GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CDC24 - CDC24 Calponin
Pfam: PF06395 (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: 89
Sequences: 1109
Seq/Len: 12.46
HH_delta: 0.072 (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
54_K61_D0.625863.474
65_F70_L0.501432.783
20_F52_A0.396252.200
68_S72_G0.348851.936
54_K64_L0.310221.722
17_C21_N0.307241.705
53_C64_L0.278641.547
10_F15_P0.271831.509
50_I64_L0.258731.436
43_K67_I0.250941.393
51_Q55_Q0.241881.343
8_K11_R0.241361.340
49_F84_V0.240641.336
74_D77_G0.238921.326
14_Y18_V0.237321.317
39_L71_Y0.231761.286
79_V84_V0.224621.247
42_C71_Y0.223981.243
51_Q54_K0.223431.240
70_L81_V0.215421.196
24_Q55_Q0.213191.183
6_L82_I0.211041.171
82_I85_V0.207581.152
28_P31_V0.20651.146
43_K47_Y0.203911.132
49_F65_F0.203281.128
8_K73_D0.198721.103
79_V83_K0.197941.099
29_L32_D0.193231.073
43_K68_S0.189771.053
39_L42_C0.186461.035
12_Q15_P0.185921.032
77_G80_K0.185731.031
79_V82_I0.184051.022
7_W60_P0.183731.020
12_Q72_G0.183721.020
52_A55_Q0.182131.011
14_Y36_S0.181661.008
7_W78_F0.177940.988
69_D81_V0.17740.985
11_R42_C0.177230.984
21_N52_A0.175260.973
10_F43_K0.175130.972
81_V84_V0.171020.949
29_L58_G0.170990.949
46_I49_F0.170640.947
30_P33_P0.170420.946
11_R43_K0.170330.945
73_D77_G0.170280.945
65_F81_V0.16930.940
51_Q57_L0.166590.925
37_D74_D0.165330.918
77_G81_V0.163720.909
8_K57_L0.162110.900
77_G84_V0.161850.898
63_E66_T0.16120.895
40_K43_K0.161010.894
24_Q51_Q0.15860.880
10_F13_G0.15830.879
40_K46_I0.157720.875
7_W36_S0.157270.873
57_L84_V0.156620.869
67_I71_Y0.154940.860
40_K44_K0.154820.859
18_V58_G0.151560.841
30_P36_S0.150860.837
50_I59_F0.148940.827
46_I71_Y0.148770.826
79_V85_V0.148570.825
14_Y74_D0.147880.821
20_F57_L0.147770.820
43_K66_T0.147520.819
17_C28_P0.147010.816
22_A33_P0.14690.815
36_S42_C0.146330.812
19_L24_Q0.146280.812
36_S39_L0.145360.807
12_Q19_L0.14530.807
21_N27_E0.143160.795
24_Q27_E0.142460.791
9_L54_K0.142410.791
13_G17_C0.142080.789
44_K48_K0.140220.778
24_Q31_V0.139980.777
23_L28_P0.139790.776
49_F70_L0.139650.775
78_F82_I0.138490.769
33_P37_D0.137550.764
19_L23_L0.137290.762
43_K46_I0.136150.756
41_V44_K0.135630.753
37_D41_V0.135020.749
43_K59_F0.132790.737
24_Q28_P0.132670.736
25_P28_P0.130920.727
40_K45_A0.130270.723
27_E52_A0.129560.719
17_C20_F0.129320.718
31_V37_D0.129280.718
49_F53_C0.129220.717
9_L15_P0.128020.711
60_P69_D0.126060.700
22_A26_E0.125630.697
18_V29_L0.124920.693
23_L57_L0.124690.692
68_S74_D0.123560.686
18_V21_N0.123240.684
24_Q36_S0.122980.683
16_L23_L0.12280.682
23_L26_E0.122670.681
28_P53_C0.121960.677
64_L67_I0.121940.677
23_L82_I0.121460.674
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
3ky9A0.966399.90.072
1p5sA0.955199.80.101
1p2xA0.955199.80.107
2rr8A0.966399.80.126
1ujoA0.943899.80.127
3i6xA0.966399.80.129
1wymA0.943899.80.136
1wypA0.943899.80.137
1wynA0.943899.80.141
1h67A0.943899.80.142

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