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This gene has the annotation "MG237 homolog, from M. genitalium".
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 | r_kim | 2003-06-10 |
| Expression tested | Done | r_kim | 2003-06-10 |
| Solubility tested | S | r_kim | 2003-06-10 |
| Purified | Done | r_kim | 2003-08-06 |
| Crystallized | Done | dhshin | 2003-12-02 |
| Diffraction quality crystals | Done | dhshin | 2004-04-22 |
| Native diffraction data | Done | dhshin | 2004-04-22 |
| Phasing diffraction data | Done | dhshin | 2004-04-22 |
| Traceable map | Done | dhshin | 2004-04-22 |
| Crystal structure | Done | dhshin | 2004-05-25 |
| In PDB | 1TD6 | dhshin | 2004-05-25 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP506 / MPN330 | -104.00 | 100.00 | 100.00 |
ATGATCAATAAGCCAAATCAGTTTGTCAACCACTTAAGTGCTTTAAAAAAACACTTTGCCTCTTATAAGGAGCTCCGTGA AGCGTTTAACGATTATCACAAGCATAACGGTGATGAGTTGACCACCTTCTTTTTGCACCAGTTTGATAAGGTGATGGAAC TAGTCAAGCAGAAGGACTTTAAAACTGCCCAGTCTCGCTGTGAGGAGGAATTAGCCGCCCCTTATCTACCAAAACCTTTA GTAAGCTTTTTCCAATCGCTACTCCAGCTCGTGAACCATGATTTATTGGAACAGCAAAACGCGGCCTTGGCTAGTTTACC CGCAGCCAAAATCATAGAGCTTGTTTTACAGGATTACCCCAATAAACTCAACATGATTCACTACCTTTTGCCCAAAACGA AGGCGTTTGTCAAACCACATTTGTTACAACGCTTACAGTTTGTGTTAACTGATTCGGAGTTGTTGGAATTAAAGCGCTTT TCCTTCTTTCAAGCACTCAACCAGATCCCGGGCTTTCAGGGTGAGCAAGTTGAGTACTTTAACAGTAAGCTCAAACAAAA GTTTACCTTGACCTTAGGGGAGTTTGAAATTGCCCAACAGCCAGATGCCAAAGCATACTTTGAGCAGTTAATTACCCAAA TCCAACAGCTCTTTTTAAAAGAGCCGGTTAACGCTGAGTTTGCCAATGAGATTATTGATGCCTTTTTGGTGAGCTATTTC CCCCTCCATCCCCCAGTACCTTTGGCACAATTAGCTGCCAAGATTTATGAGTATGTCAGCCAAATTGTGCTTAACGAAGC GGTTAACCTAAAGGATGAACTGATCAAACTAATCGTTCATACGCTTTACGAACAGTTAGATCGTCCTGTTGGGGATGAAA ATTAA
(295 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU64.4( 19) UCU6.8( 2) UAU20.3( 6) UGU3.4( 1) UUC13.6( 4) UCC3.4( 1) UAC16.9( 5) UGC0.0( 0) UUA54.2( 16) UCA0.0( 0) UAA3.4( 1) UGA0.0( 0) UUG37.3( 11) UCG6.8( 2) UAG0.0( 0) UGG0.0( 0) CUU13.6( 4) CCU13.6( 4) CAU16.9( 5) CGU6.8( 2) CUC27.1( 8) CCC16.9( 5) CAC16.9( 5) CGC10.2( 3) CUA16.9( 5) CCA16.9( 5) CAA37.3( 11) CGA0.0( 0) CUG3.4( 1) CCG6.8( 2) CAG47.5( 14) CGG0.0( 0) AUU23.7( 7) ACU6.8( 2) AAU16.9( 5) AGU10.2( 3) AUC20.3( 6) ACC16.9( 5) AAC37.3( 11) AGC10.2( 3) AUA3.4( 1) ACA0.0( 0) AAA40.7( 12) AGA0.0( 0) AUG10.2( 3) ACG6.8( 2) AAG40.7( 12) AGG0.0( 0) GUU20.3( 6) GCU13.6( 4) GAU37.3( 11) GGU6.8( 2) GUC13.6( 4) GCC37.3( 11) GAC3.4( 1) GGC3.4( 1) GUA6.8( 2) GCA13.6( 4) GAA33.9( 10) GGA0.0( 0) GUG16.9( 5) GCG13.6( 4) GAG47.5( 14) GGG6.8( 2)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
aTGATCAataagccaaatcagtttgtcaaccacttaagtgctttaaaaaaacactttgcc
3
tcttataaggagctccgtgaagcgtttaacgattatcacaagcataacggtgatgagttg
accaccttctttttgcaccagtttgataaggtgatggaactagtcaagcagaaggacttt
aaaactgcccagtctcgctgtgaggaggaattagccgccccttatctaccaaaaccttta
gtaagctttttccaatcgctactccagctcgtgaaccatgatttattggaacagcaaaac
gcggccttggctagtttacccgcagccaaaatcatagagcttgttttacaggattacccc
aataaactcaacatgattcactaccttttgcccaaaacgaaggcgtttgtcaaaccacat
ttgttacaacgcttacagtttgtgttaactgattcggagttgttggaattaaagcgcttt
tccttctttcaagcactcaaccagatcccgggctttcagggtgagcaagttgagtacttt
aacagtaagctcaaacaaaagtttaccttgaccttaggggagtttgaaattgcccaacag
ccagatgccaaagcatactttgagcagttaattacccaaatccaacagctctttttaaaa
gagccggttaacgctgagtttgccaatgagattattgatgcctttttggtgagctatttc
cccctccatcccccagtacctttggcacaattagctgccaagatttatgagtatgtcagc
