GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Arf - ADP-ribosylation factor family
Pfam: PF00025 (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: CL0023
Length: 175
Sequences: 34008
Seq/Len: 194.33
HH_delta: 0.106 (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
33_R161_G2.073142.923
154_F170_W1.747112.463
91_S122_A1.720182.425
121_L156_C1.586242.237
86_I121_L1.495992.109
88_V123_N1.45882.057
22_L99_E1.440922.032
125_Q155_S1.422162.005
30_L88_V1.36661.927
152_S170_W1.295281.826
121_L167_G1.278781.803
156_C167_G1.267931.788
122_A155_S1.247431.759
163_G166_E1.223581.725
125_Q162_E1.212861.710
29_T158_A1.187821.675
18_L82_A1.152251.625
103_E106_E1.104361.557
119_L154_F1.089861.537
91_S125_Q1.08691.532
123_N158_A1.082951.527
119_L170_W1.063321.499
100_A103_E1.042141.469
19_I86_I1.036491.461
30_L167_G1.016271.433
131_M134_E1.013031.428
132_S135_E1.010361.425
102_E106_E0.997851.407
19_I31_L0.991761.398
133_E137_K0.985791.390
135_E139_Y0.962661.357
89_V153_V0.95881.352
136_I139_Y0.957471.350
93_D96_R0.955761.348
104_L108_L0.952321.343
105_K109_N0.950181.340
30_L164_V0.947031.335
84_G171_L0.942641.329
42_T46_I0.939311.324
58_Y172_I0.934861.318
92_S127_L0.93011.311
90_D93_D0.915741.291
46_I49_N0.910631.284
33_R164_V0.904671.276
84_G119_L0.895241.262
89_V120_I0.893681.260
137_K141_G0.877871.238
42_T45_T0.867441.223
134_E138_E0.863141.217
166_E169_E0.855271.206
165_D169_E0.846141.193
86_I171_L0.841811.187
60_L172_I0.836991.180
44_P47_G0.834691.177
106_E109_N0.834241.176
52_E59_S0.827641.167
134_E137_K0.819331.155
104_L107_L0.819011.155
139_Y143_E0.816721.152
30_L158_A0.811131.144
89_V122_A0.810641.143
101_K105_K0.808991.141
101_K104_L0.800581.129
68_Q71_F0.794271.120
90_D124_K0.791751.116
43_I48_F0.788721.112
100_A104_L0.781281.102
48_F51_E0.780141.100
86_I167_G0.776051.094
42_T49_N0.775651.094
50_I61_T0.773461.091
74_L77_S0.766221.080
43_I47_G0.762791.076
140_L144_K0.754471.064
32_N36_N0.752381.061
98_Q101_K0.750071.058
43_I46_I0.739861.043
126_D157_S0.736311.038
99_E102_E0.730791.030
85_I116_I0.711951.004
34_L168_L0.708240.999
64_D67_G0.706610.996
99_E103_E0.702570.991
86_I119_L0.700980.988
30_L156_C0.697480.983
74_L78_Y0.695260.980
122_A153_V0.689410.972
56_K172_I0.688120.970
45_T51_E0.679630.958
105_K108_L0.678430.957
135_E138_E0.675640.953
120_I151_W0.67360.950
130_A133_E0.671710.947
44_P48_F0.67050.945
164_V168_L0.664180.936
157_S160_T0.662980.935
17_I84_G0.660410.931
103_E107_L0.65940.930
30_L34_L0.659370.930
131_M136_I0.653960.922
169_E172_I0.653260.921
96_R99_E0.64920.915
21_G26_G0.648040.914
75_W78_Y0.646110.911
137_K140_L0.643390.907
22_L25_S0.640160.903
167_G171_L0.637680.899
46_I51_E0.63710.898
47_G50_I0.63650.897
166_E170_W0.632310.892
