GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CutC - CutC family
Pfam: PF03932 (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: CL0036
Length: 201
Sequences: 11353
Seq/Len: 56.48
HH_delta: 0.049 (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
184_V196_I1.54893.131
14_L48_A1.458442.948
14_L18_A1.360282.749
46_R87_D1.212942.452
15_A19_G1.147692.320
17_E50_D1.125162.274
185_P189_E1.12142.267
79_R83_E1.108052.240
17_E51_I1.081982.187
161_K165_E0.998752.019
40_G43_R0.968731.958
179_V187_L0.935391.891
174_M195_E0.92291.865
106_E139_L0.904231.828
106_E110_E0.88851.796
39_L80_M0.87361.766
162_E166_Q0.872821.764
44_Q47_E0.86331.745
101_D104_A0.860461.739
188_V196_I0.843171.704
13_A24_I0.833241.684
80_M83_E0.804931.627
17_E49_V0.798751.614
164_V194_R0.793121.603
40_G44_Q0.781861.580
186_E189_E0.775031.566
135_Q139_L0.767611.551
14_L17_E0.759811.536
137_I171_I0.754071.524
13_A45_A0.744621.505
164_V173_I0.741341.498
109_I113_G0.737531.491
12_D15_A0.732591.481
158_E162_E0.716011.447
131_E134_E0.706331.428
135_Q138_E0.705771.426
78_I108_L0.7011.417
172_E194_R0.694211.403
137_I170_R0.688211.391
183_N186_E0.680411.375
162_E165_E0.67271.360
180_R183_N0.671581.357
160_L164_V0.660921.336
43_R47_E0.659111.332
53_V86_A0.653241.320
128_D131_E0.653031.320
11_E14_L0.644811.303
101_D107_E0.642661.299
15_A18_A0.642431.298
43_R84_L0.642411.298
43_R83_E0.639831.293
182_E186_E0.636461.286
34_G58_R0.625891.265
103_E107_E0.618661.250
11_E15_A0.616881.247
24_I51_I0.608091.229
187_L193_V0.608041.229
58_R100_I0.606071.225
103_E139_L0.605981.225
175_P193_V0.602841.218
161_K191_T0.599061.211
130_E162_E0.588331.189
104_A107_E0.5871.186
131_E135_Q0.580231.173
80_M84_L0.576981.166
182_E185_P0.569911.152
158_E161_K0.561541.135
107_E111_A0.561171.134
108_L111_A0.561091.134
23_R88_G0.560071.132
172_E195_E0.552521.117
164_V171_I0.549721.111
85_G113_G0.544641.101
78_I112_A0.53971.091
22_D52_P0.537751.087
159_N162_E0.534231.080
13_A49_V0.526921.065
23_R195_E0.520621.052
39_L43_R0.520581.052
38_S41_L0.518641.048
57_I81_L0.517231.045
181_A185_P0.514071.039
79_R111_A0.511691.034
79_R108_L0.511541.034
52_P87_D0.506081.023
41_L45_A0.499231.009
79_R112_A0.495671.002
127_P135_Q0.493780.998
147_S150_A0.493780.998
187_L196_I0.493430.997
145_L183_N0.490650.992
134_E166_Q0.488930.988
81_L86_A0.486360.983
17_E20_G0.475580.961
90_V118_T0.475520.961
39_L84_L0.475470.961
39_L81_L0.473310.957
134_E137_I0.471180.952
49_V52_P0.471040.952
107_E110_E0.465420.941
155_E158_E0.458930.928
130_E134_E0.455760.921
42_I84_L0.455290.920
60_R108_L0.453970.918
121_R124_D0.453550.917
157_I187_L0.45220.914
137_I169_G0.447650.905
41_L44_Q0.446830.903
157_I186_E0.444240.898
134_E138_E0.43980.889
82_R112_A0.439230.888
183_N187_L0.438990.887
32_V35_L0.434560.878
90_V141_F0.425350.860
16_A21_A0.421360.852
103_E106_E0.420270.849
54_H58_R0.415580.840
132_A135_Q0.413340.835
