GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ndr - Ndr family
Pfam: PF03096 (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: CL0028
Length: 283
Sequences: 35583
Seq/Len: 125.73
HH_delta: 0.083 (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
102_I126_G3.48974.731
64_P88_M2.461893.337
228_D254_A2.208522.994
223_L275_F2.193462.974
251_L271_A2.083192.824
264_Q267_K1.927622.613
100_S125_L1.900362.576
90_P116_F1.89892.574
103_G113_L1.85662.517
117_A127_L1.817752.464
130_V268_L1.754412.378
131_N230_S1.753312.377
102_I125_L1.6642.256
228_D252_K1.560872.116
253_V271_A1.559542.114
55_N273_K1.558062.112
90_P120_H1.520982.062
25_A57_C1.508372.045
240_N248_T1.492422.023
102_I276_L1.465661.987
94_D123_R1.43951.951
110_A132_P1.416771.921
90_P94_D1.404331.904
116_F120_H1.381821.873
129_L132_P1.379871.871
256_C264_Q1.305161.769
25_A59_Y1.289231.748
93_L101_V1.283051.739
43_F269_A1.282711.739
113_L127_L1.278731.734
115_R119_K1.275731.729
90_P123_R1.265681.716
271_A274_L1.265091.715
87_E119_K1.25821.706
128_I272_F1.252961.699
102_I128_I1.246711.690
51_E269_A1.220091.654
115_R118_L1.191581.615
270_E274_L1.186211.608
29_Y63_A1.155631.567
36_H62_D1.126841.528
223_L251_L1.125531.526
30_H63_A1.120241.519
114_A129_L1.108481.503
120_H123_R1.105571.499
30_H66_Q1.099871.491
104_F130_V1.098241.489
83_D119_K1.088071.475
214_E217_S1.087431.474
267_K271_A1.081321.466
89_L116_F1.068951.449
33_G107_G1.068861.449
28_T104_F1.064931.444
128_I223_L1.056811.433
29_Y113_L1.055331.431
92_V96_F1.046361.419
86_A115_R1.041261.412
127_L222_V1.035531.404
267_K270_E1.034611.403
31_D107_G1.03381.401
226_V252_K1.032691.400
268_L272_F1.027961.394
59_Y92_V1.010051.369
226_V250_L1.009521.369
62_D67_E1.007611.366
34_L38_S0.994451.348
26_I56_F0.983381.333
81_S84_Q0.979921.328
237_V241_S0.96091.303
36_H60_H0.960241.302
63_A112_I0.960241.302
94_D120_H0.9591.300
28_T58_I0.948321.286
24_P102_I0.936291.269
238_E242_K0.934351.267
126_G223_L0.926831.256
51_E273_K0.92361.252
36_H68_E0.923081.251
223_L249_T0.922461.251
25_A98_L0.915451.241
56_F102_I0.910611.234
107_G258_G0.907921.231
253_V256_C0.906221.229
105_G113_L0.896771.216
222_V243_L0.891071.208
126_G221_P0.890331.207
61_I89_L0.889931.206
126_G275_F0.882091.196
29_Y61_I0.867611.176
104_F128_I0.863131.170
26_I104_F0.858321.164
249_T271_A0.85691.162
237_V252_K0.854231.158
238_E241_S0.827171.121
101_V124_V0.821021.113
116_F123_R0.819331.111
98_L101_V0.81881.110
51_E54_Q0.813441.103
29_Y89_L0.801711.087
116_F124_V0.799341.084
26_I58_I0.797851.082
225_V268_L0.787791.068
91_E94_D0.784581.064
225_V253_V0.784181.063
29_Y103_G0.78171.060
90_P119_K0.774561.050
32_V108_A0.773751.049
92_V95_H0.773351.048
118_L217_S0.767011.040
56_F276_L0.765411.038
129_L224_L0.763421.035
