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This gene has the annotation "5-formyl tetrahydrofolate cyclo-ligase (HI0858) homolog; similar to GenBank Accession Number D64160, from H. influenzae".
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 | 2002-06-20 |
| Expression tested | Done | r_kim | 2002-06-20 |
| Solubility tested | S | r_kim | 2002-06-20 |
| Purified | Done | dewemmer | 2002-09-05 |
| Crystallized | Done | dhshin | 2002-12-16 |
| Diffraction quality crystals | Done | dhshin | 2002-12-16 |
| Native diffraction data | Done | dhshin | 2002-12-16 |
| Phasing diffraction data | Done | dhshin | 2002-12-16 |
| Traceable map | Done | dhshin | 2002-12-16 |
| Crystal structure | Done | dhshin | 2004-08-05 |
| NMR characterization | Done | dewemmer | 2002-09-05 |
| HSQC | Done | dewemmer | 2002-09-05 |
| In PDB | 1SBQ 1U3F 1U3G | dhshin | 2004-08-05 |
| Suggested work stop | 19182 19182 | dallen | 2003-05-20 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP488 / MPN348 | -46.40 | 100.00 | 100.00 |
ATGGACAAAAATGCCTTAAGAAAACAAATTCTGCAAAAAAGAATGGCATTAAGTACCATTGAAAAAAGTCACTTAGATCA AAAGATTAATCAAAAATTAGTTGCTTTTTTAACTCCTAAGCCATGCATTAAAACAATTGCACTTTATGAACCCATTAAAA ATGAGGTTACTTTTGTTGACTTCTTCTTTGAGTTTTTAAAGATTAACCAAATAAGAGCTGTTTACCCCAAGGTAATAAGT GATACCGAAATTATCTTTATTGATCAGGAGACAAATACATTCGAACCTAATCAAATAGACTGCTTCCTAATACCATTGGT AGGCTTTAATAAAGACAATTACCGTCTAGGCTTTGGCAAGGGCTATTATGACCGTTATTTAATGCAATTAACTAGACAAC AACCTAAAATAGGAATAGCGTACAGTTTCCAAAAAGGTGATTTTTTAGCCGATCCTTGGGATGTACAACTAGACTTAATT ATTAATGATGAATAG
(165 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU48.5( 8) UCU0.0( 0) UAU24.2( 4) UGU0.0( 0) UUC30.3( 5) UCC0.0( 0) UAC18.2( 3) UGC12.1( 2) UUA60.6( 10) UCA0.0( 0) UAA0.0( 0) UGA0.0( 0) UUG6.1( 1) UCG0.0( 0) UAG6.1( 1) UGG6.1( 1) CUU6.1( 1) CCU24.2( 4) CAU0.0( 0) CGU12.1( 2) CUC0.0( 0) CCC12.1( 2) CAC6.1( 1) CGC0.0( 0) CUA18.2( 3) CCA12.1( 2) CAA66.7( 11) CGA0.0( 0) CUG6.1( 1) CCG0.0( 0) CAG6.1( 1) CGG0.0( 0) AUU66.7( 11) ACU18.2( 3) AAU48.5( 8) AGU24.2( 4) AUC6.1( 1) ACC12.1( 2) AAC6.1( 1) AGC0.0( 0) AUA36.4( 6) ACA18.2( 3) AAA60.6( 10) AGA24.2( 4) AUG18.2( 3) ACG0.0( 0) AAG30.3( 5) AGG0.0( 0) GUU24.2( 4) GCU12.1( 2) GAU42.4( 7) GGU6.1( 1) GUC0.0( 0) GCC12.1( 2) GAC36.4( 6) GGC24.2( 4) GUA18.2( 3) GCA12.1( 2) GAA30.3( 5) GGA6.1( 1) GUG0.0( 0) GCG6.1( 1) GAG18.2( 3) GGG0.0( 0)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
atggacaaaaatgccttaagaaaacaaattctgcaaaaaagaatggcattaagtaccatt
gaaaaaagtcacttagatcaaaagattaatcaaaaattagttgcttttttaactcctaag
ccatgcattaaaacaattgcactttatgaacccattaaaaatgaggttacttttgttgac
ttcttctttgagtttttaaagattaaccaaataagagctgtttaccccaaggtaataagt
gataccgaaattatctttatTGATCAggagacaaatacattcgaacctaatcaaatagac
3
tgcttcctaataccattggtaggctttaataaagacaattaccgtctaggctttggcaag