175_P179_V0.404650.818
165_E192_G0.400930.810
42_I86_A0.399960.808
120_H123_F0.397720.804
26_L42_I0.397360.803
151_P186_E0.395360.799
163_L166_Q0.393420.795
175_P187_L0.391970.792
45_A51_I0.390440.789
160_L173_I0.389520.787
155_E159_N0.387160.783
117_V133_L0.385790.780
146_T153_A0.384040.776
152_T155_E0.383810.776
79_R115_M0.380540.769
186_E191_T0.380470.769
46_R53_V0.378620.765
91_F102_E0.37480.758
142_D160_L0.373980.756
43_R80_M0.373020.754
102_E105_L0.372880.754
159_N163_L0.370280.748
100_I108_L0.365790.739
130_E133_L0.364610.737
93_A100_I0.364420.737
52_P88_G0.362320.732
160_L193_V0.359990.728
179_V184_V0.357690.723
16_A24_I0.357210.722
102_E135_Q0.356290.720
181_A184_V0.355220.718
79_R82_R0.354360.716
13_A17_E0.354190.716
26_L45_A0.3520.711
127_P132_A0.351930.711
91_F105_L0.351420.710
55_V81_L0.349640.707
61_G105_L0.348360.704
157_I160_L0.347120.702
42_I55_V0.346790.701
46_R84_L0.346380.700
23_R172_E0.344710.697
14_L49_V0.342910.693
102_E117_V0.34050.688
42_I83_E0.340270.688
128_D132_A0.33820.684
161_K164_V0.335620.678
164_V191_T0.33480.677
44_Q48_A0.33470.676
26_L41_L0.334140.675
103_E152_T0.33410.675
105_L108_L0.333880.675
34_G59_P0.332360.672
166_Q169_G0.331230.669
93_A132_A0.330260.668
140_G171_I0.329950.667
142_D172_E0.329750.666
78_I89_F0.327530.662
105_L109_I0.327140.661
54_H57_I0.326930.661
42_I46_R0.326830.661
157_I175_P0.326780.660
154_L186_E0.326340.660
113_G142_D0.326260.659
116_P119_F0.324820.657
78_I82_R0.324480.656
25_E92_G0.32380.654
130_E166_Q0.323610.654
104_A108_L0.322950.653
157_I191_T0.320920.649
42_I81_L0.319720.646
23_R52_P0.318820.644
55_V58_R0.318570.644
108_L112_A0.318130.643
13_A53_V0.317240.641
116_P141_F0.316050.639
24_I49_V0.313650.634
20_G51_I0.312190.631
92_G176_G0.311320.629
169_G172_E0.307140.621
146_T159_N0.302160.611
88_G141_F0.299180.605
38_S80_M0.296810.600
120_H124_D0.292140.590
160_L175_P0.291550.589
143_R172_E0.291150.588
144_V173_I0.289320.585
106_E135_Q0.288820.584
184_V188_V0.287710.582
93_A102_E0.286450.579
37_P41_L0.285740.578
132_A136_L0.28420.574
161_K186_E0.28380.574
146_T175_P0.281810.570
129_P132_A0.28130.569
142_D176_G0.280450.567
23_R174_M0.279610.565
187_L191_T0.279140.564
121_R147_S0.274860.556
153_A156_G0.274080.554
115_M120_H0.273950.554
130_E135_Q0.272210.550
82_R115_M0.271840.549
83_E112_A0.271740.549
25_E176_G0.271550.549
113_G116_P0.271380.549
54_H90_V0.26890.543
136_L139_L0.264210.534
141_F195_E0.263860.533
156_G159_N0.263350.532
173_I193_V0.263260.532
129_P133_L0.263240.532
103_E135_Q0.2630.532
110_E115_M0.262160.530
144_V160_L0.261720.529
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
3iwpA11000.049
2bdqA11000.084
1twdA0.991000.09
3inpA0.870699.70.49
3ovpA0.870699.70.504
3ctlA0.870699.70.507
1h1yA0.870699.60.519
4axkA0.890599.60.524
3vndA0.915499.60.524
1tqjA0.875699.60.528

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