caaattgtgcttaacgaagcggttaacctaaaggatgaacTGATCAaactaatcgttcat
3
acgctttacgaacagttagatcgtcctgttggggatgaaaattaa
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 |
|---|---|---|
| 1260B-R1 | 60.40 | CATATGATCAATAAGCCAAATCAGTTTG |
| 1260B-R2 | 60.40 | GGATCCTTAATTTTCATCCCCAACAGGA |
| 1260B-R10 | 64.80 | GGCGGTGGTGGCGGCATGATCAATAAGCCAAATCAGTTTGTCA |
| 1260B-R11 | 64.10 | GTTCTTCTCCTTTGCGCCCCTAATTTTCATCCCCAACAGGACG |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgatcaataagccaaatcagtttgtcaaccacttaagtgctttaaaaaaacactttgcc M I N K P N Q F V N H L S A L K K H F A tcttataaggagctccgtgaagcgtttaacgattatcacaagcataacggtgatgagttg S Y K E L R E A F N D Y H K H N G D E L accaccttctttttgcaccagtttgataaggtgatggaactagtcaagcagaaggacttt T T F F L H Q F D K V M E L V K Q K D F aaaactgcccagtctcgctgtgaggaggaattagccgccccttatctaccaaaaccttta K T A Q S R C E E E L A A P Y L P K P L gtaagctttttccaatcgctactccagctcgtgaaccatgatttattggaacagcaaaac V S F F Q S L L Q L V N H D L L E Q Q N gcggccttggctagtttacccgcagccaaaatcatagagcttgttttacaggattacccc A A L A S L P A A K I I E L V L Q D Y P aataaactcaacatgattcactaccttttgcccaaaacgaaggcgtttgtcaaaccacat N K L N M I H Y L L P K T K A F V K P H ttgttacaacgcttacagtttgtgttaactgattcggagttgttggaattaaagcgcttt L L Q R L Q F V L T D S E L L E L K R F tccttctttcaagcactcaaccagatcccgggctttcagggtgagcaagttgagtacttt S F F Q A L N Q I P G F Q G E Q V E Y F aacagtaagctcaaacaaaagtttaccttgaccttaggggagtttgaaattgcccaacag N S K L K Q K F T L T L G E F E I A Q Q ccagatgccaaagcatactttgagcagttaattacccaaatccaacagctctttttaaaa P D A K A Y F E Q L I T Q I Q Q L F L K gagccggttaacgctgagtttgccaatgagattattgatgcctttttggtgagctatttc E P V N A E F A N E I I D A F L V S Y F cccctccatcccccagtacctttggcacaattagctgccaagatttatgagtatgtcagc P L H P P V P L A Q L A A K I Y E Y V S caaattgtgcttaacgaagcggttaacctaaaggatgaactgatcaaactaatcgttcat Q I V L N E A V N L K D E L I K L I V H acgctttacgaacagttagatcgtcctgttggggatgaaaattaa T L Y E Q L D R P V G D E N *
MINKPNQFVNHLSALKKHFASYKELREAFNDYHKHNGDELTTFFLHQFDKVMELVKQKDFKTAQSRCEEELAAPYLPKPL VSFFQSLLQLVNHDLLEQQNAALASLPAAKIIELVLQDYPNKLNMIHYLLPKTKAFVKPHLLQRLQFVLTDSELLELKRF SFFQALNQIPGFQGEQVEYFNSKLKQKFTLTLGEFEIAQQPDAKAYFEQLITQIQQLFLKEPVNAEFANEIIDAFLVSYF PLHPPVPLAQLAAKIYEYVSQIVLNEAVNLKDELIKLIVHTLYEQLDRPVGDEN
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 294
Molecular weight: 34135.4
Theoretical pI: 5.82
Amino acid composition:
Ala (A) 23 7.8%
Arg (R) 5 1.7%
Asn (N) 16 5.4%
Asp (D) 12 4.1%
Cys (C) 1 0.3%
Gln (Q) 25 8.5%
Glu (E) 24 8.2%
Gly (G) 5 1.7%
His (H) 10 3.4%
Ile (I) 14 4.8%
Leu (L) 45 15.3%
Lys (K) 24 8.2%
Met (M) 3 1.0%
Phe (F) 23 7.8%
Pro (P) 16 5.4%
Ser (S) 11 3.7%
Thr (T) 9 3.1%
Trp (W) 0 0.0%
Tyr (Y) 11 3.7%
Val (V) 17 5.8%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 36
Total number of positively charged residues (Arg + Lys): 29
Atomic composition:
Carbon C 1582
Hydrogen H 2444
Nitrogen N 394
Oxygen O 439
Sulfur S 4
Formula: C1582H2444N394O439S4
Total number of atoms: 4863
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 15950 15400 14795 14080 13200
Abs 0.1% (=1 g/l) 0.467 0.451 0.433 0.412 0.387
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 15950 15400 14795 14080 13200
Abs 0.1% (=1 g/l) 0.467 0.451 0.433 0.412 0.387
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 38.63
This classifies the protein as stable.
Aliphatic index: 102.86
Grand average of hydropathicity (GRAVY): -0.188