GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sugar_transport - Sugar transport protein
Pfam: PF06800 (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: CL0184
Length: 269
Sequences: 17611
Seq/Len: 65.47
HH_delta: 0.727 (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
65_S143_L1.478063.252
239_G245_E1.197682.635
214_I218_K1.173822.583
73_K140_I1.143432.516
61_G145_I1.127712.481
64_K142_A1.082992.383
61_G142_A1.058822.330
109_A265_G1.035972.279
75_M235_S0.986212.170
96_E158_K0.966892.127
85_G147_T0.953542.098
90_G96_E0.943142.075
99_T102_Q0.904111.989
214_I217_Q0.89361.966
141_L145_I0.886511.951
86_T225_F0.829741.826
89_I155_V0.829081.824
69_I139_G0.8281.822
87_S110_L0.815511.794
69_I140_I0.80481.771
81_L85_G0.796351.752
181_I184_L0.789181.736
64_K68_K0.788261.734
61_G149_G0.779941.716
163_S166_S0.77561.707
91_V98_T0.77021.695
113_I229_Q0.763951.681
100_T104_I0.737841.623
220_G223_T0.736381.620
248_T251_E0.732281.611
157_P213_L0.732251.611
57_I149_G0.730521.607
238_G242_I0.722291.589
64_K67_K0.720591.586
71_V239_G0.699131.538
137_K141_L0.685441.508
234_I238_G0.684061.505
90_G94_F0.682491.502
74_T143_L0.680811.498
68_K138_K0.660411.453
46_I50_L0.654721.441
62_Q66_F0.649791.430
66_F74_T0.633431.394
249_K257_I0.629271.385
119_L261_L0.626681.379
69_I73_K0.621771.368
85_G148_I0.610651.344
43_T46_I0.606181.334
116_G258_G0.605211.332
116_G262_I0.604441.330
252_M260_I0.595451.310
89_I152_I0.592111.303
175_M178_G0.589461.297
113_I265_G0.588941.296
176_L180_F0.588231.294
119_L250_K0.585541.288
44_S161_H0.583561.284
91_V97_W0.5831.283
85_G151_W0.58291.283
68_K142_A0.582551.282
47_V51_S0.578041.272
193_K197_K0.574991.265
247_K252_M0.572911.261
72_S236_T0.571161.257
92_L95_G0.566691.247
219_N224_A0.565191.244
147_T151_W0.563991.241
220_G224_A0.560021.232
177_I181_I0.558141.228
230_L234_I0.55771.227
68_K139_G0.556311.224
70_G73_K0.55281.216
151_W155_V0.549431.209
138_K142_A0.549141.208
47_V156_I0.543731.196
137_K140_I0.543541.196
103_K111_V0.543381.196
111_V115_I0.541651.192
50_L156_I0.538791.185
120_T258_G0.537861.183
86_T221_V0.534121.175
143_L147_T0.532431.171
247_K251_E0.529341.165
240_I247_K0.523991.153
86_T154_S0.517691.139
202_G206_G0.516221.136
76_P259_L0.513221.129
158_K221_V0.512861.128
54_F152_I0.510271.123
89_I93_F0.505571.112
86_T151_W0.502521.106
94_F155_V0.500331.101
118_I122_Y0.500261.101
180_F184_L0.499551.099
99_T103_K0.498741.097
138_K141_L0.496331.092
65_S74_T0.495421.090
89_I151_W0.486931.071
230_L233_V0.48471.066
260_I264_I0.484461.066
175_M179_A0.480911.058
77_I143_L0.469991.034
216_A220_G0.468021.030
150_Y212_Y0.46661.027
117_V121_S0.465231.024
169_L173_I0.464991.023
178_G181_I0.460481.013
215_S224_A0.457831.007
152_I156_I0.455621.002
233_V259_L0.455141.001
116_G265_G0.4551.001
69_I143_L0.453940.999
86_T155_V0.452830.996
54_F156_I0.452190.995
112_L265_G0.451720.994
162_V167_A0.451190.993
100_T103_K0.450790.992
193_K196_W0.450460.991
216_A224_A0.448980.988
174_G178_G0.448560.987
219_N223_T0.446530.982
96_E102_Q0.44450.978
89_I148_I0.444030.977
71_V243_L0.439250.966
148_I152_I0.438750.965
139_G143_L0.430260.947
177_I180_F0.428410.943
71_V245_E0.428320.942
55_W153_Y0.427460.941
44_S48_A0.423230.931
43_T47_V0.421570.928
87_S98_T0.420130.924
178_G182_F0.417450.919
202_G205_W0.416940.917
194_K197_K0.416910.917
56_A178_G0.416230.916
89_I92_L0.416030.915
49_F174_G0.41590.915
196_W200_L0.41570.915
154_S225_F0.409330.901
60_I64_K0.408740.899
63_F67_K0.408260.898
84_V113_I0.407790.897
44_S162_V0.407060.896
81_L117_V0.406410.894
76_P121_S0.405420.892
96_E222_A0.405110.891
237_L241_F0.404090.889
158_K220_G0.402930.887
238_G241_F0.402270.885
150_Y154_S0.401770.884
192_E195_S0.401020.882
57_I61_G0.400390.881
77_I144_L0.398240.876
211_F214_I0.396760.873
76_P118_I0.394160.867
