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This gene has the annotation "tRNA guanine-N1 methyltransferase".
The target was selected as part of JMC's first set.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | jmc | 2001-08-28 |
| Cloned | Done | r_kim | 2002-01-04 |
| Expression tested | Done | r_kim | 2002-01-04 |
| Solubility tested | S | r_kim | 2002-01-04 |
| Purified | Done | r_kim | 2002-02-26 |
| Crystallized | Done | weiru | 2002-05-08 |
| Diffraction quality crystals | Done | weiru | 2002-05-30 |
| Phasing diffraction data | Done | dhshin | 2002-06-10 |
| Traceable map | Done | dhshin | 2002-06-10 |
| Crystal structure | Done | dhshin | 2003-01-15 |
| In PDB | 1OY5 | dhshin | 2003-05-14 |
| Biochemical function | Done | dhshin | 2003-01-23 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP183 / MPN659 | -81.00 | 43.54 | 81.32 |
TTGAGTTCTAATCCCCTCCGCTTCTTCGTCCTCACCATATTTCCCCATATAATCTCCTGTTACTCGGAGTACGGTATAGT AAAGCAGGCTATAAAAAAGGGAAAAGTAGAAGTATATCCCATAGACCTTCGTGAGTTTGCACCAAAAGGACAAGTTGACG ACGTCCCCTACGGCGGACTTCCAGGGATGGTTTTAAAACCAGAACCCATATACGAAGCCTACGATTACGTCGTTGAAAAT TACGGAAAACCCTTCGTTTTAATTACCGAGCCCTGGGGAGAGAAACTAAACCAAAAGCTGGTAAACGAACTTTCTAAAAA GGAAAGGATAATGATAATTTGCGGGCGGTACGAGGGAGTGGACGAGAGGGTTAAGAAAATCGTGGATATGGAAATTTCTC TTGGAGACTTTATACTCTCGGGAGGTGAAATCGTAGCCCTCGCGGTAATTGACGCGGTGAGCAGGGTTCTCCCCGGAGTT TTGAGTGAACCTCAGAGCATTCAGGAAGACAGTTTTCAAAACAGGTGGCTTGGCTACCCCGTTTACACGAGACCAAGGGA ATACAGGGGGATGAAGGTTCCGGAAGAGCTCCTTTCAGGACACCACAAATTGATAGAACTCTGGAAGTTATGGCACAGGA TAGAAAACACGGTAAAAAAGAGACCGGATTTAATACCTAAAGACTTGACAGAACTTGAAAAAGACATTTTAAATAGTATA TTATCTGGAAAGTCATTCAAGGAATGGTTAAAAGAGCACAAGCACCTTCTTTAA
(258 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU15.5( 4) UCU15.5( 4) UAU3.9( 1) UGU3.9( 1) UUC15.5( 4) UCC3.9( 1) UAC42.6( 11) UGC3.9( 1) UUA27.1( 7) UCA7.8( 2) UAA3.9( 1) UGA0.0( 0) UUG15.5( 4) UCG7.8( 2) UAG0.0( 0) UGG19.4( 5) CUU34.9( 9) CCU7.8( 2) CAU3.9( 1) CGU3.9( 1) CUC27.1( 7) CCC34.9( 9) CAC19.4( 5) CGC3.9( 1) CUA3.9( 1) CCA15.5( 4) CAA11.6( 3) CGA0.0( 0) CUG3.9( 1) CCG7.8( 2) CAG11.6( 3) CGG3.9( 1) AUU23.3( 6) ACU0.0( 0) AAU11.6( 3) AGU15.5( 4) AUC11.6( 3) ACC7.8( 2) AAC15.5( 4) AGC7.8( 2) AUA50.4( 13) ACA3.9( 1) AAA50.4( 13) AGA7.8( 2) AUG15.5( 4) ACG7.8( 2) AAG42.6( 11) AGG27.1( 7) GUU34.9( 9) GCU3.9( 1) GAU11.6( 3) GGU7.8( 2) GUC11.6( 3) GCC7.8( 2) GAC34.9( 9) GGC7.8( 2) GUA27.1( 7) GCA3.9( 1) GAA65.9( 17) GGA42.6( 11) GUG11.6( 3) GCG7.8( 2) GAG31.0( 8) GGG11.6( 3)
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 |
|---|---|---|
| 1109B-R1 | 61.30 | CATATGAGTTCTAATCCCCTCCGC |
| 1109B-R2 | 60.60 | GGATCCTTAAAGAAGGTGCTTGTGCTCTTT |
| 1109B-R10 | 63.30 | GGCGGTGGTGGCGGCATGAGTTCTAATCCCCTCCGCTT |
| 1109B-R11 | 64.90 | GTTCTTCTCCTTTGCGCCCCTAAAGAAGGTGCTTGTGCTCTTTTAACC |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
