GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_q3 - NADH-ubiquinoneplastoquinone oxidoreductase chain 6
Pfam: PF00499 (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: 144
Sequences: 3595
Seq/Len: 24.97
HH_delta: 0.154 (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
127_I130_S0.425892.351
137_L141_I0.338351.868
12_S129_L0.320111.767
28_S44_F0.297451.642
47_Y58_V0.283251.564
106_S109_S0.269671.489
32_S40_G0.267521.477
10_S19_S0.265341.465
93_F97_N0.262521.449
38_W42_I0.262191.447
6_L9_F0.247271.365
82_I95_F0.243041.342
25_L60_S0.238971.319
77_F81_L0.237111.309
10_S15_Y0.235491.300
91_I94_M0.230311.271
13_P52_L0.22911.265
13_P57_Y0.224721.241
7_V20_L0.224371.239
99_S103_N0.22331.233
75_S78_S0.223121.232
101_S107_S0.221571.223
118_L126_F0.22091.219
85_L89_L0.220851.219
25_L44_F0.220811.219
13_P58_V0.22071.218
77_F80_S0.219291.211
13_P62_S0.21861.207
36_S60_S0.217841.203
32_S37_S0.21721.199
78_S82_I0.2171.198
52_L55_F0.214381.183
45_L49_G0.213581.179
84_F88_I0.213161.177
94_M99_S0.212691.174
47_Y118_L0.212611.174
85_L98_F0.208661.152
40_G136_A0.207731.147
100_F105_S0.204671.130
86_F90_I0.203671.124
6_L19_S0.203351.123
133_L137_L0.203241.122
46_V49_G0.202491.118
90_I94_M0.202161.116
73_K76_F0.201471.112
31_Y43_L0.200241.105
99_S102_L0.199391.101
26_F37_S0.199061.099
82_I89_L0.198751.097
55_F58_V0.198421.095
92_F95_F0.197691.091
103_N106_S0.196531.085
134_L137_L0.195841.081
12_S72_N0.195561.080
93_F96_S0.195181.077
40_G73_K0.194621.074
125_M130_S0.194611.074
93_F107_S0.194421.073
47_Y114_S0.194311.073
13_P55_F0.194241.072
31_Y139_G0.192541.063
77_F102_L0.190531.052
92_F99_S0.189791.048
85_L101_S0.188681.042
78_S94_M0.187711.036
117_L125_M0.187461.035
97_N100_F0.187221.034
83_L86_F0.186981.032
99_S106_S0.184461.018
76_F80_S0.183981.016
83_L90_I0.183831.015
6_L42_I0.183541.013
58_V62_S0.183051.011
135_V139_G0.182911.010
59_I65_E0.182881.010
50_G62_S0.182871.010
92_F96_S0.182611.008
82_I85_L0.182441.007
21_I52_L0.18131.001
108_S111_S0.180710.998
76_F83_L0.180590.997
6_L10_S0.180390.996
36_S127_I0.178380.985
14_L58_V0.178240.984
64_N67_F0.178090.983
50_G57_Y0.176920.977
86_F94_M0.176650.975
18_L45_L0.175590.969
73_K77_F0.175470.969
43_L55_F0.17510.967
62_S65_E0.175010.966
77_F82_I0.174940.966
15_Y45_L0.174750.965
7_V16_S0.174580.964
7_V13_P0.174070.961
17_G32_S0.173880.960
30_L33_L0.173450.958
56_L60_S0.173330.957
112_S116_F0.172520.952
98_F102_L0.172020.950
86_F95_F0.17140.946
117_L121_S0.171340.946
84_F91_I0.171280.946
6_L70_S0.17060.942
102_L106_S0.170430.941
40_G60_S0.169840.938
102_L105_S0.168810.932
36_S129_L0.168230.929
137_L142_S0.168190.928
81_L85_L0.167810.926
82_I97_N0.167470.925
78_S81_L0.167390.924
88_I92_F0.167050.922
27_I60_S0.166830.921
44_F57_Y0.166440.919
84_F87_F0.165870.916
79_L91_I0.165780.915
80_S84_F0.165370.913
49_G55_F0.165310.913
121_S128_F0.165240.912
103_N109_S0.164940.911
48_V62_S0.164230.907
97_N101_S0.164180.906
72_N75_S0.164130.906
84_F92_F0.163720.904
97_N107_S0.163160.901
33_L94_M0.163120.900
54_L57_Y0.161820.893
101_S106_S0.161440.891
94_M98_F0.160310.885
42_I136_A0.160270.885
43_L51_I0.160110.884
12_S18_L0.159940.883
17_G58_V0.159720.882
43_L140_V0.159470.880
116_F121_S0.158960.878
38_W49_G0.158910.877
54_L60_S0.158680.876
47_Y132_I0.158460.875
72_N76_F0.15840.874
76_F79_L0.158190.873
21_I51_I0.158020.872
78_S90_I0.157830.871
89_L93_F0.15770.871
92_F102_L0.157670.870
24_S43_L0.157530.870
97_N104_S0.157050.867
45_L51_I0.156880.866
50_G136_A0.156740.865
78_S105_S0.156540.864
68_K71_N0.156530.864
98_F106_S0.156320.863
103_N107_S0.156240.863
97_N102_L0.155890.861
16_S139_G0.155860.860
80_S87_F0.15480.855
81_L103_N0.154290.852
23_L26_F0.154290.852
98_F103_N0.153960.850
83_L95_F0.153870.849
86_F128_F0.153850.849
88_I94_M0.153830.849
39_Y110_L0.153710.849
18_L59_I0.153360.847
28_S47_Y0.153250.846
89_L92_F0.152910.844
79_L103_N0.152450.842
15_Y20_L0.152420.841
51_I54_L0.15160.837
52_L64_N0.151180.835
89_L99_S0.150970.833
83_L103_N0.150890.833
98_F101_S0.150740.832
85_L96_S0.150710.832
26_F30_L0.150690.832
67_F71_N0.150520.831
49_G58_V0.149310.824
20_L47_Y0.148950.822
67_F70_S0.148850.822
77_F99_S0.148770.821
83_L87_F0.148650.821
94_M100_F0.147960.817
88_I100_F0.147770.816
19_S41_L0.147620.815
51_I59_I0.147380.814
61_L118_L0.146650.810
17_G21_I0.146420.808
63_P137_L0.146190.807
82_I96_S0.146020.806
97_N106_S0.145850.805
99_S107_S0.145570.804
80_S90_I0.1450.800
39_Y130_S0.144710.799
24_S126_F0.144550.798
91_I95_F0.144540.798
55_F61_L0.144370.797
57_Y60_S0.143590.793
37_S110_L0.142430.786
87_F99_S0.142430.786
139_G142_S0.142330.786
10_S16_S0.142320.786
94_M97_N0.141990.784
80_S86_F0.141840.783
109_S112_S0.141370.780
36_S143_I0.141320.780
24_S46_V0.141070.779
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
4he8J0.986199.80.154
3rkoJ0.986199.70.197
2ks9A0.35422.30.923
4grvA0.34721.70.929
3j1rA0.18061.50.931
4ib4A0.35420.70.943
2z5eA0.28470.60.945
3eyrA0.33330.60.946
4a2nB0.50690.50.95
4ainA0.52080.40.951

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