GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CRISPR_Cas2 - CRISPR associated protein Cas2
Pfam: PF09827 (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. )
Length: 78
Sequences: 1333
Seq/Len: 17.09
HH_delta: -0.052 (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
68_C71_C0.913113.451
20_R29_R0.789042.982
13_N16_R0.67362.546
22_I50_E0.540362.042
20_R24_K0.50861.922
36_E65_Y0.501341.895
7_A34_V0.482071.822
22_I54_L0.479151.811
17_N21_K0.446721.688
6_V23_L0.439391.661
51_L62_I0.436721.650
19_V51_L0.427921.617
22_I25_S0.423611.601
30_I63_R0.393991.489
26_Y50_E0.378811.432
39_L47_L0.37221.407
25_S50_E0.36891.394
48_R64_I0.358841.356
44_L64_I0.35571.344
66_P74_K0.325881.232
46_K50_E0.321821.216
6_V64_I0.31681.197
19_V55_I0.310461.173
10_I16_R0.307891.164
56_D60_D0.301751.140
52_E57_P0.293361.109
30_I36_E0.277851.050
15_R60_D0.277791.050
52_E64_I0.276031.043
18_K54_L0.273761.035
4_Y66_P0.270941.024
44_L48_R0.270121.021
41_N45_R0.269181.017
20_R23_L0.26491.001
30_I65_Y0.261820.989
6_V27_G0.255760.967
27_G37_G0.248540.939
9_D33_S0.248520.939
24_K29_R0.248120.938
16_R20_R0.245880.929
19_V22_I0.245720.929
12_D16_R0.241320.912
49_R52_E0.23910.904
39_L43_E0.237910.899
53_K57_P0.234450.886
47_L50_E0.232320.878
16_R23_L0.23190.876
22_I47_L0.229740.868
44_L66_P0.229320.867
31_Q34_V0.226510.856
5_L67_L0.224910.850
67_L72_F0.223180.843
9_D31_Q0.222270.840
40_T43_E0.220850.835
12_D15_R0.215240.813
45_R48_R0.214710.811
5_L36_E0.214210.810
6_V37_G0.211280.798
8_Y33_S0.208990.790
4_Y41_N0.208080.786
21_K24_K0.20780.785
7_A32_Y0.205420.776
46_K49_R0.20440.772
18_K58_D0.203150.768
30_I61_S0.201710.762
55_I62_I0.200870.759
5_L65_Y0.200670.758
45_R49_R0.199470.754
70_N74_K0.199110.752
42_A46_K0.196730.743
10_I35_F0.19590.740
20_R35_F0.195530.739
51_L54_L0.1950.737
48_R51_L0.194850.736
5_L34_V0.193160.730
8_Y63_R0.191590.724
13_N17_N0.188610.713
26_Y36_E0.1870.707
22_I51_L0.186340.704
5_L63_R0.186160.704
45_R52_E0.186110.703
16_R29_R0.185180.700
10_I19_V0.183830.695
69_D72_F0.183590.694
26_Y47_L0.182140.688
8_Y60_D0.180810.683
7_A37_G0.179740.679
48_R54_L0.179010.677
4_Y39_L0.177740.672
41_N73_K0.177660.671
53_K66_P0.17480.661
29_R32_Y0.174480.659
14_K18_K0.17430.659
3_L38_N0.173740.657
23_L47_L0.173360.655
45_R50_E0.172340.651
8_Y20_R0.171910.650
38_N73_K0.17160.649
6_V48_R0.171380.648
27_G35_F0.171330.647
28_T45_R0.168010.635
46_K52_E0.167820.634
61_S65_Y0.167530.633
6_V47_L0.166280.628
32_Y44_L0.165640.626
31_Q35_F0.16520.624
24_K38_N0.16480.623
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
4es1A199.8-0.052
3oq2A199.8-0.007
3excX0.987299.80.004
2i0xA0.948799.80.027
1zpwX0.948799.70.032
2ivyA199.70.035
3ui3A196.40.698
2l69A0.884621.10.865
4irxA0.9359170.871
4iw7A0.79499.20.885

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