ttgagttctaatcccctccgcttcttcgtcctcaccatatttccccatataatctcctgt L S S N P L R F F V L T I F P H I I S C tactcggagtacggtatagtaaagcaggctataaaaaagggaaaagtagaagtatatccc Y S E Y G I V K Q A I K K G K V E V Y P atagaccttcgtgagtttgcaccaaaaggacaagttgacgacgtcccctacggcggactt I D L R E F A P K G Q V D D V P Y G G L ccagggatggttttaaaaccagaacccatatacgaagcctacgattacgtcgttgaaaat P G M V L K P E P I Y E A Y D Y V V E N tacggaaaacccttcgttttaattaccgagccctggggagagaaactaaaccaaaagctg Y G K P F V L I T E P W G E K L N Q K L gtaaacgaactttctaaaaaggaaaggataatgataatttgcgggcggtacgagggagtg V N E L S K K E R I M I I C G R Y E G V gacgagagggttaagaaaatcgtggatatggaaatttctcttggagactttatactctcg D E R V K K I V D M E I S L G D F I L S ggaggtgaaatcgtagccctcgcggtaattgacgcggtgagcagggttctccccggagtt G G E I V A L A V I D A V S R V L P G V ttgagtgaacctcagagcattcaggaagacagttttcaaaacaggtggcttggctacccc L S E P Q S I Q E D S F Q N R W L G Y P gtttacacgagaccaagggaatacagggggatgaaggttccggaagagctcctttcagga V Y T R P R E Y R G M K V P E E L L S G caccacaaattgatagaactctggaagttatggcacaggatagaaaacacggtaaaaaag H H K L I E L W K L W H R I E N T V K K agaccggatttaatacctaaagacttgacagaacttgaaaaagacattttaaatagtata R P D L I P K D L T E L E K D I L N S I ttatctggaaagtcattcaaggaatggttaaaagagcacaagcaccttctttaa L S G K S F K E W L K E H K H L L *
MSSNPLRFFVLTIFPHIISCYSEYGIVKQAIKKGKVEVYPIDLREFAPKGQVDDVPYGGLPGMVLKPEPIYEAYDYVVEN YGKPFVLITEPWGEKLNQKLVNELSKKERIMIICGRYEGVDERVKKIVDMEISLGDFILSGGEIVALAVIDAVSRVLPGV LSEPQSIQEDSFQNRWLGYPVYTRPREYRGMKVPEELLSGHHKLIELWKLWHRIENTVKKRPDLIPKDLTELEKDILNSI LSGKSFKEWLKEHKHLL
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 257
Molecular weight: 29651.5
Theoretical pI: 6.62
Amino acid composition:
Ala (A) 6 2.3%
Arg (R) 12 4.7%
Asn (N) 7 2.7%
Asp (D) 12 4.7%
Cys (C) 2 0.8%
Gln (Q) 6 2.3%
Glu (E) 25 9.7%
Gly (G) 18 7.0%
His (H) 6 2.3%
Ile (I) 22 8.6%
Leu (L) 28 10.9%
Lys (K) 24 9.3%
Met (M) 5 1.9%
Phe (F) 8 3.1%
Pro (P) 17 6.6%
Ser (S) 15 5.8%
Thr (T) 5 1.9%
Trp (W) 5 1.9%
Tyr (Y) 12 4.7%
Val (V) 22 8.6%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 37
Total number of positively charged residues (Arg + Lys): 36
Atomic composition:
Carbon C 1363
Hydrogen H 2147
Nitrogen N 347
Oxygen O 377
Sulfur S 7
Formula: C1363H2147N347O377S7
Total number of atoms: 4241
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 44545 44927 44560 43930 42520
Abs 0.1% (=1 g/l) 1.502 1.515 1.503 1.482 1.434
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 44400 44800 44440 43810 42400
Abs 0.1% (=1 g/l) 1.497 1.511 1.499 1.477 1.430
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 40.06
This classifies the protein as unstable.
Aliphatic index: 103.04
Grand average of hydropathicity (GRAVY): -0.258