GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BNR_2 - BNR repeat-like domain
Pfam: PF13088 (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: CL0434
Length: 275
Sequences: 3149
Seq/Len: 11.45
HH_delta: 0.279 (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
120_R141_D0.625024.862
86_D90_T0.4813.742
191_D195_T0.477533.715
140_S144_G0.460723.584
241_D245_T0.45533.542
60_R85_T0.44423.456
142_D146_T0.425163.307
84_S88_G0.418413.255
60_R83_R0.415083.229
27_D31_T0.414443.224
189_S193_G0.339832.644
171_R190_T0.338792.636
239_S243_G0.338532.633
171_R188_R0.299782.332
220_R240_E0.298552.322
23_S27_D0.295932.302
120_R139_Y0.294252.289
140_S146_T0.27192.115
189_S195_T0.26462.058
144_G147_W0.228621.778
239_S245_T0.226851.765
141_D148_S0.212381.652
26_T33_S0.212141.650
56_D62_W0.20721.612
117_P166_E0.204521.591
239_S246_W0.204441.590
220_R238_V0.200961.563
61_L91_W0.21.556
116_L122_I0.199081.549
53_L63_L0.193271.503
161_E177_R0.192891.501
167_L173_L0.192631.499
84_S90_T0.19021.480
187_S196_W0.185891.446
83_R95_T0.183041.424
208_N211_I0.181031.408
135_A162_P0.18051.404
216_L219_G0.179581.397
27_D30_K0.176051.370
115_Q121_L0.175311.364
173_L188_R0.175211.363
26_T89_K0.174581.358
167_L171_R0.172641.343
140_S147_W0.172591.343
240_E247_S0.172421.341
65_Y82_S0.172041.338
56_D60_R0.171471.334
122_I137_V0.171311.333
243_G246_W0.170181.324
23_S29_G0.169251.317
82_S94_P0.168441.310
57_P115_Q0.163811.274
56_D143_G0.159391.240
251_T254_D0.159211.239
62_W81_Y0.155421.209
119_G170_G0.154461.202
62_W83_R0.153491.194
139_Y148_S0.15261.187
85_T92_S0.150071.167
139_Y150_G0.149991.167
58_D143_G0.149981.167
39_A48_Y0.149931.166
88_G91_W0.147961.151
22_R26_T0.146521.140
86_D89_K0.1461.136
22_R33_S0.145381.131
190_T197_S0.1431.112
142_D145_K0.142461.108
83_R92_S0.14111.098
91_W147_W0.138971.081
64_F81_Y0.13861.078
50_N53_L0.138471.077
84_S91_W0.138241.075
189_S196_W0.138211.075
148_S194_R0.137521.070
216_L220_R0.136851.065
124_P137_V0.1361.058
50_N161_E0.134731.048
241_D244_K0.134071.043
121_L140_S0.132031.027
107_G110_R0.130281.013
187_S199_P0.130281.013
138_Y150_G0.129881.010
95_T145_K0.129831.010
197_S244_K0.129311.006
237_Y248_R0.12891.003
90_T245_T0.128811.002
174_A196_W0.128691.001
139_Y194_R0.128430.999
80_Y96_D0.128370.999
49_G68_G0.128230.998
207_P210_S0.127090.989
124_P164_I0.126730.986
122_I189_S0.126310.983
32_W196_W0.126070.981
176_F187_S0.126030.980
145_K244_K0.125250.974
164_I172_L0.124590.969
32_W147_W0.123660.962
147_W196_W0.123590.961
212_S215_R0.122710.955
175_V184_I0.122560.953
97_L100_G0.122150.950
19_V22_R0.122090.950
191_D194_R0.12180.948
204_L207_P0.121520.945
22_R38_V0.120980.941
70_S130_G0.120170.935
184_I187_S0.119890.933
222_L236_L0.119880.933
37_I40_D0.118790.924
52_S161_E0.118530.922
144_G193_G0.11770.916
111_G123_A0.117460.914
212_S216_L0.117190.912
225_Y237_Y0.117020.910
213_L221_L0.116470.906
23_S31_T0.116170.904
114_I166_E0.116040.903
146_T149_S0.114890.894
241_D246_W0.114080.887
118_D141_D0.113810.885
224_V236_L0.113580.884
142_D147_W0.113460.883
53_L226_N0.113150.880
136_F150_G0.113140.880
212_S222_L0.112910.878
105_F108_P0.112620.876
150_G153_I0.112320.874
118_D192_G0.111990.871
144_G243_G0.111880.870
249_P252_I0.111690.869
166_E192_G0.111610.868
202_T207_P0.111120.864
151_S194_R0.111040.864
172_L189_S0.110960.863
110_R210_S0.11090.863
163_S175_V0.110380.859
173_L186_I0.110030.856
27_D32_W0.109920.855
77_S107_G0.109670.853
21_R34_E0.109280.850
89_K192_G0.109150.849
235_S248_R0.108980.848
50_N162_P0.108810.846
55_V61_L0.108680.845
84_S87_G0.10860.845
51_P66_S0.108360.843
181_N203_N0.107860.839
128_E132_S0.107840.839
52_S124_P0.107390.835
211_I215_R0.107230.834
82_S93_E0.107180.834
184_I211_I0.10640.828
125_Y138_Y0.106230.826
86_D91_W0.10620.826
141_D194_R0.106020.825
35_P38_V0.105970.824
55_V59_G0.105760.823
175_V213_L0.105760.823
26_T85_T0.105470.820
62_W122_I0.105280.819
216_L222_L0.105080.817
22_R89_K0.104930.816
89_K92_S0.104760.815
203_N246_W0.104750.815
123_A185_Y0.104550.813
