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This gene has the annotation "putative 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 | 2003-02-11 |
| Expression tested | Done | r_kim | 2003-02-11 |
| Solubility tested | S | r_kim | 2003-02-11 |
| Purified | Done | dhshin | 2003-05-28 |
| Crystallized | Done | dhshin | 2003-05-28 |
| Diffraction quality crystals | Done | dhshin | 2003-05-28 |
| Native diffraction data | Done | dhshin | 2003-07-07 |
| Phasing diffraction data | Done | dhshin | 2003-07-07 |
| Traceable map | Done | dhshin | 2003-07-07 |
| Crystal structure | Done | dhshin | 2003-08-29 |
| In PDB | 1R5J | dhshin | 2003-12-15 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP296 / MPN546 | -37.30 | 17.18 | 87.92 |
| MP413 / MPN428 | -80.00 | 40.92 | 98.19 |
ATGAGTATTCGTAGTTTATTCGGTGGTTTAAGAGAAAAAATTCTTGGTAAAAACATGAAGATTGTTTTCCCAGAAGGTAA TGATGAGCGCGTCGTCCGTGCAGCTGCTCGTTTGAAATTTGAAGGACTCTTAGAACCGATTATCCTTGGACAGTCAGAAG AGGTACGCAACCTTTTGACAAAATTAGGTTTCGCTGATCAAGACTATACTATCATTAATCCAAATGAATATGCGGATTTT GACAAAATGAAAGAAGCTTTTGTTGAGGTCCGTAAAGGAAAAGCAACGCTTGAAGATGCAGATAAAATGCTTCGTGATGT TAATTACTTTGGTGTTATGTTGGTTAAAATGGGATTAGCAGATGGAATGGTATCAGGGGCTATTCATTCAACAGCTGACA CTGTTCGTCCAGCTCTTCAAATCATCAAAACTAAACCAGGTATCTCAAGAACTTCAGGTGTCTTCTTGATGAACCGCGAA AATACGAGCGAGCGTTACGTGTTTGCTGATTGTGCTATCAATATTGACCCAACAGCACAAGAATTGGCAGAAATCGCTGT TAACACAGCTGAAACAGCTAAAATCTTTGATATTGATCCTAAAATTGCTATGTTAAGCTTCTCAACAAAAGGTTCTGGTA AAGCGCCTCAAGTTGATAAGGTAAGAGAAGCAACAGAAATTGCTACAGGGTTGAACCCTGATTTGGCACTTGATGGCGAG TTGCAATTTGATGCAGCCTTTGTTCCTGAAACAGCGGCTATCAAAGCACCAGATTCAGCGGTTGCTGGTCAAGCTAATAC TTTCGTTTTCCCTGACTTGCAGTCTGGAAATATTGGTTACAAAATTGCACAACGTTTAGGAATGTTTGATGCTATTGGAC CAATCTTACAAGGATTGAACAAACCTGTTAATGATTTATCTCGTGGCTCAAGCGCTGAAGATATTTACAAACTAGCCATT ATTACAGCAGCACAAGCTATTGAAAGCCAAGGGTAA
(332 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU27.1( 9) UCU9.0( 3) UAU6.0( 2) UGU3.0( 1) UUC21.1( 7) UCC0.0( 0) UAC12.0( 4) UGC0.0( 0) UUA27.1( 9) UCA24.1( 8) UAA3.0( 1) UGA0.0( 0) UUG30.1( 10) UCG0.0( 0) UAG0.0( 0) UGG0.0( 0) CUU21.1( 7) CCU18.1( 6) CAU3.0( 1) CGU27.1( 9) CUC3.0( 1) CCC0.0( 0) CAC0.0( 0) CGC9.0( 3) CUA3.0( 1) CCA21.1( 7) CAA30.1( 10) CGA0.0( 0) CUG0.0( 0) CCG3.0( 1) CAG6.0( 2) CGG0.0( 0) AUU51.2( 17) ACU15.1( 5) AAU27.1( 9) AGU6.0( 2) AUC30.1( 10) ACC0.0( 0) AAC18.1( 6) AGC12.0( 4) AUA0.0( 0) ACA30.1( 10) AAA60.2( 20) AGA9.0( 3) AUG30.1( 10) ACG6.0( 2) AAG6.0( 2) AGG0.0( 0) GUU36.1( 12) GCU60.2( 20) GAU54.2( 18) GGU36.1( 12) GUC12.0( 4) GCC6.0( 2) GAC15.1( 5) GGC6.0( 2) GUA9.0( 3) GCA39.2( 13) GAA51.2( 17) GGA27.1( 9) GUG3.0( 1) GCG12.0( 4) GAG15.1( 5) GGG9.0( 3)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