239_G243_L0.392970.865
46_I49_F0.39220.863
153_Y213_L0.392080.863
45_F49_F0.390510.859
52_G174_G0.38470.846
183_N186_S0.384440.846
86_T90_G0.384230.845
115_I119_L0.382590.842
153_Y157_P0.382090.841
210_L214_I0.381610.840
62_Q74_T0.378190.832
215_S219_N0.375530.826
71_V75_M0.375480.826
55_W209_N0.372980.821
83_L229_Q0.370840.816
236_T247_K0.370630.815
259_L263_V0.366170.806
119_L257_I0.365720.805
68_K136_M0.36470.802
197_K200_L0.363490.800
201_T204_I0.361660.796
58_G153_Y0.356380.784
142_A145_I0.35520.782
115_I261_L0.353640.778
58_G209_N0.353470.778
236_T240_I0.352430.775
55_W59_Q0.352070.775
168_F172_A0.351820.774
119_L258_G0.350970.772
257_I261_L0.349340.769
226_T229_Q0.348630.767
81_L147_T0.348460.767
173_I177_I0.348380.767
58_G78_S0.348010.766
88_L110_L0.347720.765
182_F186_S0.346790.763
62_Q146_S0.346580.763
77_I117_V0.346390.762
45_F48_A0.344960.759
77_I140_I0.34480.759
87_S102_Q0.344590.758
135_N138_K0.34370.756
88_L92_L0.342310.753
97_W101_T0.340750.750
77_I147_T0.34040.749
237_L240_I0.340070.748
174_G177_I0.339610.747
228_S231_G0.337830.743
65_S69_I0.336470.740
200_L203_L0.336130.740
56_A182_F0.334740.737
69_I74_T0.334310.736
154_S212_Y0.332480.732
91_V95_G0.331290.729
84_V114_I0.330660.728
65_S139_G0.329230.724
204_I207_I0.32870.723
85_G144_L0.32850.723
153_Y171_Q0.328030.722
144_L147_T0.327980.722
211_F215_S0.326840.719
176_L179_A0.326610.719
249_K252_M0.326170.718
136_M140_I0.324760.715
51_S54_F0.324520.714
87_S91_V0.323360.711
173_I176_L0.323160.711
206_G210_L0.321350.707
58_G149_G0.321170.707
98_T103_K0.320470.705
207_I211_F0.320430.705
140_I144_L0.319980.704
93_F152_I0.319390.703
47_V50_L0.318740.701
192_E196_W0.318310.700
84_V110_L0.317720.699
97_W100_T0.316760.697
201_T205_W0.315680.695
157_P167_A0.314920.693
52_G56_A0.314240.691
44_S47_V0.312180.687
58_G150_Y0.30940.681
194_K198_N0.309330.681
208_G211_F0.307980.678
199_I202_G0.306160.674
94_F158_K0.30590.673
55_W58_G0.305860.673
170_P173_I0.305630.672
96_E221_V0.304540.670
157_P216_A0.304370.670
78_S146_S0.304150.669
109_A113_I0.30390.669
122_Y125_K0.30350.668
104_I112_L0.303250.667
116_G261_L0.301270.663
145_I149_G0.300870.662
114_I229_Q0.300730.662
229_Q266_A0.300190.661
76_P120_T0.299580.659
70_G74_T0.299290.659
44_S51_S0.298750.657
110_L222_A0.298590.657
83_L86_T0.298420.657
248_T252_M0.298270.656
240_I246_K0.297960.656
212_Y216_A0.297010.654
241_F244_K0.295350.650
59_Q62_Q0.29520.650
47_V159_A0.294780.649
195_S199_I0.293330.645
120_T262_I0.293230.645
54_F153_Y0.291190.641
172_A205_W0.290050.638
82_Q228_S0.289380.637
252_M257_I0.289320.637
114_I118_I0.289230.636
166_S170_P0.288020.634
66_F70_G0.287960.634
246_K249_K0.285910.629
236_T259_L0.284360.626
261_L265_G0.283950.625
240_I244_K0.282060.621
263_V267_I0.28110.619
66_F75_M0.281090.618
121_S140_I0.280530.617
208_G212_Y0.27940.615
49_F53_A0.279150.614
165_W169_L0.278660.613
236_T239_G0.277870.611
115_I118_I0.277560.611
225_F228_S0.277480.611
162_V166_S0.27720.610
81_L84_V0.27670.609
168_F213_L0.275390.606
72_S75_M0.275330.606
167_A170_P0.274470.604
191_F194_K0.274220.603
94_F159_A0.273930.603
51_S55_W0.27360.602
57_I60_I0.273380.602
121_S125_K0.273330.601
90_G222_A0.273160.601
55_W171_Q0.2730.601
229_Q262_I0.27230.599
56_A60_I0.269740.594
101_T104_I0.26910.592
113_I232_V0.268430.591
51_S157_P0.268240.590
182_F185_F0.267080.588
78_S212_Y0.26660.587
54_F149_G0.266540.586
83_L225_F0.265240.584
154_S216_A0.264940.583
196_W199_I0.26470.582
252_M259_L0.264560.582
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
2i68A0.371798.50.727
3b5dA0.408998.20.749
3b5dA0.371798.20.75
2i68A0.5093980.769
4he8J0.561322.60.924
1u7gA0.832718.50.927
3o7qA0.57995.10.942
3hrdA0.21934.60.943
2gfpA0.90334.60.943
4humA0.73613.80.946
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