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This gene has the annotation "nicotinate-nucleotide pyrophosphorylase".
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 | r_kim | 2003-09-12 |
| Crystallized | Done | dhshin | 2003-09-12 |
| Diffraction quality crystals | Done | dhshin | 2003-12-15 |
| Native diffraction data | Done | dhshin | 2003-12-15 |
| Phasing diffraction data | Done | dhshin | 2003-12-15 |
| Traceable map | Done | dhshin | 2003-12-15 |
| Crystal structure | Done | dhshin | 2004-05-26 |
| In PDB | 2I14 | dhshin | 2006-08-16 |
| Suggested work stop | 9597 9597 9597 9961 9961 17808 17808 17808 20451 21310 21310 21562 21562 22794 | dallen | 2003-12-01 |
| Override suggest work stop | Traceable map obtained | dhshin | 2004-02-17 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP107 / MPN047 | -27.52 | 15.87 | 69.67 |
ATGAAAAGATTTTACATTGCTAATGAAGATGAGATAAAGGCGGGAAAAACTACTGATGTCTATTTCTTGAGAACAAAAAA GATCCTCGAGGTTAAGAACATAAGAAAAAAGGTTCTTGCTGACGTAACAACAACCTCCCTCCCAAACAATTGGAGATGGG GAGTTTTAGTCGGGGTTGAAGAAGTAGCAAAACTATTGGAAGGAATTCCAGTTAACGTTTATGCCATGCCAGAAGGAACT ATCTTCCATCCATATGAGCCAGTGTTACAAATAGAAGGGGATTATGCAGACTTCGGTATCTATGAAACGGCCCTCCTGGG AATGCTAAGTCAAGCTAGCGGAATAGCAACAGCAGCCTTAAGAATTAAGATAGCTGCTAAGTTTAAGCCAGTGTATTCCT TCGGAATTAGGCATATGCACCCAGCAATTGCTCCGATGATTGATAGAGCCGCGTTTATTGGAGGATGTGACGGAGTTTCT GGAGTTTTGGGAGCAGAAATGATGGGAGAAAAAGCTGTGGGAACTATGCCCCACGCATTGATTATAACTGTTGGCGATCA AGTTAAAGCCTGGAAATACTTCGATGAGGTCATTGAAGAGGAAGTTCCTAGGATAGCCCTAGTAGATACATTTTACGATG AGAAGGTCGAGGCTGTTATGGCAGCTGAAGCCCTCGGCAAGAAACTATTTGCCGTGAGACTAGACACTCCAAGCTCAAGA AGAGGGAACTTCAGGAAGATAATTGAAGAAGTTAGATGGGAGTTAAAGGTTAGAGGATATGACTGGGTGAAGATATTTGT CTCAGGAGGACTTGATGAAGAGAAAATAAAGGAAATAGTTGACGTTGTAGATGCTTTTGGAGTTGGAGGAGCTATAGCAA GTGCAAAGCCAGTAGACTTTGCCCTAGACATTGTGGAAGTTGAAGGAAAGCCAATTGCAAAGAGGGGAAAGCTTAGCGGT AGGAAGCAAGTGTATAGATGTGAAAACGGACACTACCATGTAGTTCCTGCCAACAAAAAGCTTGAGAGATGTCCAGTTTG TAATGCAAAAGTTGAACCATTGTTAAAGCCAATTATCGAGAATGGAGAAATTGTAGTTGAGTTTCCAAAGGCTAGAGAGA TTAGAGAATACGTACTTGAGCAAGCTAAGAAATTTAACCTCGAGATTTGA
(390 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU25.6( 10) UCU2.6( 1) UAU20.5( 8) UGU10.3( 4) UUC15.4( 6) UCC5.1( 2) UAC12.8( 5) UGC0.0( 0) UUA12.8( 5) UCA5.1( 2) UAA0.0( 0) UGA2.6( 1) UUG12.8( 5) UCG0.0( 0) UAG0.0( 0) UGG12.8( 5) CUU12.8( 5) CCU5.1( 2) CAU7.7( 3) CGU0.0( 0) CUC12.8( 5) CCC2.6( 1) CAC7.7( 3) CGC0.0( 0) CUA15.4( 6) CCA35.9( 14) CAA12.8( 5) CGA0.0( 0) CUG2.6( 1) CCG2.6( 1) CAG0.0( 0) CGG0.0( 0) AUU41.0( 16) ACU15.4( 6) AAU10.3( 4) AGU5.1( 2) AUC10.3( 4) ACC2.6( 1) AAC17.9( 7) AGC7.7( 3) AUA30.8( 12) ACA12.8( 5) AAA33.3( 13) AGA38.5( 15) AUG23.1( 9) ACG2.6( 1) AAG56.4( 22) AGG12.8( 5) GUU56.4( 22) GCU33.3( 13) GAU25.6( 10) GGU5.1( 2) GUC12.8( 5) GCC25.6( 10) GAC20.5( 8) GGC5.1( 2) GUA20.5( 8) GCA30.8( 12) GAA56.4( 22) GGA61.5( 24) GUG17.9( 7) GCG5.1( 2) GAG38.5( 15) GGG7.7( 3)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
