GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NADH5_C - NADH dehydrogenase subunit 5 C-terminus
Pfam: PF06455 (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. )
Length: 181
Sequences: 4851
Seq/Len: 26.8
HH_delta: 0.386 (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
101_F106_W0.504912.983
75_G79_G0.416372.460
62_F66_L0.411362.431
3_F7_Y0.359812.126
161_N166_Y0.352632.084
6_I11_W0.327941.938
68_P72_I0.307021.814
38_L42_F0.305091.803
113_S117_S0.303891.796
2_S5_L0.301371.781
74_L78_L0.298771.765
32_P35_I0.295211.744
1_Y4_R0.282071.667
99_K103_S0.281451.663
3_F80_Y0.275961.631
149_M153_K0.274611.623
16_S22_S0.270981.601
34_L38_L0.26851.587
39_G43_G0.267851.583
27_K31_I0.265791.571
145_F149_M0.25561.510
137_E142_Q0.251491.486
141_P144_I0.250041.477
142_Q145_F0.24311.436
122_K126_K0.233751.381
111_L115_F0.233481.380
66_L70_L0.230861.364
92_K96_L0.230451.362
146_S150_K0.229671.357
70_L74_L0.229161.354
118_K122_K0.227491.344
164_K167_L0.227161.342
108_L112_S0.226231.337
160_S165_S0.226071.336
25_N30_N0.225131.330
100_N107_F0.223281.319
77_I81_F0.221141.307
102_F106_W0.220511.303
131_L136_L0.219951.300
73_I77_I0.218551.291
80_Y84_K0.217021.282
1_Y44_G0.213091.259
37_S40_S0.212961.258
155_F159_Q0.212071.253
29_M33_M0.20961.238
112_S116_I0.206651.221
65_K68_P0.20561.215
31_I35_I0.204221.207
2_S6_I0.203111.200
69_L72_I0.203041.200
163_L166_Y0.202091.194
162_S165_S0.202031.194
115_F119_N0.201881.193
81_F85_L0.199311.178
132_D137_E0.198721.174
105_M109_P0.198051.170
10_F109_P0.196941.164
35_I39_G0.196721.162
24_E30_N0.195021.152
45_S49_W0.191921.134
53_P59_F0.19151.132
27_K34_L0.191051.129
105_M110_F0.190741.127
30_N34_L0.190151.124
165_S169_F0.187511.108
105_M108_L0.18741.107
110_F114_Q0.187041.105
7_Y79_G0.185941.099
3_F76_I0.18571.097
36_L44_G0.185361.095
9_V12_G0.184451.090
82_L93_K0.182991.081
26_S29_M0.182741.080
2_S65_K0.182051.076
28_S32_P0.181841.074
88_K92_K0.18141.072
96_L100_N0.179771.062
32_P37_S0.179561.061
80_Y85_L0.179321.060
120_F131_L0.179091.058
153_K156_Q0.178691.056
151_L155_F0.178561.055
108_L113_S0.177981.052
40_S44_G0.17751.049
150_K153_K0.17671.044
143_G148_L0.176211.041
32_P44_G0.175951.040
155_F158_F0.175351.036
23_S147_L0.174621.032
84_K147_L0.174251.030
149_M152_S0.173891.027
84_K87_Y0.173531.025
71_I75_G0.172371.019
156_Q159_Q0.170781.009
94_M98_L0.170521.008
162_S166_Y0.170061.005
104_S110_F0.171.005
49_W58_I0.168840.998
17_N20_N0.167630.990
7_Y80_Y0.166570.984
60_L65_K0.166280.983
73_I76_I0.16590.980
68_P71_I0.165860.980
31_I34_L0.165620.979
101_F111_L0.164860.974
74_L150_K0.16470.973
116_I119_N0.164010.969
89_F116_I0.163920.969
119_N122_K0.163640.967
25_N29_M0.163190.964
58_I63_F0.162780.962
104_S107_F0.162140.958
132_D135_W0.161310.953
12_G15_N0.161280.953
69_L73_I0.158820.938
3_F6_I0.156110.922
1_Y36_L0.155670.920
63_F170_F0.154360.912
33_M105_M0.153880.909
82_L88_K0.15380.909
39_G42_F0.153680.908
75_G132_D0.153330.906
121_L125_S0.153020.904
134_G172_I0.153020.904
143_G147_L0.15160.896
36_L40_S0.151550.895
126_K139_F0.15150.895
116_I123_L0.151030.892
34_L144_I0.150350.888
7_Y11_W0.150040.887
47_L51_L0.148460.877
145_F148_L0.147690.873
