GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CNH - CNH domain
Pfam: PF00780 (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: CL0186
Length: 275
Sequences: 36901
Seq/Len: 134.19
HH_delta: 0.245 (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
40_Q53_L1.844932.726
11_L43_V1.742242.574
143_S154_G1.739672.570
11_L20_V1.697132.508
42_S97_A1.696332.506
97_A145_A1.688652.495
34_K52_V1.674212.474
152_C161_L1.6482.435
51_L60_V1.581432.337
12_V21_Y1.544972.283
18_L52_V1.487432.198
116_I153_V1.42772.109
117_L134_E1.39582.062
51_L101_G1.327061.961
58_L110_V1.323611.956
242_I251_V1.318461.948
11_L50_L1.29721.917
137_L153_V1.296211.915
160_Y169_P1.269261.875
160_Y172_L1.258471.859
44_L101_G1.256371.856
109_C146_F1.250331.847
153_V162_I1.236251.827
110_V119_Y1.229911.817
95_F111_A1.223781.808
52_V61_Y1.204721.780
131_L134_E1.197781.770
120_E123_D1.19191.761
62_D65_S1.185841.752
233_S244_F1.185141.751
117_L131_L1.182621.747
89_E110_V1.180281.744
142_S156_S1.159231.713
19_Y28_K1.144261.691
109_C118_I1.140961.686
59_Y86_K1.137371.680
102_H146_F1.114251.646
51_L108_L1.103871.631
243_A252_R1.055121.559
210_G243_A1.0531.556
227_W243_A1.052671.555
12_V19_Y1.045771.545
11_L41_L1.036531.531
13_G38_I1.032551.526
163_D166_T1.030311.522
89_E93_V1.029561.521
109_C151_I1.029391.521
137_L155_T1.028281.519
211_V219_P1.010411.493
22_D25_D0.98481.455
169_P172_L0.97791.445
109_C144_I0.973971.439
13_G41_L0.970931.435
137_L141_P0.955471.412
28_K31_R0.953131.408
19_Y31_R0.949531.403
211_V224_T0.938071.386
204_L236_Y0.918531.357
237_S240_Y0.884061.306
159_F205_C0.872711.289
227_W231_P0.867211.281
133_K167_G0.866991.281
189_S192_L0.851221.258
205_C213_V0.850121.256
162_I169_P0.836791.236
155_T158_G0.829561.226
12_V16_D0.825371.219
111_A141_P0.817861.208
152_C203_L0.816051.206
149_N165_N0.805411.190
10_L23_L0.79581.176
57_Q86_K0.792441.171
204_L212_F0.792391.171
51_L96_F0.792381.171
54_S57_Q0.791251.169
34_K38_I0.789471.166
213_V219_P0.786951.163
34_K54_S0.785161.160
112_V115_K0.763611.128
115_K134_E0.760021.123
147_L150_K0.75811.120
59_Y70_S0.756721.118
97_A144_I0.752011.111
44_L48_N0.751521.110
123_D130_K0.750041.108
119_Y131_L0.748561.106
109_C112_V0.747261.104
189_S197_L0.74681.103
145_A194_I0.746711.103
40_Q95_F0.739191.092
194_I235_A0.729111.077
42_S96_F0.72281.068
40_Q96_F0.720661.065
95_F143_S0.708281.046
210_G234_V0.705121.042
53_L96_F0.702531.038
107_R132_L0.700131.034
204_L241_L0.698331.032
150_K161_L0.698111.031
102_H106_R0.690261.020
9_R20_V0.685541.013
106_R122_N0.681481.007
240_Y251_V0.677591.001
103_E148_G0.674350.996
43_V63_L0.674260.996
18_L41_L0.673930.996
150_K170_S0.672260.993
44_L49_L0.668880.988
95_F144_I0.663670.981
53_L93_V0.662910.979
52_V59_Y0.657940.972
153_V160_Y0.649740.960
101_G121_W0.647440.957
227_W245_S0.645860.954
22_D29_P0.639830.945
70_S86_K0.6360.940
44_L47_L0.635520.939
202_F205_C0.635190.939
34_K59_Y0.634650.938
207_D211_V0.632880.935
14_T19_Y0.632230.934
103_E146_F0.630250.931
137_L162_I0.626620.926
29_P33_L0.626310.925
65_S69_V0.624230.922
204_L234_V0.619240.915
50_L63_L0.618490.914
245_S248_S0.616580.911
212_F236_Y0.616460.911
111_A144_I0.616150.910
118_I135_I0.616040.910
194_I234_V0.614050.907
146_F164_L0.613620.907
115_K136_S0.613420.906
14_T17_G0.609660.901
236_Y254_L0.608420.899
43_V50_L0.602720.891
44_L51_L0.602590.890
219_P224_T0.602280.890
21_Y28_K0.600290.887
194_I197_L0.599130.885
201_E214_N0.598030.884
196_Q199_D0.593840.877
139_D156_S0.589590.871
89_E113_K0.587160.868
196_Q236_Y0.582530.861
243_A250_E0.581580.859
102_H105_S0.580810.858
116_I135_I0.579390.856
152_C195_F0.578820.855
45_P105_S0.577880.854
140_P156_S0.577590.853
116_I144_I0.57620.851
214_N220_S0.574360.849
94_S142_S0.573210.847
15_E37_S0.570860.843
41_L52_V0.570570.843
89_E117_L0.570290.843