atgaaaagattttacattgctaatgaagatgagataaaggcgggaaaaactactgatgtc
tatttcttgagaacaaaaaagatcctcgaggttaagaacataagaaaaaaggttcttgct
gacgtaacaacaacctccctcccaaacaattggagatggggagttttagtcggggttgaa
gaagtagcaaaactattggaaggaattccagttaacgtttatgccatgccagaaggaact
atcttccatcCATATGagccagtgttacaaatagaaggggattatgcagacttcggtatc
1
tatgaaacggccctcctgggaatgctaagtcaagctagcggaatagcaacagcagcctta
agaattaagatagctgctaagtttaagccagtgtattccttcggaattaggCATATGcac
1
ccagcaattgctccgatgattgatagagccgcgtttattggaggatgtgacggagtttct
ggagttttgggagcagaaatgatgggagaaaaagctgtgggaactatgccccacgcattg
attataactgttggcgatcaagttaaagcctggaaatacttcgatgaggtcattgaagag
gaagttcctaggatagccctagtagatacattttacgatgagaaggtcgaggctgttatg
gcagctgaagccctcggcaagaaactatttgccgtgagactagacactccaagctcaaga
agagggaacttcaggaagataattgaagaagttagatgggagttaaaggttagaggatat
gactgggtgaagatatttgtctcaggaggacttgatgaagagaaaataaaggaaatagtt
gacgttgtagatgcttttggagttggaggagctatagcaagtgcaaagccagtagacttt
gccctagacattgtggaagttgaaggaaagccaattgcaaagaggggaaagcttagcggt
aggaagcaagtgtatagatgtgaaaacggacactaccatgtagttcctgccaacaaaaag
cttgagagatgtccagtttgtaatgcaaaagttgaaccattgttaaagccaattatcgag
aatggagaaattgtagttgagtttccaaaggctagagagattagagaatacgtacttgag
caagctaagaaatttaacctcgagatttga
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 |
|---|---|---|
| 1367B-R1 | 60.80 | CATATGAAAAGATTTTACATTGCTAATGAAGA |
| 1367B-R2 | 61.60 | GGATCCTTAAATCTCGAGGTTAAATTTCTTAGCTTG |
| 1367B-R10 | 64.10 | GGCGGTGGTGGCGGCATGAAAAGATTTTACATTGCTAATGAAGATGA |
| 1367B-R11 | 64.20 | GTTCTTCTCCTTTGCGCCCCTAAATCTCGAGGTTAAATTTCTTAGCTTGC |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgaaaagattttacattgctaatgaagatgagataaaggcgggaaaaactactgatgtc M K R F Y I A N E D E I K A G K T T D V tatttcttgagaacaaaaaagatcctcgaggttaagaacataagaaaaaaggttcttgct Y F L R T K K I L E V K N I R K K V L A gacgtaacaacaacctccctcccaaacaattggagatggggagttttagtcggggttgaa D V T T T S L P N N W R W G V L V G V E gaagtagcaaaactattggaaggaattccagttaacgtttatgccatgccagaaggaact E V A K L L E G I P V N V Y A M P E G T atcttccatccatatgagccagtgttacaaatagaaggggattatgcagacttcggtatc I F H P Y E P V L Q I E G D Y A D F G I tatgaaacggccctcctgggaatgctaagtcaagctagcggaatagcaacagcagcctta Y E T A L L G M L S Q A S G I A T A A L agaattaagatagctgctaagtttaagccagtgtattccttcggaattaggcatatgcac R I K I A A K F K P V Y S F G I R H M H ccagcaattgctccgatgattgatagagccgcgtttattggaggatgtgacggagtttct P A I A P M I D R A A F I G G C D G V S ggagttttgggagcagaaatgatgggagaaaaagctgtgggaactatgccccacgcattg