44_P51_E0.631510.890
133_E136_I0.627170.884
46_I50_I0.625970.883
82_A85_I0.624610.881
72_R75_W0.623820.880
132_S136_I0.621830.877
158_A161_G0.621160.876
124_K127_L0.620040.874
54_K57_G0.619990.874
154_F163_G0.616240.869
133_E155_S0.613620.865
96_R100_A0.607190.856
102_E105_K0.604890.853
168_L171_L0.604230.852
45_T49_N0.603090.850
141_G144_K0.60180.849
42_T47_G0.597420.842
97_L100_A0.596640.841
131_M135_E0.591830.834
71_F75_W0.585050.825
54_K59_S0.584740.824
47_G51_E0.582270.821
103_E108_L0.581540.820
44_P49_N0.575520.811
17_I171_L0.573830.809
120_I153_V0.572080.807
18_L65_L0.565840.798
35_K39_I0.562450.793
42_T51_E0.5620.792
136_I140_L0.560080.790
51_E55_Y0.554570.782
31_L62_I0.553710.781
143_E146_K0.55340.780
32_N41_E0.552370.779
87_F100_A0.550790.777
55_Y169_E0.549140.774
161_G164_V0.542380.765
97_L101_K0.541040.763
160_T163_G0.535960.756
52_E55_Y0.531210.749
21_G27_K0.529520.747
119_L167_G0.529210.746
84_G167_G0.526250.742
146_K150_P0.524470.739
17_I60_L0.518330.731
168_L172_I0.51820.731
139_Y144_K0.518050.730
135_E140_L0.517990.730
33_R158_A0.515610.727
90_D123_N0.513510.724
134_E139_Y0.510730.720
138_E141_G0.510660.720
28_T32_N0.50950.718
51_E54_K0.509050.718
98_Q102_E0.508650.717
37_G41_E0.50730.715
121_L154_F0.506960.715
154_F166_E0.50590.713
23_D68_Q0.505440.713
32_N38_E0.505330.712
75_W79_F0.505030.712
87_F120_I0.504960.712
88_V156_C0.504180.711
42_T50_I0.501370.707
33_R37_G0.49710.701
96_R101_K0.495920.699
71_F74_L0.489090.690
30_L121_L0.489010.689
132_S139_Y0.485190.684
128_P131_M0.483720.682
45_T48_F0.482880.681
87_F104_L0.480720.678
137_K143_E0.479140.676
17_I62_I0.47310.667
29_T32_N0.472660.666
45_T50_I0.468680.661
129_D132_S0.467920.660
69_E72_R0.466240.657
108_L118_I0.461630.651
68_Q75_W0.460960.650
32_N35_K0.459620.648
136_I141_G0.457860.646
131_M137_K0.456610.644
38_E41_E0.452790.638
140_L143_E0.452760.638
140_L145_L0.450840.636
56_K169_E0.449390.634
25_S28_T0.447850.631
79_F82_A0.447130.630
94_P98_Q0.444650.627
138_E144_K0.443940.626
152_S155_S0.442720.624
137_K155_S0.441580.623
43_I51_E0.44120.622
84_G117_P0.441020.622
50_I53_I0.439640.620
141_G146_K0.436260.615
159_K162_E0.434980.613
162_E166_E0.43330.611
70_S74_L0.430580.607
43_I49_N0.430370.607
22_L93_D0.428460.604
122_A125_Q0.427510.603
164_V167_G0.424070.598
118_I151_W0.422240.595
58_Y61_T0.42020.592
49_N55_Y0.420150.592
50_I55_Y0.419610.592
73_P76_K0.419390.591
52_E61_T0.416490.587
33_R159_K0.415960.586
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
2b6hA0.988699.90.106
3lvqE0.994399.90.107
1f6bA199.90.108
1fzqA0.994399.90.109
1m2oB199.90.11
1mozA0.994399.90.116
3o47A0.988699.90.12
2x77A0.994399.90.12
1kshA0.988699.90.122
1zj6A0.982999.90.122

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