120_E132_L0.56990.842
110_V117_L0.569620.842
144_I153_V0.566910.838
89_E112_V0.565210.835
48_N64_D0.562820.832
11_L63_L0.561730.830
88_P119_Y0.560420.828
106_R109_C0.559850.827
49_L60_V0.558970.826
93_V96_F0.556060.822
209_I224_T0.556040.822
189_S195_F0.554350.819
197_L236_Y0.553990.819
154_G189_S0.551290.815
155_T160_Y0.550950.814
146_F151_I0.547180.808
8_D22_D0.546860.808
46_E49_L0.546410.807
43_V101_G0.544940.805
23_L26_P0.543780.803
97_A146_F0.542490.802
34_K61_Y0.542340.801
89_E119_Y0.541810.801
163_D170_S0.540650.799
62_D69_V0.539180.797
28_K33_L0.538710.796
227_W250_E0.536140.792
58_L96_F0.531420.785
41_L50_L0.529580.782
164_L167_G0.529130.782
147_L152_C0.526060.777
142_S232_Q0.52380.774
240_Y244_F0.521060.770
147_L195_F0.521010.770
173_L176_S0.519660.768
102_H107_R0.517280.764
152_C159_F0.514640.760
176_S205_C0.512940.758
199_D202_F0.512770.758
9_R43_V0.512330.757
8_D24_S0.510940.755
54_S59_Y0.510450.754
13_G52_V0.507910.750
175_P213_V0.507890.750
216_N219_P0.507040.749
107_R110_V0.506850.749
27_S32_I0.503660.744
145_A195_F0.501520.741
39_T94_S0.501220.741
191_P197_L0.500330.739
108_L121_W0.498240.736
45_P101_G0.497650.735
137_L160_Y0.496390.733
154_G192_L0.494060.730
9_R29_P0.493450.729
234_V243_A0.492720.728
34_K55_D0.490820.725
29_P32_I0.48720.720
107_R118_I0.486720.719
227_W252_R0.485190.717
60_V87_L0.484920.716
20_V43_V0.484070.715
151_I164_L0.48270.713
141_P155_T0.480730.710
112_V117_L0.478720.707
171_E217_G0.477440.705
122_N165_N0.477290.705
42_S101_G0.475930.703
60_V121_W0.475580.703
42_S51_L0.475140.702
142_S190_K0.471010.696
240_Y243_A0.469680.694
161_L171_E0.468310.692
137_L157_K0.466390.689
205_C211_V0.46580.688
18_L50_L0.464450.686
38_I52_V0.45720.676
150_K215_K0.456350.674
161_L173_L0.455850.674
59_Y68_P0.454940.672
60_V101_G0.453770.670
121_W124_P0.453770.670
6_W9_R0.453460.670
17_G37_S0.453430.670
22_D27_S0.453050.669
48_N62_D0.449690.664
97_A109_C0.449520.664
97_A101_G0.448370.662
231_P234_V0.447230.661
102_H109_C0.446310.659
235_A242_I0.444750.657
43_V236_Y0.443260.655
64_D122_N0.440220.650
111_A116_I0.439990.650
158_G174_D0.437630.647
189_S196_Q0.435790.644
141_P153_V0.435270.643
101_G146_F0.431830.638
44_L105_S0.430360.636
144_I151_I0.428260.633
191_P233_S0.427730.632
111_A153_V0.42730.631
135_I162_I0.426910.631
27_S31_R0.425480.629
147_L200_N0.423130.625
212_F225_I0.421010.622
96_F110_V0.417870.617
202_F212_F0.417860.617
195_F236_Y0.416290.615
241_L254_L0.416280.615
104_G107_R0.416250.615
8_D23_L0.414910.613
30_T33_L0.414660.613
120_E130_K0.413750.611
154_G205_C0.412140.609
210_G213_V0.411390.608
227_W246_S0.410460.606
13_G17_G0.41030.606
58_L93_V0.409240.605
201_E204_L0.406270.600
36_S54_S0.40620.600
236_Y241_L0.405810.600
16_D19_Y0.404430.598
9_R22_D0.404430.598
118_I133_K0.404260.597
192_L197_L0.403770.597
152_C215_K0.403190.596
245_S250_E0.402870.595
39_T92_G0.402680.595
53_L110_V0.401390.593
18_L38_I0.400380.592
209_I226_Q0.40020.591
113_K117_L0.398860.589
191_P195_F0.398580.589
221_R225_I0.398230.588
96_F108_L0.39790.588
145_A152_C0.393340.581
220_S224_T0.392780.580
27_S33_L0.392210.579
171_E176_S0.391340.578
101_G108_L0.391230.578
194_I236_Y0.390950.578
96_F101_G0.390850.577
51_L58_L0.389590.576
94_S140_P0.38840.574
25_D29_P0.388270.574
157_K160_Y0.386140.571
15_E39_T0.382760.566
145_A192_L0.382580.565
114_K140_P0.381540.564
139_D155_T0.381250.563
158_G172_L0.380420.562
36_S39_T0.380250.562
118_I146_F0.37760.558
217_G220_S0.375440.555
131_L169_P0.374860.554
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
4gqbB0.90181000.245
1nr0A0.87641000.27
4gqbB0.85821000.28
4j73A0.89091000.281
2ynnA0.89091000.284
1vyhC0.88361000.285
4j87A0.91271000.286
1erjA0.90551000.287
1vyhC0.807399.90.299
3dm0A0.887399.90.307

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