24_P125_L0.762141.033
24_P100_S0.760431.031
25_A101_V0.756831.026
27_L101_V0.753821.022
106_V261_L0.74831.014
225_V271_A0.747871.014
105_G109_G0.745661.011
266_G270_E0.744481.009
229_N255_D0.738331.001
128_I276_L0.736350.998
87_E91_E0.734930.996
256_C260_V0.734110.995
86_A112_I0.733070.994
131_N227_G0.733010.994
103_G124_V0.732060.992
199_A203_N0.726640.985
93_L98_L0.725780.984
54_Q273_K0.718150.974
256_C263_E0.717450.973
237_V250_L0.712850.966
30_H61_I0.711950.965
53_L58_I0.711870.965
228_D255_D0.707080.959
91_E95_H0.703850.954
83_D115_R0.698740.947
105_G110_A0.696450.944
224_L248_T0.695970.944
28_T40_F0.695810.943
118_L214_E0.695730.943
106_V131_N0.687660.932
38_S261_L0.685710.930
93_L116_F0.680820.923
59_Y96_F0.677160.918
183_Q187_Q0.675330.916
257_G263_E0.674280.914
27_L93_L0.670720.909
27_L103_G0.667230.905
226_V235_D0.667160.904
178_N181_L0.665850.903
103_G116_F0.665610.902
251_L274_L0.663860.900
270_E273_K0.663310.899
253_V267_K0.657660.892
84_Q87_E0.652290.884
61_I92_V0.643920.873
86_A90_P0.643470.872
106_V259_L0.643380.872
24_P56_F0.64320.872
106_V130_V0.637840.865
85_L108_A0.637050.864
104_F272_F0.63610.862
87_E90_P0.626920.850
107_G259_L0.625740.848
28_T60_H0.617790.838
88_M92_V0.617670.837
63_A108_A0.617640.837
251_L267_K0.616170.835
63_A66_Q0.616050.835
235_D252_K0.613090.831
51_E266_G0.612090.830
227_G260_V0.612010.830
130_V261_L0.608770.825
253_V264_Q0.604710.820
269_A273_K0.603550.818
117_A220_C0.603540.818
200_L203_N0.601570.816
240_N250_L0.599960.813
184_T187_Q0.598960.812
49_M60_H0.595470.807
115_R214_E0.590460.800
41_Q60_H0.588260.797
271_A275_F0.587410.796
56_F273_K0.58730.796
27_L89_L0.584060.792
86_A119_K0.578380.784
131_N226_V0.574550.779
49_M53_L0.572380.776
57_C98_L0.5710.774
239_M244_D0.570370.773
179_S183_Q0.569650.772
49_M52_I0.569480.772
117_A124_V0.563980.765
127_L220_C0.560910.760
25_A56_F0.560310.760
63_A85_L0.554650.752
117_A218_L0.552980.750
86_A116_F0.551220.747
62_D69_G0.546790.741
128_I225_V0.545140.739
128_I275_F0.540440.733
40_F43_F0.539570.731
197_N200_L0.539130.731
226_V233_V0.538310.730
33_G108_A0.535340.726
125_L128_I0.534870.725
130_V260_V0.533460.723
59_Y98_L0.530890.720
101_V125_L0.530490.719
181_L184_T0.529610.718
213_I216_P0.526830.714
237_V240_N0.526330.714
249_T274_L0.525460.712
183_Q186_R0.521660.707
225_V251_L0.518890.703
196_K199_A0.518530.703
33_G66_Q0.516190.700
27_L59_Y0.516190.700
130_V225_V0.511350.693
30_H35_N0.510730.692
224_L250_L0.509690.691
26_I276_L0.508750.690
88_M91_E0.507990.689
49_M58_I0.507440.688
198_L201_F0.503740.683
83_D87_E0.501090.679
121_P124_V0.500850.679
196_K200_L0.49830.676
224_L240_N0.497430.674
26_I102_I0.497090.674
31_D106_V0.496860.674
126_G276_L0.492950.668
131_N260_V0.492310.667
