|
|
This gene has the annotation "conserved hypothetical protein".
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 | 2003-09-12 |
| Crystallized | Done | dhshin | 2003-09-12 |
| Diffraction quality crystals | Done | dhshin | 2004-01-27 |
| Native diffraction data | Done | dhshin | 2004-01-27 |
| Phasing diffraction data | Done | dhshin | 2004-01-27 |
| Traceable map | Done | dhshin | 2004-02-13 |
| Crystal structure | Done | dhshin | 2004-10-04 |
| In PDB | 1YT5 | dhshin | 2005-02-10 |
| Suggested work stop | 9402 9402 9402 11558 11558 11558 11834 11834 11834 11834 12057 12057 12057 12057 13225 13225 16927 16927 16927 16927 24001 24001 | dallen | 2004-02-10 |
| Override suggest work stop | Traceable map obtained | dhshin | 2004-02-13 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP566 / MPN267 | -47.22 | 21.12 | 97.29 |
ATGAAAATCGCCATTCTCTACAGAGAAGAGCGGGAAAAAGAGGGAGAGTTCTTGAAAGAAAAGATTTCAAAAGAACACGA AGTAATCGAGTTCGGTGAAGCGAACGCTCCAGGAAGGGTTACGGCAGATTTGATAGTGGTGGTTGGAGGAGACGGAACCG TGCTCAAGGCAGCGAAAAAAGCGGCCGATGGAACACCGATGGTGGGCTTCAAGGCAGGCAGACTGGGGTTCCTCACATCC TACACCCTCGATGAGATAGATCGATTTCTCGAGGATCTCAGAAACTGGAACTTCCGGGAAGAAACAAGATGGTTCATACA GATCGAAAGTGAACTCGGAAACCATCTCGCCCTGAACGATGTCACCCTCGAACGTGACCTGAGTGGAAAGATGGTCGAAA TAGAGGTCGAGGTGGAGCACCACTCTTCCATGTGGTTCTTCGCAGACGGAGTGGTGATTTCCACACCGACAGGTTCCACG GCTTATTCTCTTTCCATAGGAGGTCCCATAATATTCCCGGAATGCGAGGTGCTGGAGATCTCTCCCATTGCACCACAATT CTTTCTCACCCGAAGCGTTGTGATACCCTCGAATTTCAAAGTGGTGGTTGAATCCCAGAGAGATATAAACATGCTGGTGG ATGGAGTCCTGACGGGAAAAACAAAACGAATCGAAGTAAAGAAATCCAGAAGATACGTTAGAATTCTGAGACCTCCTGAG TACGATTACGTGACGGTGATAAGAGACAAACTCGGTTACGGGAGGCGTATCGAGTGA
(259 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU7.7( 2) UCU11.6( 3) UAU3.9( 1) UGU0.0( 0) UUC42.5( 11) UCC27.0( 7) UAC23.2( 6) UGC3.9( 1) UUA0.0( 0) UCA3.9( 1) UAA0.0( 0) UGA3.9( 1) UUG7.7( 2) UCG3.9( 1) UAG0.0( 0) UGG11.6( 3) CUU3.9( 1) CCU7.7( 2) CAU3.9( 1) CGU7.7( 2) CUC42.5( 11) CCC11.6( 3) CAC11.6( 3) CGC0.0( 0) CUA0.0( 0) CCA7.7( 2) CAA3.9( 1) CGA11.6( 3) CUG27.0( 7) CCG11.6( 3) CAG7.7( 2) CGG7.7( 2) AUU19.3( 5) ACU0.0( 0) AAU3.9( 1) AGU7.7( 2) AUC23.2( 6) ACC15.4( 4) AAC23.2( 6) AGC3.9( 1) AUA38.6( 10) ACA23.2( 6) AAA42.5( 11) AGA38.6( 10) AUG19.3( 5) ACG15.4( 4) AAG19.3( 5) AGG7.7( 2) GUU19.3( 5) GCU7.7( 2) GAU34.7( 9) GGU15.4( 4) GUC15.4( 4) GCC11.6( 3) GAC15.4( 4) GGC7.7( 2) GUA7.7( 2) GCA19.3( 5) GAA57.9( 15) GGA46.3( 12) GUG54.1( 14) GCG11.6( 3) GAG50.2( 13) GGG7.7( 2)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
atgaaaatcgccattctctacagagaagagcgggaaaaagagggagagttcttgaaagaa
aagatttcaaaagaacacgaagtaatcgagttcggtgaagcgaacgctccaggaagggtt
acggcagatttgatagtggtggttggaggagacggaaccgtgctcaaggcagcgaaaaaa
gcggccgatggaacaccgatggtgggcttcaaggcaggcagactggggttcctcacatcc
tacaccctcgatgagatagatcgatttctcgaggatctcagaaactggaacttccgggaa
gaaacaagatggttcatacagatcgaaagtgaactcggaaaccatctcgccctgaacgat
gtcaccctcgaacgtgacctgagtggaaagatggtcgaaatagaggtcgaggtggagcac
cactcttccatgtggttcttcgcagacggagtggtgatttccacaccgacaggttccacg
gcttattctctttccataggaggtcccataatattcccggaatgcgaggtgctggAGATC
4
Tctcccattgcaccacaattctttctcacccgaagcgttgtgataccctcgaatttcaaa
gtggtggttgaatcccagagagatataaacatgctggtggatggagtcctgacgggaaaa
