GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RIO1 - RIO1 family
Pfam: PF01163 (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: CL0016
Length: 188
Sequences: 6871
Seq/Len: 36.55
HH_delta: 0.176 (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
139_L148_I1.170313.612
4_H12_E0.92612.858
4_H87_Y0.798932.466
141_D144_K0.782082.414
132_D137_N0.738852.280
110_E114_E0.721112.226
6_I12_E0.717182.214
88_I146_Y0.706382.180
121_K125_K0.70482.175
141_D146_Y0.691962.136
86_E146_Y0.674942.083
119_I122_M0.664372.051
114_E145_V0.663472.048
14_A87_Y0.611381.887
94_P97_R0.607181.874
138_I145_V0.591261.825
7_D13_V0.583861.802
5_A13_V0.558221.723
72_V75_P0.557011.719
15_V84_V0.550361.699
5_A15_V0.53451.650
102_D108_P0.533951.648
11_E74_K0.529581.635
76_Y86_E0.503311.553
97_R100_D0.499861.543
131_G152_Q0.477581.474
137_N149_D0.474331.464
120_I124_H0.473161.460
12_E89_G0.466991.441
93_V97_R0.466071.438
66_Y74_K0.455241.405
13_V84_V0.454881.404
128_I153_A0.452081.395
74_K86_E0.451341.393
113_E117_E0.445481.375
89_G142_D0.441311.362
88_I148_I0.438761.354
132_D149_D0.437471.350
150_F153_A0.434881.342
133_L147_I0.433961.339
115_I138_I0.431531.332
64_R155_D0.427311.319
71_P144_K0.422741.305
119_I123_L0.420131.297
7_D11_E0.415211.282
28_R31_Y0.411391.270
62_L75_P0.403811.246
121_K126_A0.40081.237
73_P76_Y0.398671.230
26_K29_K0.395061.219
94_P99_K0.393651.215
49_Y52_R0.390551.205
29_K33_D0.389541.202
71_P75_P0.387851.197
134_S137_N0.386171.192
17_I82_V0.380961.176
29_K32_R0.378521.168
129_V154_V0.377381.165
114_E144_K0.371561.147
59_F63_K0.37071.144
58_E61_N0.366121.130
63_K66_Y0.36511.127
23_T26_K0.359911.111
119_I147_I0.356571.101
18_Y81_N0.354041.093
68_A126_A0.351521.085
49_Y53_E0.350741.083
131_G154_V0.350061.080
51_I57_K0.347141.071
88_I141_D0.345241.066
95_L99_K0.342641.058
71_P86_E0.340211.050
98_L102_D0.337561.042
111_L145_V0.336361.038
104_S107_E0.335031.034
63_K67_E0.328181.013
115_I145_V0.327271.010
51_I54_W0.32431.001
69_G114_E0.323911.000
29_K36_Y0.322980.997
93_V104_S0.321390.992
120_I123_L0.318110.982
58_E132_D0.316520.977
105_P108_P0.312780.965
58_E65_L0.311890.963
110_E113_E0.31020.957
105_P109_K0.309340.955
46_S49_Y0.307750.950
28_R36_Y0.302960.935
29_K34_Y0.301780.931
119_I124_H0.296410.915
134_S149_D0.295420.912
97_R101_V0.294180.908
109_K113_E0.29360.906
70_V75_P0.291490.900
2_V14_A0.291070.898
30_K33_D0.289990.895
113_E116_L0.289040.892
28_R32_R0.285370.881
95_L140_V0.283060.874
61_N64_R0.281230.868
60_R63_K0.279690.863
7_D10_G0.277240.856
11_E76_Y0.276930.855
108_P111_L0.274980.849
99_K103_L0.272240.840
61_N65_L0.271150.837
61_N153_A0.270820.836
27_R31_Y0.27060.835
132_D151_G0.270150.834
78_Y84_V0.270030.833
140_V145_V0.269780.833