G V L G A E M M G E K A V G T M P H A L attataactgttggcgatcaagttaaagcctggaaatacttcgatgaggtcattgaagag I I T V G D Q V K A W K Y F D E V I E E gaagttcctaggatagccctagtagatacattttacgatgagaaggtcgaggctgttatg E V P R I A L V D T F Y D E K V E A V M gcagctgaagccctcggcaagaaactatttgccgtgagactagacactccaagctcaaga A A E A L G K K L F A V R L D T P S S R agagggaacttcaggaagataattgaagaagttagatgggagttaaaggttagaggatat R G N F R K I I E E V R W E L K V R G Y gactgggtgaagatatttgtctcaggaggacttgatgaagagaaaataaaggaaatagtt D W V K I F V S G G L D E E K I K E I V gacgttgtagatgcttttggagttggaggagctatagcaagtgcaaagccagtagacttt D V V D A F G V G G A I A S A K P V D F gccctagacattgtggaagttgaaggaaagccaattgcaaagaggggaaagcttagcggt A L D I V E V E G K P I A K R G K L S G aggaagcaagtgtatagatgtgaaaacggacactaccatgtagttcctgccaacaaaaag R K Q V Y R C E N G H Y H V V P A N K K cttgagagatgtccagtttgtaatgcaaaagttgaaccattgttaaagccaattatcgag L E R C P V C N A K V E P L L K P I I E aatggagaaattgtagttgagtttccaaaggctagagagattagagaatacgtacttgag N G E I V V E F P K A R E I R E Y V L E caagctaagaaatttaacctcgagatttga Q A K K F N L E I *
MKRFYIANEDEIKAGKTTDVYFLRTKKILEVKNIRKKVLADVTTTSLPNNWRWGVLVGVEEVAKLLEGIPVNVYAMPEGT IFHPYEPVLQIEGDYADFGIYETALLGMLSQASGIATAALRIKIAAKFKPVYSFGIRHMHPAIAPMIDRAAFIGGCDGVS GVLGAEMMGEKAVGTMPHALIITVGDQVKAWKYFDEVIEEEVPRIALVDTFYDEKVEAVMAAEALGKKLFAVRLDTPSSR RGNFRKIIEEVRWELKVRGYDWVKIFVSGGLDEEKIKEIVDVVDAFGVGGAIASAKPVDFALDIVEVEGKPIAKRGKLSG RKQVYRCENGHYHVVPANKKLERCPVCNAKVEPLLKPIIENGEIVVEFPKAREIREYVLEQAKKFNLEI
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 389
Molecular weight: 43367.5
Theoretical pI: 7.03
Amino acid composition:
Ala (A) 37 9.5%
Arg (R) 20 5.1%
Asn (N) 11 2.8%
Asp (D) 18 4.6%
Cys (C) 4 1.0%
Gln (Q) 5 1.3%
Glu (E) 37 9.5%
Gly (G) 31 8.0%
His (H) 6 1.5%
Ile (I) 32 8.2%
Leu (L) 27 6.9%
Lys (K) 35 9.0%
Met (M) 9 2.3%
Phe (F) 16 4.1%
Pro (P) 18 4.6%
Ser (S) 10 2.6%
Thr (T) 13 3.3%
Trp (W) 5 1.3%
Tyr (Y) 13 3.3%
Val (V) 42 10.8%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 55
Total number of positively charged residues (Arg + Lys): 55
Atomic composition:
Carbon C 1974
Hydrogen H 3143
Nitrogen N 517
Oxygen O 552
Sulfur S 13
Formula: C1974H3143N517O552S13
Total number of atoms: 6199
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 46140 46454 46025 45330 43840
Abs 0.1% (=1 g/l) 1.064 1.071 1.061 1.045 1.011
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 45850 46200 45785 45090 43600
Abs 0.1% (=1 g/l) 1.057 1.065 1.056 1.040 1.005
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 35.88
This classifies the protein as stable.
Aliphatic index: 99.97
Grand average of hydropathicity (GRAVY): -0.032