acaaaacgaatcgaagtaaagaaatccagaagatacgttagaattctgagacctcctgag
tacgattacgtgacggtgataagagacaaactcggttacgggaggcgtatcgagtga
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 |
|---|---|---|
| 1316B-R1 | 61.20 | CATATGAAAATCGCCATTCTCTACAGA |
| 1316B-R2 | 60.40 | GGATCCTTACTCGATACGCCTCCCGT |
| 1316B-R10 | 63.50 | GGCGGTGGTGGCGGCATGAAAATCGCCATTCTCTACAGAGA |
| 1316B-R11 | 65.60 | GTTCTTCTCCTTTGCGCCCCTACTCGATACGCCTCCCGTAACC |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgaaaatcgccattctctacagagaagagcgggaaaaagagggagagttcttgaaagaa M K I A I L Y R E E R E K E G E F L K E aagatttcaaaagaacacgaagtaatcgagttcggtgaagcgaacgctccaggaagggtt K I S K E H E V I E F G E A N A P G R V acggcagatttgatagtggtggttggaggagacggaaccgtgctcaaggcagcgaaaaaa T A D L I V V V G G D G T V L K A A K K gcggccgatggaacaccgatggtgggcttcaaggcaggcagactggggttcctcacatcc A A D G T P M V G F K A G R L G F L T S tacaccctcgatgagatagatcgatttctcgaggatctcagaaactggaacttccgggaa Y T L D E I D R F L E D L R N W N F R E gaaacaagatggttcatacagatcgaaagtgaactcggaaaccatctcgccctgaacgat E T R W F I Q I E S E L G N H L A L N D gtcaccctcgaacgtgacctgagtggaaagatggtcgaaatagaggtcgaggtggagcac V T L E R D L S G K M V E I E V E V E H cactcttccatgtggttcttcgcagacggagtggtgatttccacaccgacaggttccacg H S S M W F F A D G V V I S T P T G S T gcttattctctttccataggaggtcccataatattcccggaatgcgaggtgctggagatc A Y S L S I G G P I I F P E C E V L E I tctcccattgcaccacaattctttctcacccgaagcgttgtgataccctcgaatttcaaa S P I A P Q F F L T R S V V I P S N F K gtggtggttgaatcccagagagatataaacatgctggtggatggagtcctgacgggaaaa V V V E S Q R D I N M L V D G V L T G K acaaaacgaatcgaagtaaagaaatccagaagatacgttagaattctgagacctcctgag T K R I E V K K S R R Y V R I L R P P E tacgattacgtgacggtgataagagacaaactcggttacgggaggcgtatcgagtga Y D Y V T V I R D K L G Y G R R I E *
MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTS YTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGST AYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPE YDYVTVIRDKLGYGRRIE
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 258
Molecular weight: 29241.5
Theoretical pI: 5.48
Amino acid composition:
Ala (A) 13 5.0%
Arg (R) 19 7.4%
Asn (N) 7 2.7%
Asp (D) 13 5.0%
Cys (C) 1 0.4%
Gln (Q) 3 1.2%
Glu (E) 28 10.9%
Gly (G) 20 7.8%
His (H) 4 1.6%
Ile (I) 21 8.1%
Leu (L) 21 8.1%
Lys (K) 16 6.2%
Met (M) 5 1.9%
Phe (F) 13 5.0%
Pro (P) 10 3.9%
Ser (S) 15 5.8%
Thr (T) 14 5.4%
Trp (W) 3 1.2%
Tyr (Y) 7 2.7%
Val (V) 25 9.7%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 41
Total number of positively charged residues (Arg + Lys): 35
Atomic composition:
Carbon C 1317
Hydrogen H 2092
Nitrogen N 352
Oxygen O 387
Sulfur S 6
Formula: C1317H2092N352O387S6
Total number of atoms: 4154
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 26350 26600 26395 26030 25200
Abs 0.1% (=1 g/l) 0.901 0.910 0.903 0.890 0.862
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 26350 26600 26395 26030 25200
Abs 0.1% (=1 g/l) 0.901 0.910 0.903 0.890 0.862
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 40.07
This classifies the protein as unstable.
Aliphatic index: 96.63
Grand average of hydropathicity (GRAVY): -0.177