GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CH - Calponin homology (CH) domain
Pfam: PF00307 (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: CL0188
Length: 108
Sequences: 3365
Seq/Len: 31.16
HH_delta: 0.041 (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
60_D63_E0.563952.218
70_E74_K0.557822.194
65_I88_V0.523472.058
73_E80_P0.500841.970
14_K36_K0.476731.875
62_L66_E0.471371.854
66_E70_E0.46881.844
87_L96_V0.45441.787
11_H40_K0.404461.591
35_C68_A0.400651.576
5_L9_N0.397141.562
35_C67_L0.395751.556
21_V33_V0.389041.530
29_R61_K0.38571.517
92_D95_S0.359251.413
11_H37_L0.359121.412
66_E84_P0.356921.404
70_E73_E0.353471.390
39_N44_G0.35331.389
65_I69_L0.342251.346
23_N26_E0.335631.320
101_W104_F0.323261.271
98_S101_W0.32261.269
48_L51_I0.318971.254
25_S93_E0.311881.226
9_N15_Y0.310611.221
47_D50_K0.30681.206
4_L104_F0.304461.197
32_V36_K0.298661.174
62_L84_P0.293561.154
69_L73_E0.288451.134
93_E101_W0.28821.133
73_E79_P0.285371.122
71_A76_L0.282311.110
15_Y36_K0.281911.109
34_L65_I0.280471.103
95_S98_S0.279871.101
19_R33_V0.279681.100
98_S102_Q0.278321.094
10_S13_E0.276651.088
4_L100_L0.275321.083
9_N12_L0.273421.075
39_N45_T0.272451.071
68_A72_A0.267231.051
62_L88_V0.266371.047
35_C71_A0.26581.045
38_I72_A0.264631.041
93_E103_L0.261471.028
38_I103_L0.261361.028
19_R27_D0.255071.003
46_I67_L0.25491.002
2_K6_K0.254871.002
86_D95_S0.254611.001
5_L24_F0.252270.992
91_G98_S0.251240.988
6_K10_S0.249780.982
83_S86_D0.249530.981
61_K88_V0.249080.979
21_V27_D0.248690.978
86_D92_D0.247020.971
38_I71_A0.246010.967
91_G96_V0.245530.966
23_N27_D0.243810.959
3_E6_K0.240630.946
26_E29_R0.239910.943
34_L96_V0.239120.940
91_G94_K0.235760.927
92_D96_V0.234440.922
87_L99_F0.233050.916
8_I33_V0.232960.916
68_A99_F0.231470.910
69_L72_A0.230850.908
35_C46_I0.22940.902
29_R91_G0.225310.886
5_L21_V0.22360.879
82_L99_F0.222840.876
66_E83_S0.222270.874
95_S101_W0.221830.872
72_A99_F0.221770.872
19_R36_K0.221050.869
49_K52_N0.217790.856
42_F45_T0.217570.856
92_D99_F0.21680.853
39_N48_L0.216590.852
52_N67_L0.215640.848
91_G99_F0.215020.846
72_A78_I0.214940.845
35_C51_I0.214560.844
97_L101_W0.213840.841
45_T76_L0.211990.834
20_R23_N0.210940.830
63_E66_E0.210920.829
46_I51_I0.210520.828
61_K64_N0.209070.822
15_Y19_R0.208780.821
62_L85_E0.208560.820
82_L102_Q0.206520.812
50_K66_E0.205870.810
63_E67_L0.202890.798
30_D33_V0.20150.792
86_D96_V0.201010.790
58_P90_K0.200880.790
39_N46_I0.199060.783
9_N19_R0.198450.780
15_Y39_N0.197570.777
22_T27_D0.196850.774
11_H20_R0.196660.773
5_L27_D0.196640.773
14_K18_G0.194780.766
14_K40_K0.193260.760
8_I12_L0.191190.752
69_L84_P0.189980.747
44_G71_A0.189450.745
41_L103_L0.189370.745
2_K10_S0.187990.739
97_L102_Q0.187640.738
58_P62_L0.186850.735
38_I68_A0.185970.731
15_Y23_N0.185880.731
8_I34_L0.185820.731
90_K94_K0.185480.729
24_F97_L0.183590.722
24_F28_L0.183490.722
8_I28_L0.183310.721
59_F64_N0.182870.719
95_S99_F0.182640.718
2_K5_L0.181760.715
63_E86_D0.18010.708
52_N62_L0.179320.705
8_I11_H0.178330.701
4_L97_L0.178280.701
65_I68_A0.178140.701
65_I84_P0.177440.698
35_C39_N0.176690.695
34_L100_L0.174210.685
4_L24_F0.173880.684
59_F82_L0.173450.682
11_H14_K0.173430.682
61_K65_I0.172830.680
77_G86_D0.171760.675
90_K102_Q0.171640.675
44_G76_L0.171530.675
58_P88_V0.170260.670
6_K11_H0.169940.668
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
1wylA0.944499.60.041
2d88A0.944499.60.054
1bhdA0.944499.60.059
1wyqA0.944499.60.059
2d87A0.944499.60.06
2d89A0.935299.60.062
1bkrA0.944499.60.062
3f7pA0.944499.50.073
1sjjA0.944499.50.076
1rt8A0.935299.50.079

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