GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrom_B_N - Cytochrome b(N-terminal)b6petB
Pfam: PF00033 (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: CL0328
Length: 188
Sequences: 3021
Seq/Len: 16.07
HH_delta: 0.224 (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
21_L53_L0.497842.433
172_I176_F0.448942.194
5_S67_W0.423132.068
15_N60_L0.409622.002
5_S8_T0.404741.978
8_T67_W0.367851.798
58_L121_A0.365391.786
119_L156_L0.362561.772
15_N61_F0.359631.758
151_L154_F0.353921.730
142_P145_L0.341061.667
168_I171_A0.339051.657
155_I159_L0.336771.646
164_I168_I0.335561.640
120_M156_L0.33381.631
66_L70_F0.331041.618
7_F67_W0.329211.609
19_F117_L0.328641.606
10_L14_L0.31611.545
57_F117_L0.312361.527
180_G183_R0.310611.518
166_I170_A0.307881.505
120_M157_A0.303921.485
22_L57_F0.303561.484
112_A163_F0.301281.472
26_G29_L0.301111.472
175_H180_G0.29941.463
5_S71_S0.299221.462
61_F121_A0.297721.455
111_W115_L0.297551.454
104_P107_K0.287441.405
175_H181_V0.284681.391
165_I169_Y0.283141.384
122_I126_I0.282521.381
58_L125_L0.282341.380
61_F117_L0.280771.372
16_A20_I0.269741.318
173_F177_R0.26731.306
106_Q110_Y0.260451.273
162_A166_I0.259291.267
14_L60_L0.258921.265
6_L10_L0.255461.248
41_P44_Q0.253341.238
99_S102_Y0.250361.224
175_H183_R0.24961.220
160_L164_I0.246321.204
109_V166_I0.245681.201
175_H182_L0.242711.186
112_A116_L0.242281.184
61_F118_L0.241321.179
18_L53_L0.240761.177
127_M150_R0.240491.175
109_V163_F0.238561.166
170_A174_H0.237931.163
15_N57_F0.235721.152
158_Y162_A0.235681.152
68_R114_Y0.235491.151
15_N117_L0.235091.149
110_Y171_A0.234631.147
6_L9_R0.234621.147
20_I24_I0.231081.129
49_L53_L0.228991.119
13_W16_A0.228911.119
22_L25_T0.228811.118
54_G57_F0.22881.118
8_T71_S0.228681.118
120_M160_L0.228551.117
7_F10_L0.226611.107
41_P45_L0.226281.106
108_L111_W0.225741.103
4_F8_T0.223081.090
148_W152_I0.222761.089
23_L158_Y0.219891.075
67_W71_S0.217181.061
120_M125_L0.215051.051
104_P108_L0.214161.047
123_T149_A0.213911.045
123_T152_I0.212541.039
19_F160_L0.211931.036
57_F121_A0.211931.036
28_Y41_P0.211841.035
103_N107_K0.211771.035
126_I149_A0.211221.032
123_T127_M0.21061.029
102_Y106_Q0.21011.027
55_I59_A0.208931.021
43_R46_L0.208521.019
100_G104_P0.208431.019
116_L159_L0.207711.015
108_L112_A0.205111.002
12_H167_H0.204891.001
106_Q109_V0.203320.994
23_L161_L0.202070.988
183_R187_S0.200870.982
44_Q48_W0.199620.976
40_F44_Q0.199470.975
110_Y174_H0.198750.971
152_I155_I0.19770.966
49_L52_S0.196740.961
17_L21_L0.196660.961
147_E150_R0.19650.960
4_F102_Y0.196380.960
171_A182_L0.191360.935
115_L119_L0.190010.929
152_I156_L0.189040.924
113_L163_F0.189020.924
171_A174_H0.188390.921
147_E151_L0.18830.920
119_L152_I0.187490.916
155_I158_Y0.187490.916
181_V184_S0.186640.912
41_P46_L0.186530.912
116_L163_F0.185960.909
154_F157_A0.184380.901
