GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CLP_protease - Clp protease
Pfam: PF00574 (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: CL0127
Length: 182
Sequences: 13484
Seq/Len: 74.09
HH_delta: 0.138 (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
79_T96_G2.325993.579
103_A175_I2.307483.551
108_R163_W1.950343.001
105_P180_E1.744422.684
41_E74_K1.686442.595
38_L69_A1.647512.535
168_E171_E1.522992.343
34_I69_A1.418562.183
165_S168_E1.397852.151
167_E171_E1.273231.959
102_Y179_I1.257251.935
86_A110_M1.219451.876
81_V85_A1.200671.847
168_E172_Y1.171891.803
103_A109_F1.150261.770
155_E159_D1.135031.746
153_E172_Y1.118431.721
105_P167_E1.118311.721
170_L175_I1.109011.706
153_E156_E1.102761.697
102_Y177_E1.094231.684
156_E162_T1.089041.676
141_N145_E1.080971.663
81_V93_F1.039991.600
151_K155_E1.013441.559
70_I77_V0.991971.526
55_S89_A0.981871.511
28_E32_R0.979121.507
76_P97_D0.97221.496
41_E69_A0.970251.493
18_I52_Y0.961711.480
170_L178_I0.957741.474
49_I73_S0.939971.446
37_L73_S0.934771.438
20_F52_Y0.916431.410
68_D72_S0.915081.408
78_T102_Y0.894541.376
157_L172_Y0.887771.366
167_E170_L0.886191.364
39_Y43_E0.869741.338
84_L108_R0.8651.331
40_L49_I0.861691.326
98_K177_E0.852581.312
34_I38_L0.846611.303
26_D29_S0.841721.295
48_P76_P0.84041.293
32_R36_Q0.831051.279
82_L106_N0.830931.279
48_P78_T0.830541.278
170_L177_E0.814911.254
166_A178_I0.806051.240
82_L104_S0.801411.233
157_L164_L0.792561.220
19_I36_Q0.782681.204
46_N75_A0.78021.201
103_A107_S0.778941.199
41_E73_S0.775731.194
52_Y82_L0.775121.193
90_T111_I0.773061.190
156_E176_D0.767681.181
41_E75_A0.766711.180
162_T168_E0.748471.152
63_G88_A0.746071.148
27_E31_N0.746061.148
50_N80_V0.740411.139
114_P161_D0.726151.117
27_E62_A0.725211.116
90_T143_Y0.721381.110
153_E168_E0.695451.070
43_E46_N0.688741.060
77_V96_G0.686711.057
141_N151_K0.680291.047
152_E176_D0.675851.040
36_Q39_Y0.671781.034
91_L142_I0.666261.025
164_L172_Y0.661021.017
81_V107_S0.658831.014
110_M163_W0.65141.002
94_L146_R0.65021.000
147_T153_E0.648480.998
38_L42_N0.64560.993
50_N78_T0.643620.990
98_K176_D0.636320.979
71_R145_E0.628340.967
169_A174_I0.621840.957
121_N124_E0.606520.933
156_E177_E0.605410.932
77_V97_D0.603380.928
87_S112_H0.597660.920
18_I80_V0.593170.913
34_I65_A0.589040.906
80_V102_Y0.586890.903
90_T109_F0.5810.894
143_Y147_T0.580070.893
30_A34_I0.579020.891
23_G26_D0.569130.876
52_Y80_V0.566830.872
31_N35_S0.566760.872
36_Q40_L0.566550.872
152_E155_E0.566360.871
49_I75_A0.559680.861
21_L29_S0.559640.861
21_L55_S0.556280.856
81_V109_F0.556260.856
44_D75_A0.553540.852
175_I178_I0.549540.846
37_L70_I0.54530.839
50_N54_N0.540610.832
167_E178_I0.538940.829
86_A112_H0.537360.827
21_L51_I0.534360.822
35_S39_Y0.53370.821
51_I77_V0.53080.817
141_N144_A0.518920.798
29_S32_R0.518210.797
23_G29_S0.513970.791
94_L174_I0.511340.787
53_I84_L0.510950.786
169_A175_I0.507610.781
105_P178_I0.494320.761
25_I30_A0.492370.758
67_Y71_R0.491230.756
88_A91_L0.490530.755
166_A175_I0.490450.755
43_E75_A0.487970.751
93_F109_F0.48120.740
93_F96_G0.479410.738
71_R142_I0.475320.731
18_I50_N0.474610.730
85_A89_A0.473580.729
108_R165_S0.472890.728
98_K102_Y0.472440.727
30_A66_I0.470870.725
143_Y154_I0.470390.724
94_L143_Y0.469220.722
69_A72_S0.463060.713
59_D62_A0.461140.710
84_L163_W0.459540.707
51_I54_N0.45640.702
71_R95_A0.45630.702
115_S163_W0.454350.699
120_G124_E0.450420.693
67_Y95_A0.448410.690
54_N82_L0.447140.688
147_T157_L0.445730.686
37_L77_V0.444890.685
32_R35_S0.444420.684
73_S77_V0.435870.671
147_T154_I0.435380.670
69_A73_S0.433660.667
33_L66_I0.42880.660
28_E31_N0.428660.660
144_A151_K0.426720.657
120_G125_L0.421580.649
40_L73_S0.417020.642
144_A154_I0.415340.639
144_A147_T0.412620.635
90_T93_F0.412410.635
164_L169_A0.410980.632
110_M161_D0.40920.630
143_Y146_R0.404830.623
58_G87_S0.404230.622
19_I40_L0.400420.616
156_E160_R0.399640.615
103_A170_L0.399290.614
40_L75_A0.399150.614
86_A163_W0.399020.614
111_I158_M0.398490.613
148_G153_E0.398230.613
86_A113_Q0.396170.610
91_L113_Q0.393820.606
142_I146_R0.393120.605
25_I29_S0.392970.605
48_P54_N0.391980.603
26_D62_A0.389550.599
91_L94_L0.38830.597
104_S107_S0.387550.596
87_S111_I0.387540.596
35_S38_L0.386980.595
49_I77_V0.38680.595
103_A166_A0.384830.592
40_L46_N0.383450.590
58_G120_G0.38220.588
21_L25_I0.379150.583
85_A93_F0.377810.581
122_A125_L0.377690.581
64_L67_Y0.372590.573
68_D71_R0.37180.572
30_A62_A0.370850.571
113_Q119_G0.370630.570
51_I79_T0.370080.569
112_H116_T0.369830.569
91_L111_I0.368660.567
39_Y42_N0.36790.566
166_A170_L0.366180.563
90_T94_L0.365760.563
156_E159_D0.36510.562
54_N57_G0.363160.559
37_L49_I0.361420.556
23_G59_D0.361210.556
109_F169_A0.360530.555
19_I37_L0.358980.552
27_E30_A0.357930.551
146_R152_E0.357630.550
46_N49_I0.357090.549
91_L122_A0.356860.549
103_A178_I0.355150.546
146_R176_D0.35240.542
143_Y158_M0.346020.532
88_A113_Q0.344760.530
64_L68_D0.342270.527
147_T174_I0.340110.523
67_Y146_R0.340020.523
71_R146_R0.338070.520
94_L142_I0.3340.514
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
1tg6A11000.138
4jcqA0.99451000.139
1y7oA11000.144
3qwdA11000.148
3p2lA11000.149
4gm2A11000.156
1yg6A11000.158
2cbyA11000.163
2f6iA0.99451000.183
3vivA0.945199.90.293

Page generated in 0.0153 seconds.