GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gmad1 - Lipoprotein LpqB beta-propeller domain
Pfam: PF10647 (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: 253
Sequences: 43060
Seq/Len: 170.2
HH_delta: 0.127 (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
28_S41_V1.586352.310
70_R83_D1.581192.302
72_S118_R1.549262.256
39_A73_W1.546092.251
30_A72_S1.517652.210
81_T119_V1.513622.204
48_R52_V1.509592.198
74_D119_V1.484852.162
172_A215_A1.438612.095
118_R172_A1.419622.067
116_A129_V1.391462.026
81_T91_V1.370631.996
127_A173_W1.329081.935
39_A52_V1.322921.926
170_D183_G1.300811.894
82_V92_V1.28861.876
32_S73_W1.267171.845
174_S216_V1.214651.769
48_R51_Y1.195391.740
181_V216_V1.193281.737
69_T85_G1.180771.719
39_A80_W1.17911.717
120_S173_W1.16031.689
213_V226_T1.151061.676
40_A53_G1.132651.649
136_G140_V1.122931.635
136_G139_Y1.120811.632
191_V203_P1.101831.604
164_L182_L1.082981.577
50_L82_V1.05551.537
181_V192_R1.041441.516
66_G82_V1.033061.504
207_V225_V1.022711.489
191_V200_P1.015791.479
89_V128_V1.006891.466
29_P40_A1.001781.459
217_A221_S0.991361.443
127_A140_V0.987561.438
135_G139_Y0.985821.435
81_T117_L0.982471.430
172_A214_V0.981551.429
190_V225_V0.978231.424
54_P57_G0.97281.416
84_D88_G0.969961.412
32_S36_S0.960671.399
27_T46_G0.954581.390
81_T126_V0.950041.383
30_A71_P0.926411.349
170_D213_V0.9141.331
182_L194_V0.901551.313
200_P203_P0.900721.311
164_L184_R0.895051.303
118_R171_V0.871131.268
72_S117_L0.868691.265
70_R116_A0.85811.249
28_S70_R0.857231.248
68_L71_P0.855981.246
39_A71_P0.850551.238
139_Y160_V0.847531.234
83_D114_I0.838111.220
125_R128_V0.830171.209
51_Y62_V0.827711.205
169_T185_S0.81951.193
128_V141_A0.814871.186
217_A222_T0.810431.180
40_A51_Y0.809381.178
59_V62_V0.806891.175
42_S47_G0.806671.175
74_D78_W0.805131.172
93_R96_A0.792541.154
157_P160_V0.791051.152
191_V194_V0.780351.136
110_L128_V0.77971.135
83_D117_L0.774021.127
174_S177_S0.773261.126
217_A220_P0.770821.122
26_V40_A0.770351.122
130_V135_G0.762131.110
127_A180_V0.759651.106
118_R173_W0.758481.104
31_V38_V0.75231.095
172_A216_V0.749971.092
174_S178_T0.741941.080
30_A73_W0.741471.080
89_V93_R0.738071.075
142_G148_D0.736061.072
41_V68_L0.732011.066
116_A170_D0.731571.065
125_R140_V0.730571.064
74_D79_V0.725131.056
120_S123_G0.721931.051
120_S125_R0.721181.050
181_V214_V0.720441.049
93_R97_S0.716761.044
122_D125_R0.714621.040
195_S198_G0.714231.040
84_D90_R0.713991.040
181_V223_V0.703711.025
138_V182_L0.702231.022
175_D220_P0.697951.016
126_V129_V0.696641.014
129_V168_V0.691871.007
47_G51_Y0.690271.005
120_S124_T0.689531.004
28_S71_P0.689491.004
33_P73_W0.689411.004
33_P77_G0.686871.000
37_R52_V0.683520.995
175_D216_V0.682820.994
137_R160_V0.682630.994
207_V211_V0.681890.993
32_S37_R0.679720.990
183_G211_V0.67170.978
184_R187_G0.671480.978
41_V71_P0.671410.978
90_R100_G0.667620.972
211_V214_V0.665050.968
183_G214_V0.663160.966
66_G84_D0.658190.958
127_A171_V0.655030.954
179_L182_L0.652840.951
82_V90_R0.652220.950
34_D37_R0.647660.943
31_V55_A0.647380.943
173_W196_V0.646510.941
188_G191_V0.645650.940
179_L192_R0.637310.928
36_S56_G0.634540.924
169_T212_P0.631760.920
139_Y157_P0.631210.919
130_V139_Y0.628880.916
219_S222_T0.625420.911
85_G113_R0.621560.905
107_W110_L0.617020.898
70_R117_L0.615350.896
51_Y59_V0.614080.894
115_T169_T0.613260.893
103_V106_D0.61250.892
195_S201_S0.612270.891
75_P123_G0.610360.889
52_V55_A0.607830.885
42_S49_S0.605390.881