23_L164_I0.184010.899
154_F158_Y0.183070.895
145_L148_W0.182570.892
67_W70_F0.182450.892
62_L66_L0.182150.890
127_M149_A0.181550.887
168_I172_I0.180580.883
123_T157_A0.178580.873
114_Y118_L0.177230.866
11_L15_N0.177070.865
13_W185_M0.176970.865
110_Y163_F0.176510.863
18_L57_F0.175330.857
11_L63_L0.174310.852
11_L60_L0.173890.850
90_L93_R0.172410.843
50_H54_G0.172060.841
45_L49_L0.17160.839
4_F67_W0.171550.838
134_P137_P0.171110.836
64_R114_Y0.171040.836
124_G153_H0.170810.835
119_L123_T0.169740.830
169_Y173_F0.169450.828
52_S56_V0.169050.826
56_V60_L0.168790.825
42_G46_L0.166370.813
40_F43_R0.165810.810
117_L121_A0.165730.810
66_L69_L0.165240.808
106_Q181_V0.164920.806
65_I111_W0.164020.802
143_P147_E0.162990.797
168_I182_L0.162720.795
99_S104_P0.162080.792
182_L186_V0.161680.790
15_N54_G0.161490.789
141_P145_L0.16120.788
27_L157_A0.161020.787
146_A150_R0.160740.786
28_Y42_G0.160690.785
156_L159_L0.160040.782
62_L159_L0.159430.779
47_R150_R0.159420.779
162_A165_I0.15770.771
125_L138_W0.15760.770
174_H184_S0.156920.767
42_G45_L0.156590.765
159_L166_I0.156390.764
21_L25_T0.156320.764
64_R68_R0.156180.763
120_M123_T0.15610.763
116_L160_L0.155540.760
117_L160_L0.15510.758
22_L53_L0.154760.756
109_V170_A0.153350.749
63_L67_W0.153190.749
50_H124_G0.152390.745
54_G68_R0.151550.741
109_V113_L0.151420.740
107_K111_W0.151380.740
6_L63_L0.150870.737
50_H153_H0.150490.735
43_R47_R0.15010.734
18_L56_V0.149460.730
26_G41_P0.149080.729
150_R154_F0.148660.727
21_L49_L0.147830.722
19_F61_F0.14570.712
139_L142_P0.145150.709
27_L30_M0.14420.705
23_L26_G0.144020.704
26_G30_M0.142680.697
61_F114_Y0.142220.695
136_P152_I0.141860.693
29_L43_R0.141280.690
45_L48_W0.141020.689
156_L160_L0.140390.686
11_L67_W0.140170.685
175_H184_S0.140.684
99_S162_A0.139470.682
144_G148_W0.139160.680
135_L138_W0.138810.678
15_N22_L0.138750.678
11_L110_Y0.138730.678
9_R187_S0.138350.676
57_F60_L0.138270.676
146_A149_A0.137310.671
24_I151_L0.137250.671
122_I125_L0.13710.670
23_L160_L0.137030.670
161_L165_I0.136850.669
119_L122_I0.13680.669
133_W136_P0.135930.664
141_P144_G0.135710.663
124_G127_M0.13570.663
15_N19_F0.134930.659
19_F157_A0.134870.659
9_R168_I0.13470.658
30_M41_P0.134630.658
8_T114_Y0.134380.657
9_R186_V0.134140.656
23_L157_A0.133330.652
26_G161_L0.133170.651
43_R150_R0.132980.650
170_A181_V0.131710.644
4_F107_K0.13140.642
26_G123_T0.131290.642
102_Y173_F0.130680.639
125_L137_P0.130090.636
41_P187_S0.130010.635
65_I118_L0.129960.635
7_F63_L0.129930.635
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
4gd3A199.90.224
1kqfC0.946899.90.235
4gd3A0.537296.90.813
1kqfC0.537296.30.826
4h44A0.819193.50.855
4h44A0.606490.70.867
3cx5C0.968182.40.882
3cx5C0.590481.60.883
1pp9C0.851179.20.886
2qjyA0.8564740.891

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