149_S152_P0.104220.811
62_W121_L0.103940.809
160_C175_V0.103930.808
165_V242_G0.103930.808
215_R242_G0.10380.807
167_L242_G0.10360.806
190_T244_K0.103540.805
235_S251_T0.102970.801
65_Y125_Y0.102650.799
19_V37_I0.102160.795
114_I164_I0.102030.794
191_D196_W0.101930.793
175_V224_V0.101910.793
140_S145_K0.101210.787
164_I181_N0.101060.786
219_G244_K0.101050.786
209_S212_S0.10090.785
179_E182_D0.100450.781
235_S249_P0.099650.775
235_S246_W0.099060.771
66_S108_P0.098350.765
165_V168_P0.098180.764
162_P174_A0.098140.763
91_W176_F0.097880.761
88_G147_W0.097630.759
122_I172_L0.09760.759
166_E172_L0.097550.759
26_T29_G0.09740.758
50_N210_S0.097330.757
22_R53_L0.097250.757
206_N209_S0.096930.754
89_K145_K0.096880.754
97_L127_H0.096810.753
159_E176_F0.096620.752
223_L226_N0.096540.751
148_S198_P0.096020.747
161_E231_R0.095950.746
231_R234_L0.095880.746
151_S184_I0.095710.745
212_S224_V0.09570.744
98_P105_F0.095670.744
114_I199_P0.095550.743
166_E221_L0.095340.742
71_G75_S0.095160.740
188_R199_P0.095130.740
227_N233_N0.095070.740
78_R96_D0.094780.737
89_K197_S0.094650.736
29_G32_W0.094590.736
177_R226_N0.094290.733
226_N234_L0.094270.733
90_T146_T0.094230.733
135_A156_G0.094160.732
51_P55_V0.094050.732
30_K197_S0.094020.731
111_G115_Q0.093960.731
222_L238_V0.093920.731
87_G145_K0.093590.728
201_P204_L0.093420.727
30_K89_K0.093410.727
21_R27_D0.093370.726
177_R231_R0.093350.726
138_Y142_D0.093310.726
26_T34_E0.093290.726
165_V213_L0.093280.726
135_A176_F0.0930.723
34_E39_A0.092870.722
247_S250_K0.092530.720
37_I42_P0.09250.720
125_Y176_F0.092460.719
87_G94_P0.09230.718
31_T219_G0.092190.717
50_N68_G0.092160.717
22_R35_P0.0920.716
171_R174_A0.091980.716
60_R145_K0.091610.713
114_I163_S0.091590.712
140_S143_G0.091430.711
64_F68_G0.091180.709
164_I167_L0.091020.708
68_G76_G0.090890.707
166_E169_D0.090710.706
163_S212_S0.090660.705
188_R244_K0.090550.704
86_D142_D0.090180.702
91_W196_W0.090110.701
207_P212_S0.09010.701
148_S151_S0.090070.701
26_T31_T0.090030.700
124_P211_I0.089420.696
21_R35_P0.089360.695
175_V186_I0.089190.694
64_F161_E0.089160.694
76_G79_I0.089110.693
37_I89_K0.089090.693
115_Q118_D0.089090.693
146_T195_T0.0890.692
129_S132_S0.088860.691
87_G240_E0.088710.690
111_G184_I0.088560.689
206_N218_D0.08850.688
91_W246_W0.088490.688
69_S72_G0.088170.686
218_D238_V0.087890.684
81_Y111_G0.087810.683
193_G243_G0.087750.683
21_R48_Y0.087620.682
160_C209_S0.087480.681
145_K148_S0.087350.680
240_E248_R0.087350.680
69_S75_S0.087220.678
141_D170_G0.087020.677
108_P126_Y0.086740.675
33_S36_R0.086450.673
66_S126_Y0.08640.672
125_Y161_E0.086230.671
164_I174_A0.086160.670
53_L184_I0.086130.670
89_K93_E0.085970.669
139_Y149_S0.085890.668
58_D62_W0.085730.667
128_E196_W0.085690.667
49_G160_C0.085670.666
221_L225_Y0.085580.666
123_A137_V0.085410.664
26_T190_T0.085170.663
58_D61_L0.085170.663
211_I216_L0.085120.662
20_I53_L0.085050.662
61_L64_F0.085010.661
52_S147_W0.084930.661
57_P61_L0.084860.660
194_R200_Q0.084850.660
62_W173_L0.08460.658
58_D91_W0.084580.658
59_G85_T0.084520.657
85_T190_T0.08450.657
135_A138_Y0.08450.657
185_Y198_P0.084460.657
210_S226_N0.084330.656
67_A125_Y0.084250.655
121_L144_G0.084230.655
237_Y246_W0.084190.655
125_Y133_F0.084120.654
61_L88_G0.084090.654
159_E162_P0.084090.654
84_S89_K0.08390.653
226_N237_Y0.083820.652
34_E42_P0.083540.650
166_E170_G0.083460.649
218_D240_E0.083360.648
151_S154_P0.08320.647
59_G170_G0.082780.644
189_S192_G0.082490.642
208_N213_L0.082460.641
47_R50_N0.082440.641
23_S32_W0.082250.640
39_A65_Y0.081860.637
173_L236_L0.081820.636
32_W47_R0.08170.636
110_R161_E0.081610.635
238_V247_S0.081460.634
95_T105_F0.081340.633
92_S200_Q0.08110.631
209_S224_V0.081010.630
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
4fj6A0.98551000.279
1w0pA0.98181000.304
4j9tA0.97091000.306
2w20A0.97821000.315
2jkbA0.97451000.327
2bf6A0.98181000.333
1w8oA0.96361000.342
2sliA0.97091000.358
1so7A0.967399.90.372
2xziA0.938299.90.381

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