120_S127_A0.603950.879
60_R63_L0.601930.876
184_R191_V0.597210.870
194_V200_P0.596430.868
148_D156_G0.594880.866
121_P177_S0.59160.861
32_S35_G0.586260.854
48_R53_G0.585820.853
129_V171_V0.584080.850
170_D214_V0.582820.849
124_T144_V0.580510.845
74_D77_G0.577630.841
190_V214_V0.577060.840
36_S54_P0.575840.838
174_S179_L0.575360.838
42_S51_Y0.572740.834
168_V171_V0.567840.827
75_P119_V0.56760.826
179_L183_G0.564860.822
67_S85_G0.563760.821
49_S62_V0.562190.819
222_T225_V0.561380.817
97_S100_G0.560320.816
136_G141_A0.55960.815
79_V91_V0.55880.814
26_V29_P0.55870.813
184_R188_G0.557180.811
171_V182_L0.555970.809
121_P173_W0.55280.805
197_D200_P0.551830.803
74_D81_T0.55030.801
73_W80_W0.545160.794
176_D179_L0.54430.793
38_V55_A0.543880.792
72_S119_V0.543370.791
40_A47_G0.542530.790
217_A224_Y0.540910.788
180_V196_V0.540470.787
119_V143_V0.538850.785
37_R40_A0.536410.781
160_V163_P0.535090.779
59_V63_L0.533440.777
78_W96_A0.533070.776
89_V117_L0.532410.775
163_P194_V0.531770.774
71_P82_V0.530760.773
51_Y60_R0.529090.770
212_P227_D0.52450.764
108_P111_R0.522090.760
117_L128_V0.520920.758
195_S199_G0.519660.757
104_E107_W0.517240.753
182_L191_V0.51650.752
29_P38_V0.515580.751
115_T134_G0.512120.746
116_A171_V0.507020.738
78_W93_R0.506910.738
37_R41_V0.505990.737
110_L130_V0.503890.734
37_R73_W0.50370.733
48_R55_A0.503430.733
84_D87_G0.501040.730
46_G67_S0.496550.723
71_P80_W0.494720.720
192_R202_T0.491110.715
185_S210_G0.487530.710
37_R54_P0.484550.706
90_R103_V0.483610.704
156_G161_A0.483290.704
125_R129_V0.481950.702
76_D79_V0.477680.696
27_T69_T0.477250.695
144_V148_D0.474440.691
166_S185_S0.474270.691
222_T226_T0.471040.686
68_L82_V0.470290.685
126_V143_V0.468850.683
168_V182_L0.46660.679
47_G52_V0.464890.677
178_T195_S0.464460.676
135_G141_A0.464450.676
66_G90_R0.460310.670
136_G182_L0.459320.669
110_L114_I0.45870.668
57_G61_P0.458620.668
27_T67_S0.458270.667
215_A224_Y0.457170.666
174_S181_V0.457110.666
214_V218_A0.45530.663
64_T82_V0.454710.662
69_T115_T0.454650.662
199_G203_P0.452990.660
158_R161_A0.452030.658
86_S90_R0.448240.653
101_E105_V0.446740.650
228_D232_L0.444160.647
31_V216_V0.443080.645
57_G63_L0.443040.645
182_L186_A0.441790.643
72_S81_T0.440840.642
68_L84_D0.440440.641
227_D230_G0.440140.641
102_P106_D0.438690.639
55_A58_P0.437840.637
192_R204_L0.435510.634
32_S39_A0.434020.632
26_V42_S0.433380.631
183_G187_G0.431320.628
214_V225_V0.430790.627
25_D46_G0.42940.625
114_I117_L0.429010.625
216_V223_V0.428870.624
164_L168_V0.427020.622
100_G103_V0.426030.620
92_V100_G0.424670.618
119_V126_V0.42150.614
103_V107_W0.42090.613
164_L194_V0.420450.612
198_G202_T0.420240.612
224_Y231_V0.418270.609
79_V119_V0.417110.607
42_S48_R0.416430.606
90_R106_D0.412810.601
52_V73_W0.411670.599
172_A181_V0.41080.598
115_T167_D0.410270.597
225_V232_L0.407910.594
173_W216_V0.406780.592
125_R158_R0.405350.590
221_S224_Y0.4040.588
128_V139_Y0.40350.587
200_P204_L0.402870.587
199_G204_L0.402750.586
114_I128_V0.402350.586
52_V61_P0.401850.585
138_V171_V0.400610.583
167_D185_S0.40020.583
34_D77_G0.398160.580
100_G104_E0.397530.579
130_V137_R0.396180.577
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
2ymuA0.81421000.127
2ymuA0.88541000.128
1nr0A0.893399.90.139
1vyhC0.897299.90.144
4gqbB0.893399.90.145
3dm0A0.91399.90.145
3ow8A0.897299.90.15
1vyhC0.897299.90.157
4j87A0.932899.90.164
3ow8A0.83499.90.165

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