60_L66_L0.147530.872
6_I10_F0.147350.871
40_S103_S0.147110.869
52_F144_I0.147020.869
161_N165_S0.146820.868
141_P152_S0.146720.867
82_L132_D0.146710.867
133_Q148_L0.146440.865
81_F86_S0.14640.865
1_Y5_L0.146060.863
162_S167_L0.145710.861
121_L124_S0.145340.859
78_L81_F0.145120.857
63_F70_L0.144910.856
153_K157_K0.144730.855
97_F100_N0.143930.850
43_G47_L0.143070.845
75_G137_E0.1430.845
150_K157_K0.1430.845
60_L64_L0.142650.843
144_I171_F0.14250.842
63_F67_L0.142320.841
51_L136_L0.142010.839
146_S149_M0.141970.839
168_L172_I0.141570.837
33_M37_S0.141210.834
61_P64_L0.140860.832
5_L33_M0.140720.831
164_K169_F0.140390.830
147_L150_K0.140140.828
5_L8_Y0.139330.823
49_W133_Q0.139320.823
54_F60_L0.139280.823
169_F172_I0.139060.822
116_I120_F0.138680.819
55_P59_F0.138570.819
156_Q160_S0.138240.817
88_K91_S0.137780.814
2_S164_K0.137770.814
34_L109_P0.137440.812
131_L134_G0.137310.811
129_K133_Q0.137030.810
117_S120_F0.136980.809
162_S168_L0.136760.808
41_I48_S0.136730.808
144_I147_L0.136430.806
14_P19_L0.135910.803
33_M68_P0.135210.799
145_F152_S0.135210.799
20_N110_F0.135170.799
2_S163_L0.134870.797
97_F122_K0.134120.792
168_L171_F0.133630.790
159_Q162_S0.133390.788
10_F13_S0.132830.785
100_N104_S0.132810.785
61_P65_K0.132340.782
14_P20_N0.131830.779
131_L135_W0.131230.775
160_S166_Y0.131050.774
33_M44_G0.130960.774
8_Y11_W0.130850.773
126_K130_S0.130250.770
23_S29_M0.129350.764
154_K157_K0.128780.761
93_K96_L0.12860.760
10_F152_S0.128570.760
81_F84_K0.128560.760
5_L99_K0.128490.759
105_M112_S0.128460.759
72_I76_I0.128060.757
114_Q121_L0.127870.756
143_G146_S0.127780.755
138_Y150_K0.127560.754
84_K116_I0.127430.753
26_S30_N0.127390.753
114_Q117_S0.126820.749
158_F169_F0.126590.748
128_F131_L0.126580.748
98_L147_L0.126360.747
127_S130_S0.125770.743
136_L173_W0.125490.742
139_F159_Q0.12540.741
5_L109_P0.125350.741
110_F127_S0.125340.741
112_S162_S0.125260.740
148_L152_S0.125080.739
85_L88_K0.125060.739
10_F156_Q0.125010.739
28_S163_L0.124910.738
36_L166_Y0.124870.738
89_F94_M0.124830.738
16_S19_L0.124730.737
22_S25_N0.124680.737
146_S154_K0.124470.735
91_S111_L0.124440.735
120_F124_S0.12430.734
145_F150_K0.123370.729
86_S151_L0.122540.724
17_N144_I0.122470.724
124_S164_K0.12180.720
96_L169_F0.121770.720
67_L71_I0.121320.717
78_L97_F0.121220.716
153_K158_F0.121010.715
134_G138_Y0.1210.715
19_L22_S0.120680.713
13_S70_L0.120660.713
6_I72_I0.120450.712
137_E141_P0.119980.709
157_K169_F0.119870.708
98_L102_F0.119830.708
2_S16_S0.11920.704
69_L86_S0.119190.704
144_I162_S0.118260.699
5_L9_V0.118220.699
141_P164_K0.118220.699
79_G83_Y0.118140.698
63_F66_L0.117790.696
82_L90_S0.117040.692
62_F96_L0.116780.690
29_M106_W0.116730.690
17_N148_L0.116640.689
33_M141_P0.116360.688
90_S94_M0.115870.685
53_P60_L0.115730.684
158_F172_I0.115170.681
88_K94_M0.11510.680
157_K160_S0.115010.680
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
3rkoL0.955899.50.386
4he8L0.955899.40.441
3rkoN0.33765.70.861
3rkoM0.408857.10.868
4he8M0.359132.10.886
2iubA0.4532.60.93
2iruA0.30392.50.93
4ev6A0.45861.80.935
4i0uA0.46411.50.938
2kbgA0.20991.40.939

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