2gnx Results: Difference between revisions

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   15: 3256-A 2oew-A  6.1  2.8  119  358    8      0      0    12 S    PROTEIN TRANSPORT programmed cell death 6-interacting  
   15: 3256-A 2oew-A  6.1  2.8  119  358    8      0      0    12 S    PROTEIN TRANSPORT programmed cell death 6-interacting  


However, a Dali analysis with the C-terminus of the protein showed us that
However, a Dali analysis carried out with the C-terminus of the protein produced one significant structural match, this being the GAF protein.

Revision as of 05:44, 11 June 2007

Structural analysis

A Dali analysis (Table 1) of our protein was highly inconclusive and there were no significant structural matches to our hypothetical protein.

Table 1: A Dali analysis of the 2GNX protein

NR. STRID1 STRID2  Z   RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
 1: 3023-A 2gnx-A 42.9  0.0  280   280  100      0      0     1 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	hypothetical pro
 2: 3023-A 2cmr-A  5.7  3.5  114   192   11      0      0    11 S    IMMUNOGLOBULIN COMPLEX 	d5 (fab heavy chain) d5 (fab li
 3: 3023-A 1j3w-A  5.7  3.2   99   134   12      0      0     9 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	giding protein-m
 4: 3023-A 1jmr-A  5.5  3.0   94   246    9      0      0    12 S    
 5: 3023-A 1f5m-B  5.5  5.0  107   177    9      0      0    13 S    SIGNALING PROTEIN 	gaf 	(saccharomyces cerevisiae) yeas
 6: 3023-A 1vcs-A  5.0  4.7   82   102    9      0      0     8 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	vesicle transpor
 7: 3023-A 1kt0-A  4.9  2.8   81   357    6      0      0     7 S    ISOMERASE 	51 kda fk506-binding protein (fkbp51) Mutant
 8: 3023-A 1e2a-A  4.9  4.5   80   102    9      0      0     6 S    TRANSFERASE 	enzyme iia (enzyme iii, lactose-specific i
 9: 3023-A 2d2s-A  4.8  3.1   75   217   11      0      0     5 S    ENDOCYTOSIS/EXOCYTOSIS 	exocyst complex component exo84
10: 3023-A 2oew-A  4.7  2.8  119   358    8      0      0    12 S    PROTEIN TRANSPORT 	programmed cell death 6-interacting 
11: 3023-A 1h3q-A  4.7  4.2   92   140    4      0      0    11 S    TRANSPORT 	sedlin (sedl) 	(mus musculus) mouse 	S.B.Jan
12: 3023-A 2oev-A  4.5 36.5  151   697    7      0      0    14 S    PROTEIN TRANSPORT 	programmed cell death 6-interacting 
13: 3023-A 2cwy-A  4.5  2.4   82    92   20      0      0     7 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	hypothetical pro
14: 3023-A 2c5i-T  4.5  2.8   75    93   11      0      0     5 S    PROTEIN TRANSPORT/COMPLEX 	t-snare affecting a late gol
15: 3023-A 3nul    4.4  3.4   93   130    5      0      0    11 S    ACTIN-BINDING PROTEIN 	profilin i 	(arabidopsis thalian

A Dali analysis carried out separately with only the N-terminus (Table 2) of our protein also did not produce any significant structural matches.

Table 2: Dali analysis of N-terminal domain

 NR. STRID1 STRID2  Z   RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
  1: 3256-A 2gnx-A 23.2  0.0  173   280  100      0      0     1 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	hypothetical pro
  2: 3256-A 1e2a-A  7.5  4.5   80   102    9      0      0     6 S    TRANSFERASE 	enzyme iia (enzyme iii, lactose-specific i
  3: 3256-A 1kt0-A  7.4  2.8   81   357    6      0      0     7 S    ISOMERASE 	51 kda fk506-binding protein (fkbp51) Mutant
  4: 3256-A 2d2s-A  7.3  3.1   75   217   11      0      0     5 S    ENDOCYTOSIS/EXOCYTOSIS 	exocyst complex component exo84
  5: 3256-A 1vcs-A  7.3  4.7   78   102    9      0      0     7 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION 	vesicle transpor
  6: 3256-A 2cmr-A  6.9  3.2  104   192   11      0      0     9 S    IMMUNOGLOBULIN COMPLEX 	d5 (fab heavy chain) d5 (fab li
  7: 3256-A 2c5i-T  6.9  2.8   75    93   11      0      0     5 S    PROTEIN TRANSPORT/COMPLEX 	t-snare affecting a late gol
  8: 3256-A 2h7o-A  6.8  3.0   81   270    5      0      0     7 S    SIGNALING PROTEIN 	protein kinase ypka fragment (protei
  9: 3256-A 2h7v-C  6.6  4.2   76   269   13      0      0     5 S    SIGNALING PROTEIN 	migration-inducing protein 5 (ras-re
 10: 3256-A 2dnx-A  6.5  4.9   80   130    6      0      0     6 S    TRANSPORT PROTEIN 	syntaxin-12 fragment 	(homo sapiens)
 11: 3256-A 1hg5-A  6.5  3.2   85   263    9      0      0     6 S     ENDOCYTOSIS 	clathrin assembly protein short form frag
 12: 3256-A 1a17    6.4  2.5   71   159    3      0      0     5 S    HYDROLASE 	serineTHREONINE PROTEIN PHOSPHATASE 5 fragme
 13: 3256-A 2if4-A  6.3  2.5   82   258    7      0      0     7 S    SIGNALING PROTEIN 	atfkbp42 fragment (twd1 (twisted dwa
 14: 3256-A 1owa-A  6.2  3.3   76   156   12      0      0     6 S    CYTOKINE 	spectrin alpha chain, erythrocyte fragment (e
 15: 3256-A 2oew-A  6.1  2.8  119   358    8      0      0    12 S    PROTEIN TRANSPORT 	programmed cell death 6-interacting 

However, a Dali analysis carried out with the C-terminus of the protein produced one significant structural match, this being the GAF protein.