( 0) AUU24.7( 8) ACU12.3( 4) AAU18.5( 6) AGU6.2( 2) AUC37.0( 12) ACC0.0( 0) AAC27.8( 9) AGC12.3( 4) AUA0.0( 0) ACA24.7( 8) AAA74.1( 24) AGA3.1( 1) AUG18.5( 6) ACG6.2( 2) AAG9.3( 3) AGG0.0( 0) GUU12.3( 4) GCU37.0( 12) GAU27.8( 9) GGU6.2( 2) GUC6.2( 2) GCC6.2( 2) GAC34.0( 11) GGC37.0( 12) GUA37.0( 12) GCA52.5( 17) GAA64.8( 21) GGA27.8( 9) GUG27.8( 9) GCG34.0( 11) GAG24.7( 8) GGG3.1( 1)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
gtggcagatttattttcaacagtgcaagaaaaagtagctggaaaagacgttaaaattgta
tttcctgaaggcttagacgagcgtattttagaagcggtcagcaagcttgcaggaaacaaa
gtgctgaatccgattgtgatcggcaatgaaaatgagatccaagcaaaagcaaaagaattg
aaccttacgctgggcggcgttaagatttatgatcctcataCATATGaaggcatggaagac
1
cttgtacaagcattcgtagaacgccgcaaaggcaaagcgactgaagaacaggctcgtaaa
gcattattagacgagaactacttcggtacaatgctggtgtataaaggacttgcagacgga
cttgtaagcggagctgctcactcaactgctgacactgtccgcccggctcttcaaatcatc
aaaacaaaagaaggcgtgaaaaagacttcaggcgtgttcatcatggctcgcggagaagag
caatacgtattcgcagattgcgcgatcaacattgcacctgacagccaAGATCTtgccgag
4
attgcgatcgaaagtgccaatacggcaaaaatgttcgacattgagcctcgcgtggcaatg
ctcagcttctctacaaaaggctcagcaaaatctgatgaaacagaaaaagtagcggatgca
gtgaaaatcgcgaaagaaaaagcgcctgaactgacacttgacggcgaattccaatttgat
gctgcatttgttccatctgtagctgagaaaaaagcgccggattccgagatcaaaggggac
gctaacgtattcgtattcccaagtcttgaagcaggaaacatcggctataaaatcgctcag
cgtttgggcaactttgaagcggtaggaccaatcctgcaaggtttaaatatgcctgtaaac
gacctttcaagaggatgtaacgctgaagatgtttacaatctcgcattaattacagcggcg
caagcactgtaa
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 |
|---|---|---|
| 1347B-R1 | 62.40 | CATATGGCAGATTTATTTTCAACAGTGC |
| 1347B-R2 | 60.50 | GGATCCTTACAGTGCTTGCGCCG |
| 1347B-R10 | 64.70 | GGCGGTGGTGGCGGCATGGCAGATTTATTTTCAACAGTGCA |
| 1347B-R11 | 63.30 | GTTCTTCTCCTTTGCGCCCCTACAGTGCTTGCGCCGC |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
gtggcagatttattttcaacagtgcaagaaaaagtagctggaaaagacgttaaaattgta V A D L F S T V Q E K V A G K D V K I V tttcctgaaggcttagacgagcgtattttagaagcggtcagcaagcttgcaggaaacaaa F P E G L D E R I L E A V S K L A G N K gtgctgaatccgattgtgatcggcaatgaaaatgagatccaagcaaaagcaaaagaattg V L N P I V I G N E N E I Q A K A K E L aaccttacgctgggcggcgttaagatttatgatcctcatacatatgaaggcatggaagac N L T L G G V K I Y D P H T Y E G M E D cttgtacaagcattcgtagaacgccgcaaaggcaaagcgactgaagaacaggctcgtaaa L V Q A F V E R R K G K A T E E Q A R K gcattattagacgagaactacttcggtacaatgctggtgtataaaggacttgcagacgga A L L D E N Y F G T M L V Y K G L A D G cttgtaagcggagctgctcactcaactgctgacactgtccgcccggctcttcaaatcatc L V S G A A H S T A D T V R P A L Q I I aaaacaaaagaaggcgtgaaaaagacttcaggcgtgttcatcatggctcgcggagaagag K T K E G V K K T S G V F I M A R G E E caatacgtattcgcagattgcgcgatcaacattgcacctgacagccaagatcttgccgag Q Y V F A D C A I N I A P D S Q D L A E attgcgatcgaaagtgccaatacggcaaaaatgttcgacattgagcctcgcgtggcaatg I A I E S A N T A K M F D I E P R V A M ctcagcttctctacaaaaggctcagcaaaatctgatgaaacagaaaaagtagcggatgca L S F S T K G S A K S D E T E K V A D A gtgaaaatcgcgaaagaaaaagcgcctgaactgacacttgacggcgaattccaatttgat V K I A K E K A P E L T L D G E F Q F D gctgcatttgttccatctgtagctgagaaaaaagcgccggattccgagatcaaaggggac A A F V P S V A E K K A P D S E I K G D gctaacgtattcgtattcccaagtcttgaagcaggaaacatcggctataaaatcgctcag A N V F V F P S L E A G N I G Y K I A Q cgtttgggcaactttgaagcggtaggaccaatcctgcaaggtttaaatatgcctgtaaac R L G N F E A V G P I L Q G L N M P V N gacctttcaagaggatgtaacgctgaagatgtttacaatctcgcattaattacagcggcg D L S R G C N A E D V Y N L A L I T A A caagcactgtaa Q A L *
MADLFSTVQEKVAGKDVKIVFPEGLDERILEAVSKLAGNKVLNPIVIGNENEIQAKAKELNLTLGGVKIYDPHTYEGMED LVQAFVERRKGKATEEQARKALLDENYFGTMLVYKGLADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARGEE QYVFADCAINIAPDSQDLAEIAIESANTAKMFDIEPRVAMLSFSTKGSAKSDETEKVADAVKIAKEKAPELTLDGEFQFD AAFVPSVAEKKAPDSEIKGDANVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGLNMPVNDLSRGCNAEDVYNLALITAA QAL
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 323
Molecular weight: 34790.6
Theoretical pI: 4.84
Amino acid composition:
Ala (A) 42 13.0%
Arg (R) 9 2.8%
Asn (N) 15 4.6%
Asp (D) 20 6.2%
Cys (C) 2 0.6%
Gln (Q) 11 3.4%
Glu (E) 29 9.0%
Gly (G) 24 7.4%
His (H) 2 0.6%
Ile (I) 20 6.2%
Leu (L) 27 8.4%
Lys (K) 27 8.4%
Met (M) 7 2.2%
Phe (F) 14 4.3%
Pro (P) 12 3.7%
Ser (S) 15 4.6%
Thr (T) 14 4.3%
Trp (W) 0 0.0%
Tyr (Y) 7 2.2%
Val (V) 26 8.0%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 49
Total number of positively charged residues (Arg + Lys): 36
Atomic composition:
Carbon C 1545
Hydrogen H 2481
Nitrogen N 407
Oxygen O 484
Sulfur S 9
Formula: C1545H2481N407O484S9
Total number of atoms: 4926
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 10295 9927 9535 9080 8520
Abs 0.1% (=1 g/l) 0.296 0.285 0.274 0.261 0.245
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 10150 9800 9415 8960 8400
Abs 0.1% (=1 g/l) 0.292 0.282 0.271 0.258 0.241
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 33.38
This classifies the protein as stable.
Aliphatic index: 93.10
Grand average of hydropathicity (GRAVY): -0.122