atgagtattcgtagtttattcggtggtttaagagaaaaaattcttggtaaaaacatgaag
attgttttcccagaaggtaatgatgagcgcgtcgtccgtgcagctgctcgtttgaaattt
gaaggactcttagaaccgattatccttggacagtcagaagaggtacgcaaccttttgaca
aaattaggtttcgcTGATCAagactatactatcattaatccaaatgaatatgcggatttt
3
gacaaaatgaaagaagcttttgttgaggtccgtaaaggaaaagcaacgcttgaagatgca
gataaaatgcttcgtgatgttaattactttggtgttatgttggttaaaatgggattagca
gatggaatggtatcaggggctattcattcaacagctgacactgttcgtccagctcttcaa
atcatcaaaactaaaccaggtatctcaagaacttcaggtgtcttcttgatgaaccgcgaa
aatacgagcgagcgttacgtgtttgctgattgtgctatcaatattgacccaacagcacaa
gaattggcagaaatcgctgttaacacagctgaaacagctaaaatctttgatattgatcct
aaaattgctatgttaagcttctcaacaaaaggttctggtaaagcgcctcaagttgataag
gtaagagaagcaacagaaattgctacagggttgaaccctgatttggcacttgatggcgag
ttgcaatttgatgcagcctttgttcctgaaacagcggctatcaaagcaccagattcagcg
gttgctggtcaagctaatactttcgttttccctgacttgcagtctggaaatattggttac
aaaattgcacaacgtttaggaatgtttgatgctattggaccaatcttacaaggattgaac
aaacctgttaatgatttatctcgtggctcaagcgctgaagatatttacaaactagccatt
attacagcagcacaagctattgaaagccaagggtaa
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 |
|---|---|---|
| 1324B-R1 | 60.70 | CATATGAGTATTCGTAGTTTATTCGGTGG |
| 1324B-R2 | 60.30 | GGATCCTTACCCTTGGCTTTCAATAGCTT |
| 1324B-R10 | 63.20 | GGCGGTGGTGGCGGCATGAGTATTCGTAGTTTATTCGGTGGTTT |
| 1324B-R11 | 64.50 | GTTCTTCTCCTTTGCGCCCCTACCCTTGGCTTTCAATAGCTTGTG |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgagtattcgtagtttattcggtggtttaagagaaaaaattcttggtaaaaacatgaag M S I R S L F G G L R E K I L G K N M K attgttttcccagaaggtaatgatgagcgcgtcgtccgtgcagctgctcgtttgaaattt I V F P E G N D E R V V R A A A R L K F gaaggactcttagaaccgattatccttggacagtcagaagaggtacgcaaccttttgaca E G L L E P I I L G Q S E E V R N L L T aaattaggtttcgctgatcaagactatactatcattaatccaaatgaatatgcggatttt K L G F A D Q D Y T I I N P N E Y A D F gacaaaatgaaagaagcttttgttgaggtccgtaaaggaaaagcaacgcttgaagatgca D K M K E A F V E V R K G K A T L E D A gataaaatgcttcgtgatgttaattactttggtgttatgttggttaaaatgggattagca D K M L R D V N Y F G V M L V K M G L A gatggaatggtatcaggggctattcattcaacagctgacactgttcgtccagctcttcaa D G M V S G A I H S T A D T V R P A L Q atcatcaaaactaaaccaggtatctcaagaacttcaggtgtcttcttgatgaaccgcgaa