|
|
This gene has the annotation "N utilization substance protein A".
The target was selected as part of Igor's sets.
Available sections:
| Experiment | Result | User | Experiment Date |
|---|---|---|---|
| Selected | Done | shkim | 2001-08-24 |
| Cloned | Done | abwaight | 2001-08-24 |
| Expression tested | Done | abwaight | 2001-08-24 |
| Solubility tested | S | abwaight | 2001-08-24 |
| Purified | Done | abwaight | 2001-08-24 |
| Crystallized | Done | abwaight | 2001-08-24 |
| Diffraction quality crystals | Done | abwaight | 2001-08-24 |
| Phasing diffraction data | Done | abwaight | 2001-08-24 |
| Traceable map | Done | abwaight | 2001-08-24 |
| Crystal structure | Done | weiru | 2001-12-03 |
| In PDB | 1L2F | weiru | 2002-04-08 |
| Biochemical function | Done | dhshin | 2001-07-07 |
| MP gene | log10(PSIBLAST E) | % identical | % coverage (of MP gene) |
|---|---|---|---|
| MP589 / MPN243 | -4.52 | 8.62 | 33.72 |
| MP677 / MPN154 | -55.22 | 31.56 | 98.55 |
ATGAACATAGGCTTGCTGGAAGCCCTCGACCAGCTGGAGGAAGAAAAAGGAATTTCCAAAGAAGAGGTCATTCCTATCCT TGAAAAAGCACTGGTGAGCGCTTACAGGAAGAACTTTGGAAATTCCAAGAACGTGGAGGTTGTTATAGATAGGAACACGG GAAACATAAAAGTGTATCAGCTCCTCGAAGTTGTGGAAGAAGTGGAAGATCCAGCAACACAGATATCTCTCGAGGAGGCG AAAAAGATCGACCCCCTCGCGGAAGTTGGGTCTATTGTGAAGAAGGAACTGAACGTTAAGAATTTTGGAAGAATAGCCGC GCAGACGGCGAAGCAGGTTCTCATTCAGAGAATCAGAGAACTCGAGAAGGAGAAACAGTTCGAGAAGTATTCCGAACTCA AAGGAACGGTTACAACCGCTGAAGTCATAAGAGTCATGGGCGAGTGGGCAGACATCAGAATAGGAAAGCTCGAGACAAGG CTTCCAAAGAAAGAGTGGATCCCCGGTGAGGAAATCAAAGCCGGTGATCTGGTGAAGGTCTACATCATCGATGTGGTTAA AACAACCAAGGGGCCGAAGATACTCGTGAGCAGGAGAGTACCGGAGTTCGTAATTGGCCTGATGAAACTCGAAATTCCGG AAGTGGAGAATGGAATCGTGGAAATAAAGGCTATCGCCAGAGAACCCGGTGTTCGAACAAAGGTGGCAGTTGCATCGAAC GATCCGAACGTGGATCCCATAGGTGCCTGCATCGGTGAAGGAGGATCGAGGATAGCCGCCATACTGAAGGAGCTCAAGGG TGAAAAACTCGACGTTCTGAAGTGGTCGGACGATCCCAAACAGCTCATAGCGAACGCCCTTGCGCCGGCTACCGTCATAG AAGTGGAGATACTCGACAAAGAGAACAAGGCCGCACGCGTTCTAGTTCCTCCGACACAGCTTTCCCTCGCCATAGGAAAA GGAGGGCAGAACGCGAGACTCGCTGCAAAGCTCACAGGATGGAAAATAGACATAAAACCGATCATGAACCTGTGA
(345 codons) fields: [triplet] [frequency: per thousand] ([number]) UUU5.8( 2) UCU5.8( 2) UAU5.8( 2) UGU0.0( 0) UUC5.8( 2) UCC11.6( 4) UAC5.8( 2) UGC2.9( 1) UUA0.0( 0) UCA0.0( 0) UAA0.0( 0) UGA2.9( 1) UUG2.9( 1) UCG8.7( 3) UAG0.0( 0) UGG11.6( 4) CUU11.6( 4) CCU5.8( 2) CAU0.0( 0) CGU0.0( 0) CUC52.2( 18) CCC14.5( 5) CAC0.0( 0) CGC2.9( 1) CUA2.9( 1) CCA5.8( 2) CAA0.0( 0) CGA2.9( 1) CUG26.1( 9) CCG20.3( 7) CAG29.0( 10) CGG0.0( 0) AUU17.4( 6) ACU0.0( 0) AAU8.7( 3) AGU0.0( 0) AUC34.8( 12) ACC8.7( 3) AAC34.8( 12) AGC5.8( 2) AUA52.2( 18) ACA20.3( 7) AAA49.3( 17) AGA23.2( 8) AUG11.6( 4) ACG8.7( 3) AAG60.9( 21) AGG14.5( 5) GUU37.7( 13) GCU14.5( 5) GAU20.3( 7) GGU17.4( 6) GUC14.5( 5) GCC29.0( 10) GAC20.3( 7) GGC8.7( 3) GUA5.8( 2) GCA20.3( 7) GAA63.8( 22) GGA34.8( 12) GUG40.6( 14) GCG20.3( 7) GAG49.3( 17) GGG8.7( 3)