ggctattatgaccgttatttaatgcaattaactagacaacaacctaaaataggaatagcg
tacagtttccaaaaaggtgattttttagccgatccttgggatgtacaactagacttaatt
attaatgatgaatag
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 |
|---|---|---|
| 1151B-R1 | 60.10 | CATATGGACAAAAATGCCTTAAGAAAA |
| 1151B-R2 | 60.80 | GGATCCTTATTCATCATTAATAATTAAGTCTAGTTGTACATCC |
| 1151B-R3 | 60.80 | GGATCCTTATTCATCATTAATAATTAAGTCTAGTTGTACATCC |
| 1151B-R10 | 63.00 | GGCGGTGGTGGCGGCATGGACAAAAATGCCTTAAGAAAACA |
| 1151B-R11 | 63.40 | GTTCTTCTCCTTTGCGCCCCTATTCATCATTAATAATTAAGTCTAGTTGTACATCCC |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atggacaaaaatgccttaagaaaacaaattctgcaaaaaagaatggcattaagtaccatt M D K N A L R K Q I L Q K R M A L S T I gaaaaaagtcacttagatcaaaagattaatcaaaaattagttgcttttttaactcctaag E K S H L D Q K I N Q K L V A F L T P K ccatgcattaaaacaattgcactttatgaacccattaaaaatgaggttacttttgttgac P C I K T I A L Y E P I K N E V T F V D ttcttctttgagtttttaaagattaaccaaataagagctgtttaccccaaggtaataagt F F F E F L K I N Q I R A V Y P K V I S gataccgaaattatctttattgatcaggagacaaatacattcgaacctaatcaaatagac D T E I I F I D Q E T N T F E P N Q I D tgcttcctaataccattggtaggctttaataaagacaattaccgtctaggctttggcaag C F L I P L V G F N K D N Y R L G F G K ggctattatgaccgttatttaatgcaattaactagacaacaacctaaaataggaatagcg G Y Y D R Y L M Q L T R Q Q P K I G I A tacagtttccaaaaaggtgattttttagccgatccttgggatgtacaactagacttaatt Y S F Q K G D F L A D P W D V Q L D L I attaatgatgaatag I N D E *
MDKNALRKQILQKRMALSTIEKSHLDQKINQKLVAFLTPKPCIKTIALYEPIKNEVTFVDFFFEFLKINQIRAVYPKVIS DTEIIFIDQETNTFEPNQIDCFLIPLVGFNKDNYRLGFGKGYYDRYLMQLTRQQPKIGIAYSFQKGDFLADPWDVQLDLI INDE
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 164
Molecular weight: 19265.3
Theoretical pI: 6.60
Amino acid composition:
Ala (A) 7 4.3%
Arg (R) 6 3.7%
Asn (N) 9 5.5%
Asp (D) 13 7.9%
Cys (C) 2 1.2%
Gln (Q) 12 7.3%
Glu (E) 8 4.9%
Gly (G) 6 3.7%
His (H) 1 0.6%
Ile (I) 18 11.0%
Leu (L) 16 9.8%
Lys (K) 15 9.1%
Met (M) 3 1.8%
Phe (F) 13 7.9%
Pro (P) 8 4.9%
Ser (S) 4 2.4%
Thr (T) 8 4.9%
Trp (W) 1 0.6%
Tyr (Y) 7 4.3%
Val (V) 7 4.3%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 21
Total number of positively charged residues (Arg + Lys): 21
Atomic composition:
Carbon C 888
Hydrogen H 1381
Nitrogen N 221
Oxygen O 247
Sulfur S 5
Formula: C888H1381N221O247S5
Total number of atoms: 2742
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 15695 15527 15195 14770 14120
Abs 0.1% (=1 g/l) 0.815 0.806 0.789 0.767 0.733
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 15550 15400 15075 14650 14000
Abs 0.1% (=1 g/l) 0.807 0.799 0.782 0.760 0.727
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 17.46
This classifies the protein as stable.
Aliphatic index: 97.50
Grand average of hydropathicity (GRAVY): -0.237