I I K T K P G I S R T S G V F L M N R E aatacgagcgagcgttacgtgtttgctgattgtgctatcaatattgacccaacagcacaa N T S E R Y V F A D C A I N I D P T A Q gaattggcagaaatcgctgttaacacagctgaaacagctaaaatctttgatattgatcct E L A E I A V N T A E T A K I F D I D P aaaattgctatgttaagcttctcaacaaaaggttctggtaaagcgcctcaagttgataag K I A M L S F S T K G S G K A P Q V D K gtaagagaagcaacagaaattgctacagggttgaaccctgatttggcacttgatggcgag V R E A T E I A T G L N P D L A L D G E ttgcaatttgatgcagcctttgttcctgaaacagcggctatcaaagcaccagattcagcg L Q F D A A F V P E T A A I K A P D S A gttgctggtcaagctaatactttcgttttccctgacttgcagtctggaaatattggttac V A G Q A N T F V F P D L Q S G N I G Y aaaattgcacaacgtttaggaatgtttgatgctattggaccaatcttacaaggattgaac K I A Q R L G M F D A I G P I L Q G L N aaacctgttaatgatttatctcgtggctcaagcgctgaagatatttacaaactagccatt K P V N D L S R G S S A E D I Y K L A I attacagcagcacaagctattgaaagccaagggtaa I T A A Q A I E S Q G *
MSIRSLFGGLREKILGKNMKIVFPEGNDERVVRAAARLKFEGLLEPIILGQSEEVRNLLTKLGFADQDYTIINPNEYADF DKMKEAFVEVRKGKATLEDADKMLRDVNYFGVMLVKMGLADGMVSGAIHSTADTVRPALQIIKTKPGISRTSGVFLMNRE NTSERYVFADCAINIDPTAQELAEIAVNTAETAKIFDIDPKIAMLSFSTKGSGKAPQVDKVREATEIATGLNPDLALDGE LQFDAAFVPETAAIKAPDSAVAGQANTFVFPDLQSGNIGYKIAQRLGMFDAIGPILQGLNKPVNDLSRGSSAEDIYKLAI ITAAQAIESQG
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 331
Molecular weight: 35824.0
Theoretical pI: 5.01
Amino acid composition:
Ala (A) 39 11.8%
Arg (R) 15 4.5%
Asn (N) 15 4.5%
Asp (D) 23 6.9%
Cys (C) 1 0.3%
Gln (Q) 12 3.6%
Glu (E) 22 6.6%
Gly (G) 26 7.9%
His (H) 1 0.3%
Ile (I) 27 8.2%
Leu (L) 28 8.5%
Lys (K) 22 6.6%
Met (M) 10 3.0%
Phe (F) 16 4.8%
Pro (P) 14 4.2%
Ser (S) 17 5.1%
Thr (T) 17 5.1%
Trp (W) 0 0.0%
Tyr (Y) 6 1.8%
Val (V) 20 6.0%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 45
Total number of positively charged residues (Arg + Lys): 37
Atomic composition:
Carbon C 1589
Hydrogen H 2561
Nitrogen N 427
Oxygen O 489
Sulfur S 11
Formula: C1589H2561N427O489S11
Total number of atoms: 5077
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 8700 8400 8070 7680 7200
Abs 0.1% (=1 g/l) 0.243 0.234 0.225 0.214 0.201
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 8700 8400 8070 7680 7200
Abs 0.1% (=1 g/l) 0.243 0.234 0.225 0.214 0.201
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 37.12
This classifies the protein as stable.
Aliphatic index: 94.11
Grand average of hydropathicity (GRAVY): -0.079