Details (problem DNA region is in upper case, with the key on the line below):
Key:
atgaacataggcttgctggaagccctcgaccagctggaggaagaaaaaggaatttccaaa
gaagaggtcattcctatccttgaaaaagcactggtgagcgcttacaggaagaactttgga
aattccaagaacgtggaggttgttatagataggaacacgggaaacataaaagtgtatcag
ctcctcgaagttgtggaagaagtggaagatccagcaacacagatatctctcgaggaggcg
aaaaagatcgaccccctcgcggaagttgggtctattgtgaagaaggaactgaacgttaag
aattttggaagaatagccgcgcagacggcgaagcaggttctcattcagagaatcagagaa
ctcgagaaggagaaacagttcgagaagtattccgaactcaaaggaacggttacaaccgct
gaagtcataagagtcatgggcgagtgggcagacatcagaataggaaagctcgagacaagg
cttccaaagaaagagtGGATCCccggtgaggaaatcaaagccggtgatctggtgaaggtc
2
tacatcatcgatgtggttaaaacaaccaaggggccgaagatactcgtgagcaggagagta
ccggagttcgtaattggcctgatgaaactcgaaattccggaagtggagaatggaatcgtg
gaaataaaggctatcgccagagaacccggtgttcgaacaaaggtggcagttgcatcgaac
gatccgaacgtGGATCCcataggtgcctgcatcggtgaaggaggatcgaggatagccgcc
2
atactgaaggagctcaagggtgaaaaactcgacgttctgaagtggtcggacgatcccaaa
cagctcatagcgaacgcccttgcgccggctaccgtcatagaagtggagatactcgacaaa
gagaacaaggccgcacgcgttctagttcctccgacacagctttccctcgccataggaaaa
ggagggcagaacgcgagactcgctgcaaagctcacaggatggaaaatagacataaaaccg
atcatgaacctgtga
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 |
|---|---|---|
| 1102B-R1 | 60.50 | CATATGAACATAGGCTTGCTGGAAG |
| 1102B-R2 | 60.70 | AGATCTTTATCACAGGTTGATCGGTTTTATGT |
| 1102B-R3 | 60.00 | AGATCTTTACAGGTTCATGATCGGTTTTATG |
| 1102B-R10 | 63.80 | GGCGGTGGTGGCGGCATGAACATAGGCTTGCTGGAAGC |
| 1102B-R11 | 63.10 | GTTCTTCTCCTTTGCGCCCCTACAGGTTCATGATCGGTTTTATGTCT |
Note: This was generated using the standard codon usage table; UGA codons in MP/MP genes will show up as terminators ("*")
atgaacataggcttgctggaagccctcgaccagctggaggaagaaaaaggaatttccaaa M N I G L L E A L D Q L E E E K G I S K gaagaggtcattcctatccttgaaaaagcactggtgagcgcttacaggaagaactttgga E E V I P I L E K A L V S A Y R K N F G aattccaagaacgtggaggttgttatagataggaacacgggaaacataaaagtgtatcag N S K N V E V V I D R N T G N I K V Y Q ctcctcgaagttgtggaagaagtggaagatccagcaacacagatatctctcgaggaggcg L L E V V E E V E D P A T Q I S L E E A aaaaagatcgaccccctcgcggaagttgggtctattgtgaagaaggaactgaacgttaag K K I D P L A E V G S I V K K E L N V K aattttggaagaatagccgcgcagacggcgaagcaggttctcattcagagaatcagagaa N F G R I A A Q T A K Q V L I Q R I R E ctcgagaaggagaaacagttcgagaagtattccgaactcaaaggaacggttacaaccgct L E K E K Q F E K Y S E L K G T V T T A