72_V76_Y0.268370.828
33_D36_Y0.264850.817
112_L115_I0.264560.817
61_N128_I0.264020.815
5_A84_V0.263650.814
45_S48_R0.259920.802
55_A58_E0.256150.791
111_L140_V0.255680.789
93_V99_K0.255110.787
31_Y34_Y0.25490.787
58_E151_G0.254180.785
35_D43_H0.253340.782
43_H46_S0.252970.781
138_I147_I0.25290.781
89_G141_D0.252720.780
99_K102_D0.251470.776
70_V73_P0.251420.776
114_E117_E0.251240.775
78_Y81_N0.250250.772
26_K30_K0.249330.770
67_E71_P0.249160.769
120_I133_L0.248570.767
16_K149_D0.247440.764
28_R35_D0.247140.763
131_G134_S0.246660.761
100_D104_S0.246540.761
115_I133_L0.244850.756
18_Y55_A0.244540.755
25_F28_R0.243290.751
36_Y43_H0.242240.748
9_D12_E0.241760.746
18_Y21_G0.240080.741
11_E86_E0.239380.739
34_Y37_R0.238770.737
112_L120_I0.238520.736
75_P83_I0.237520.733
71_P146_Y0.237160.732
130_H137_N0.236520.730
32_R35_D0.235740.728
24_S27_R0.235330.726
134_S148_I0.234720.724
24_S29_K0.233640.721
32_R36_Y0.23150.715
62_L150_F0.231040.713
20_T25_F0.230130.710
93_V101_V0.229180.707
69_G110_E0.228960.707
47_W52_R0.227550.702
59_F83_I0.2260.698
88_I139_L0.224230.692
130_H133_L0.224180.692
59_F62_L0.223940.691
148_I152_Q0.22260.687
60_R64_R0.219140.676
33_D37_R0.218510.674
21_G24_S0.218360.674
36_Y48_R0.217930.673
147_I150_F0.217530.671
107_E110_E0.215020.664
112_L116_L0.212230.655
52_R55_A0.211140.652
134_S151_G0.210720.650
31_Y35_D0.209480.647
114_E143_G0.206980.639
54_W57_K0.206760.638
48_R53_E0.206470.637
98_L108_P0.206170.636
122_M126_A0.205960.636
117_E121_K0.205410.634
69_G117_E0.204520.631
65_L68_A0.204140.630
107_E111_L0.203550.628
48_R51_I0.203340.628
149_D153_A0.203010.627
100_D103_L0.203010.627
132_D153_A0.202070.624
106_E110_E0.201690.623
24_S32_R0.201620.622
34_Y43_H0.201530.622
44_K49_Y0.201520.622
71_P141_D0.200930.620
108_P112_L0.200910.620
25_F31_Y0.200370.618
58_E62_L0.199740.616
77_D80_R0.199720.616
19_R138_I0.199150.615
71_P74_K0.19910.615
62_L153_A0.198490.613
57_K61_N0.198480.613
43_H47_W0.198380.612
111_L115_I0.197740.610
36_Y47_W0.197270.609
49_Y56_K0.196690.607
25_F29_K0.194650.601
105_P112_L0.194110.599
97_R142_D0.194040.599
64_R126_A0.193530.597
32_R37_R0.193480.597
116_L124_H0.192340.594
29_K37_R0.192040.593
62_L85_M0.191610.591
102_D106_E0.191450.591
69_G144_K0.191310.590
93_V98_L0.190230.587
4_H14_A0.18920.584
43_H48_R0.18750.579
122_M125_K0.186030.574
149_D152_Q0.185180.572
3_Y17_I0.185130.571
28_R33_D0.185130.571
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
4fieA0.835199.90.176
4fihA0.835199.90.183
4g3fA0.808599.90.2
4im0A0.840499.90.206
4g31A0.840499.90.21
3ubdA0.845799.90.215
4aojA0.835199.90.217
4ic7A0.845799.90.218
3hyhA0.851199.90.219
4b99A0.845799.90.221

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