GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sdh_cyt - Succinate dehydrogenaseFumarate reductase transmembrane subunit
Pfam: PF01127 (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: CL0335
Length: 121
Sequences: 1422
Seq/Len: 11.75
HH_delta: 0.041 (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
16_F20_T0.498622.785
104_R108_L0.358872.005
17_H20_T0.352971.972
101_K105_R0.35151.964
16_F21_W0.339091.894
82_H86_G0.323921.809
87_I91_L0.323441.807
102_N106_S0.319581.785
10_H13_I0.311261.739
30_G86_G0.289041.615
29_T78_A0.271991.519
28_I31_I0.26071.456
26_Q85_N0.259781.451
6_P9_P0.250261.398
21_W25_L0.247851.385
89_H92_E0.244261.364
30_G82_H0.241861.351
22_A81_F0.238571.333
57_D60_V0.234411.309
107_G110_I0.233831.306
101_K104_R0.232811.301
60_V64_S0.232161.297
102_N105_R0.231691.294
9_P14_Y0.230511.288
105_R108_L0.228131.274
57_D61_A0.224871.256
39_H42_I0.222381.242
6_P27_R0.220731.233
74_L78_A0.215611.204
69_A73_F0.214911.201
60_V66_P0.21411.196
88_R106_S0.21261.188
84_L110_I0.2121.184
104_R107_G0.20841.164
27_R88_R0.208371.164
54_I58_E0.207971.162
8_S13_I0.205361.147
91_L94_W0.204881.144
101_K106_S0.200231.119
77_V81_F0.199331.113
32_I35_L0.196791.099
5_R11_R0.196771.099
38_L42_I0.195221.091
16_F19_G0.190311.063
97_G106_S0.189781.060
88_R93_D0.189371.058
85_N110_I0.189191.057
103_R107_G0.189141.057
53_P57_D0.18861.054
105_R109_L0.184921.033
103_R106_S0.184881.033
81_F85_N0.181691.015
9_P13_I0.180881.010
11_R24_I0.179521.003
89_H93_D0.178550.997
90_I94_W0.17770.993
5_R10_H0.177070.989
101_K109_L0.175670.981
77_V80_F0.175020.978
18_S104_R0.173690.970
61_A64_S0.173290.968
73_F77_V0.172830.965
62_F68_W0.172220.962
54_I57_D0.171020.955
106_S109_L0.170240.951
32_I69_A0.170180.951
70_I74_L0.168340.940
37_F79_F0.167730.937
56_Y60_V0.167410.935
106_S110_I0.167210.934
31_I35_L0.166540.930
103_R110_I0.166360.929
72_Y76_L0.166350.929
71_L75_L0.164720.920
8_S14_Y0.162440.907
102_N108_L0.161920.905
23_W89_H0.159730.892
92_E103_R0.159490.891
15_R18_S0.15720.878
72_Y75_L0.155530.869
19_G23_W0.154970.866
20_T23_W0.153160.856
58_E61_A0.152570.852
66_P70_I0.152240.850
37_F41_H0.151510.846
53_P60_V0.151230.845
11_R14_Y0.150880.843
10_H14_Y0.149210.834
62_F65_S0.149190.833
14_Y27_R0.148260.828
25_L29_T0.146150.816
72_Y78_A0.145950.815
5_R8_S0.145050.810
9_P23_W0.144340.806
5_R27_R0.143510.802
35_L75_L0.143280.800
102_N110_I0.142090.794
26_Q30_G0.14130.789
91_L106_S0.141090.788
23_W92_E0.141020.788
18_S84_L0.140940.787
104_R109_L0.140390.784
5_R9_P0.140230.783
25_L28_I0.140060.782
27_R31_I0.140060.782
22_A107_G0.139330.778
55_S58_E0.139220.778
18_S21_W0.138940.776
48_A52_G0.137440.768
51_G56_Y0.136430.762
35_L59_V0.136430.762
8_S92_E0.136210.761
51_G63_F0.135640.758
94_W102_N0.135570.757
7_R11_R0.135550.757
30_G85_N0.135540.757
88_R92_E0.134950.754
52_G57_D0.134540.752
59_V63_F0.134340.750
33_L79_F0.134290.750
102_N109_L0.134150.749
42_I62_F0.133780.747
103_R109_L0.13370.747
81_F107_G0.133270.744
83_A105_R0.132930.743
5_R19_G0.132050.738
61_A65_S0.131890.737
22_A92_E0.131590.735
25_L54_I0.131130.733
15_R96_I0.13070.730
69_A93_D0.130560.729
89_H107_G0.129840.725
26_Q93_D0.12980.725
32_I96_I0.12980.725
86_G90_I0.129480.723
75_L85_N0.127480.712
43_W48_A0.127210.711
63_F75_L0.127150.710
87_I90_I0.126940.709
51_G64_S0.126340.706
71_L74_L0.126220.705
61_A105_R0.126130.705
21_W81_F0.126130.705
83_A102_N0.125790.703
47_S58_E0.125720.702
32_I78_A0.125630.702
98_L102_N0.125260.700
70_I105_R0.125160.699
23_W26_Q0.124960.698
26_Q89_H0.123730.691
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
3vr8C0.958799.90.041
2wdqC0.983599.90.044
1zoyC0.958799.90.068
2h88C0.958799.90.069
2wdqD0.884399.20.517
2bs2C0.958799.10.536
1kf6D0.87696.30.785
2bs2C0.983594.80.809
2h88D0.68692.20.828
1kf6C0.966980.10.857

Page generated in 0.035 seconds.