gaagtcataagagtcatgggcgagtgggcagacatcagaataggaaagctcgagacaagg E V I R V M G E W A D I R I G K L E T R cttccaaagaaagagtggatccccggtgaggaaatcaaagccggtgatctggtgaaggtc L P K K E W I P G E E I K A G D L V K V tacatcatcgatgtggttaaaacaaccaaggggccgaagatactcgtgagcaggagagta Y I I D V V K T T K G P K I L V S R R V ccggagttcgtaattggcctgatgaaactcgaaattccggaagtggagaatggaatcgtg P E F V I G L M K L E I P E V E N G I V gaaataaaggctatcgccagagaacccggtgttcgaacaaaggtggcagttgcatcgaac E I K A I A R E P G V R T K V A V A S N gatccgaacgtggatcccataggtgcctgcatcggtgaaggaggatcgaggatagccgcc D P N V D P I G A C I G E G G S R I A A atactgaaggagctcaagggtgaaaaactcgacgttctgaagtggtcggacgatcccaaa I L K E L K G E K L D V L K W S D D P K cagctcatagcgaacgcccttgcgccggctaccgtcatagaagtggagatactcgacaaa Q L I A N A L A P A T V I E V E I L D K gagaacaaggccgcacgcgttctagttcctccgacacagctttccctcgccataggaaaa E N K A A R V L V P P T Q L S L A I G K ggagggcagaacgcgagactcgctgcaaagctcacaggatggaaaatagacataaaaccg G G Q N A R L A A K L T G W K I D I K P atcatgaacctgtga I M N L *
MNIGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEVVEEVEDPATQISLEEA KKIDPLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETR LPKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEVENGIVEIKAIAREPGVRTKVAVASN DPNVDPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKENKAARVLVPPTQLSLAIGK GGQNARLAAKLTGWKIDIKPIMNL
This information was obtained using the Protein Parameters tool on the ExPASy Molecular Biology Server.
Number of amino acids: 344
Molecular weight: 37920.3
Theoretical pI: 6.61
Amino acid composition:
Ala (A) 29 8.4%
Arg (R) 15 4.4%
Asn (N) 15 4.4%
Asp (D) 14 4.1%
Cys (C) 1 0.3%
Gln (Q) 10 2.9%
Glu (E) 39 11.3%
Gly (G) 24 7.0%
His (H) 0 0.0%
Ile (I) 36 10.5%
Leu (L) 33 9.6%
Lys (K) 38 11.0%
Met (M) 4 1.2%
Phe (F) 4 1.2%
Pro (P) 16 4.7%
Ser (S) 11 3.2%
Thr (T) 13 3.8%
Trp (W) 4 1.2%
Tyr (Y) 4 1.2%
Val (V) 34 9.9%
Asx (B) 0 0.0%
Glx (Z) 0 0.0%
Xaa (X) 0 0.0%
Total number of negatively charged residues (Asp + Glu): 53
Total number of positively charged residues (Arg + Lys): 53
Atomic composition:
Carbon C 1702
Hydrogen H 2844
Nitrogen N 456
Oxygen O 504
Sulfur S 5
Formula: C1702H2844N456O504S5
Total number of atoms: 5511
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 27400 28000 28020 27880 27200
Abs 0.1% (=1 g/l) 0.723 0.738 0.739 0.735 0.717
276 278 279 280 282
nm nm nm nm nm
Ext. coefficient 27400 28000 28020 27880 27200
Abs 0.1% (=1 g/l) 0.723 0.738 0.739 0.735 0.717
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 22.19
This classifies the protein as stable.
Aliphatic index: 115.32
Grand average of hydropathicity (GRAVY): -0.136