GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PuR_N - Bacterial purine repressor N-terminal
Pfam: PF09182 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0123
Length: 70
Sequences: 28816
Seq/Len: 411.66
HH_delta: 0.145 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
12_Y29_R2.871982.630
23_L38_S2.726462.497
35_S38_S2.427082.223
22_S25_Y2.033531.862
57_E67_R1.700911.558
12_Y21_I1.682151.541
25_Y29_R1.679211.538
6_L40_D1.633251.496
20_L67_R1.613691.478
23_L34_K1.603721.469
12_Y16_N1.603521.469
27_A34_K1.484671.360
40_D43_I1.483581.359
59_V67_R1.475981.352
24_T34_K1.457951.335
12_Y30_F1.43051.310
16_N21_I1.357731.243
34_K38_S1.35551.241
6_L43_I1.343611.231
33_A36_S1.282711.175
16_N19_K1.274641.167
9_I26_F1.23481.131
26_F37_I1.161181.063
36_S40_D1.144851.049
39_E42_S1.138071.042
12_Y15_E1.135061.040
11_K15_E1.125171.030
20_L65_G1.118941.025
38_S42_S1.115161.021
8_A11_K1.114611.021
41_L66_V1.111261.018
9_I37_I1.08140.990
24_T28_E1.07180.982
35_S39_E1.064540.975
56_I65_G1.060820.972
7_V11_K1.052010.963
39_E43_I1.042180.954
23_L27_A1.032650.946
13_L21_I1.025540.939
36_S39_E0.976070.894
8_A12_Y0.970930.889
25_Y28_E0.965370.884
8_A30_F0.928850.851
22_S65_G0.905350.829
32_A36_S0.900630.825
56_I67_R0.898750.823
20_L59_V0.891550.817
27_A37_I0.878680.805
12_Y26_F0.871370.798
42_S49_E0.868660.796
19_K25_Y0.857210.785
21_I25_Y0.843810.773
21_I29_R0.837010.767
53_L68_Y0.823420.754
43_I51_E0.819760.751
33_A40_D0.800870.733
20_L62_A0.795410.728
32_A37_I0.785890.720
14_L68_Y0.783090.717
9_I40_D0.778610.713
32_A40_D0.764450.700
30_F37_I0.762170.698
24_T27_A0.752980.690
49_E57_E0.75290.690
49_E52_G0.74340.681
10_T53_L0.734740.673
16_N25_Y0.722210.661
16_N29_R0.712630.653
13_L56_I0.702930.644
59_V62_A0.689470.631
61_G65_G0.685220.628
13_L20_L0.672050.615
11_K14_L0.668650.612
10_T68_Y0.653110.598
49_E58_T0.644310.590
58_T66_V0.63890.585
26_F41_L0.637230.584
23_L41_L0.630090.577
11_K51_E0.627030.574
23_L66_V0.623020.571
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
1biaA0.8714980.145
1o57A1980.151
3rkxA0.8857980.153
3k69A0.914397.90.165
3sqnA0.997.90.18
2y75A0.914397.80.184
1j5yA0.871497.80.197
4hf0A0.914397.80.203
1ylfA0.997.80.203
3r4kA0.885797.80.205

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