113_L129_L0.491050.666
244_D248_T0.490180.665
187_Q190_D0.489970.664
228_D235_D0.489780.664
84_Q88_M0.486990.660
90_P93_L0.48690.660
124_V220_C0.485070.658
26_I52_I0.484260.656
109_G113_L0.483640.656
63_A89_L0.483140.655
88_M95_H0.483110.655
240_N244_D0.482330.654
223_L271_A0.480940.652
62_D68_E0.480510.651
50_Q53_L0.479780.650
199_A202_L0.479230.650
93_L123_R0.478730.649
29_Y112_I0.477060.647
64_P85_L0.476580.646
248_T251_L0.475390.644
101_V123_R0.473570.642
216_P242_K0.473190.641
38_S106_V0.472120.640
129_L222_V0.471760.640
30_H40_F0.470620.638
254_A267_K0.470010.637
260_V268_L0.469050.636
230_S258_G0.467960.634
111_N133_T0.466130.632
108_A112_I0.465260.631
111_N114_A0.464070.629
113_L117_A0.461970.626
40_F104_F0.461040.625
221_P247_K0.459840.623
36_H61_I0.458090.621
201_F205_Y0.454310.616
253_V260_V0.453750.615
118_L218_L0.453350.615
179_S182_V0.451010.611
105_G129_L0.448630.608
223_L226_V0.448120.608
265_P269_A0.446880.606
121_P219_G0.445450.604
110_A129_L0.445190.604
37_K41_Q0.445110.603
114_A132_P0.443210.601
243_L248_T0.442080.599
126_G129_L0.44190.599
27_L61_I0.440940.598
85_L112_I0.440450.597
180_D184_T0.43820.594
69_G72_T0.437960.594
93_L124_V0.436390.592
34_L259_L0.43570.591
186_R190_D0.434470.589
89_L93_L0.432610.586
42_G50_Q0.426710.578
50_Q54_Q0.426490.578
114_A134_C0.426310.578
97_G100_S0.423810.575
99_K123_R0.422690.573
184_T188_H0.419340.568
119_K214_E0.416690.565
200_L204_S0.415820.564
52_I272_F0.415550.563
249_T275_F0.415540.563
201_F204_S0.414550.562
34_L37_K0.414340.562
132_P230_S0.413710.561
180_D183_Q0.41370.561
244_D247_K0.413430.560
145_Q148_S0.410950.557
38_S259_L0.410540.557
182_V186_R0.409840.556
52_I55_N0.409670.555
230_S233_V0.407940.553
202_L205_Y0.406490.551
239_M243_L0.405860.550
143_F147_L0.40580.550
93_L96_F0.404840.549
85_L88_M0.403020.546
51_E55_N0.400530.543
102_I275_F0.400120.542
259_L262_E0.400110.542
232_H257_G0.398310.540
272_F276_L0.397470.539
32_V66_Q0.397030.538
107_G131_N0.3960.537
32_V107_G0.392230.532
40_F106_V0.39060.530
114_A239_M0.390440.529
105_G117_A0.38970.528
255_D264_Q0.386220.524
82_M115_R0.386010.523
41_Q50_Q0.384670.521
82_M108_A0.384120.521
143_F146_K0.383960.521
163_D166_L0.383740.520
207_S210_D0.383620.520
182_V185_Y0.382290.518
66_Q108_A0.3820.518
261_L268_L0.381820.518
164_Y168_H0.381040.517
210_D214_E0.38090.516
210_D213_I0.378510.513
108_A111_N0.377420.512
227_G255_D0.376710.511
144_Y148_S0.376690.511
58_I61_I0.376050.510
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
3om8A0.91171000.083
3afiE0.9471000.098
3v48A0.92231000.099
3nwoA0.95761000.109
2yysA0.93291000.111
2xuaA0.92231000.115
3w04A0.92931000.118
1b6gA0.93291000.122
2wueA0.91871000.124
4b9eA0.95051000.125

Page generated in 0.0312 seconds.