GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NADHdh - NADH dehydrogenase
Pfam: PF00146 (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: 311
Sequences: 3467
Seq/Len: 11.15
HH_delta: 0.044 (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
161_S166_E0.656544.470
238_A261_F0.460623.136
21_T48_P0.45313.085
28_L277_A0.405912.763
188_F271_I0.392172.670
31_I277_A0.389442.651
184_F240_F0.373122.540
130_S215_T0.351062.390
238_A265_V0.344172.343
174_F178_F0.335312.283
49_F52_L0.321482.189
192_L275_I0.314222.139
195_T272_F0.305342.079
241_S261_F0.298642.033
245_L268_V0.298562.033
189_I295_L0.293391.997
237_S268_V0.291871.987
234_F269_M0.29021.976
82_S232_K0.283771.932
159_T176_F0.283561.930
56_F223_A0.279961.906
177_I184_F0.272111.852
211_S214_N0.270711.843
170_Y176_F0.268871.830
70_L120_L0.263531.794
155_V167_I0.262691.788
82_S231_L0.257651.754
191_L236_L0.256941.749
188_F192_L0.256641.747
31_I274_W0.251791.714
17_V231_L0.251261.711
241_S245_L0.249671.700
166_E169_N0.248731.693
87_A106_F0.23241.582
106_F110_L0.2321.579
54_K58_K0.228091.553
187_F240_F0.224661.529
155_V180_M0.222991.518
60_I221_Y0.222711.516
49_F53_I0.220451.501
181_P185_I0.219331.493
23_I270_F0.216381.473
78_A117_G0.215031.464
85_A235_F0.21371.455
74_A120_L0.212741.448
17_V227_L0.209831.428
154_A183_A0.209151.424
30_R35_K0.20731.411
169_N172_S0.206681.407
150_L303_L0.206111.403
78_A228_A0.201751.373
205_A209_L0.201471.372
175_W246_G0.198231.350
104_L164_L0.197451.344
159_T170_Y0.197161.342
40_V47_Q0.197031.341
35_K38_N0.195171.329
88_F106_F0.194271.323
63_P71_F0.193751.319
47_Q51_D0.193421.317
20_L269_M0.191411.303
222_F226_F0.191341.303
151_I186_A0.18841.283
177_I245_L0.187981.280
274_W278_S0.185851.265
100_F106_F0.185681.264
152_L243_L0.184051.253
147_P190_A0.183961.252
56_F220_P0.18081.231
183_A302_N0.179111.219
77_L81_L0.178751.217
175_W264_K0.178041.212
133_G203_P0.17781.210
188_F240_F0.176851.204
268_V271_I0.176281.200
165_S169_N0.175491.195
104_L156_A0.175161.192
140_Q196_N0.174781.190
284_Y288_M0.174621.189
298_L302_N0.173621.182
94_N99_D0.17341.180
79_F228_A0.173391.180
113_L294_I0.172771.176
147_P291_C0.171671.169
140_Q287_L0.171171.165
84_L106_F0.169961.157
147_P299_S0.169411.153
158_L180_M0.169011.151
187_F191_L0.168991.150
154_A303_L0.166871.136
122_G134_A0.166411.133
283_R288_M0.166011.130
19_F48_P0.165721.128
241_S265_V0.165721.128
79_F83_L0.165191.125
11_L15_L0.165121.124
233_L269_M0.164861.122
174_F179_S0.164581.120
29_A35_K0.163671.114
202_I287_L0.163011.110
202_I286_Q0.162931.109
137_E205_A0.162911.109
22_L28_L0.162451.106
154_A299_S0.162431.106
27_I270_F0.160581.093
155_V243_L0.160481.093
259_L263_I0.160121.090
13_V231_L0.159881.088
121_A124_S0.159681.087
214_N222_F0.159471.086
191_L240_F0.158931.082
22_L48_P0.158671.080
168_V246_G0.158361.078
183_A244_F0.158171.077
242_V247_G0.157741.074
281_R285_D0.157631.073
127_S130_S0.157211.070
202_I282_F0.157121.070
137_E203_P0.156511.065
108_L149_M0.156041.062
27_I273_V0.155911.061
163_S166_E0.155671.060
74_A117_G0.155161.056
180_M183_A0.1551.055
208_E281_R0.153861.047
205_A208_E0.153721.046
96_I165_S0.152391.037
115_V141_M0.152161.036
171_Q246_G0.150821.027
172_S249_F0.150611.025
156_A162_F0.15061.025
58_K293_K0.150571.025
27_I31_I0.150451.024
15_L49_F0.150121.022
11_L14_L0.149431.017
25_R34_R0.149231.016
290_F295_L0.149231.016
78_A114_S0.148911.014
159_T167_I0.148471.011
93_P248_W0.148121.008
240_F268_V0.147971.007
223_A227_L0.146720.999
166_E262_L0.146590.998
263_I266_L0.145890.993
201_D204_E0.145760.992
285_D288_M0.145570.991
161_S167_I0.14430.982
181_P184_F0.144070.981
72_F76_I0.1440.980
233_L272_F0.143340.976
84_L110_L0.143050.974
154_A180_M0.142960.973
133_G137_E0.142560.971
147_P296_L0.141910.966
210_V215_T0.141840.966
21_T230_Y0.139760.951
69_W73_L0.139520.950
30_R38_N0.139450.949
55_L226_F0.13850.943
89_I238_A0.138220.941
150_L300_L0.137970.939
267_I271_I0.137930.939
269_M273_V0.137320.935
238_A242_V0.136960.932
71_F75_P0.136790.931
184_F245_L0.136760.931
55_L223_A0.13670.931
23_I273_V0.136110.927
148_L190_A0.135920.925
107_F235_F0.13580.925
185_I303_L0.135370.922
209_L213_F0.135330.921
188_F268_V0.134960.919
85_A232_K0.134790.918
72_F221_Y0.134650.917
146_V186_A0.134530.916
62_I68_K0.134410.915
143_S288_M0.134130.913
42_P46_L0.134120.913
103_G163_S0.133530.909
52_L57_S0.133170.907
81_L110_L0.132760.904
231_L234_F0.132550.902
180_M302_N0.13250.902
116_Y284_Y0.132230.900
123_W126_N0.131780.897
14_L18_A0.131630.896
99_D165_S0.131170.893
22_L30_R0.130850.891
52_L56_F0.130740.890
273_V276_R0.130590.889
230_Y276_R0.130450.888
245_L267_I0.130190.886
65_S113_L0.12990.884
266_L270_F0.129850.884
68_K157_L0.129620.882
204_E212_G0.129520.882
187_F236_L0.129340.881
96_I266_L0.129180.879
52_L227_L0.128620.876
16_S19_F0.128310.874
198_S279_F0.127820.870
52_L83_L0.127490.868
79_F224_L0.127460.868
27_I43_M0.127210.866
203_P213_F0.12670.863
220_P223_A0.12650.861
21_T24_E0.126460.861
91_F95_F0.126320.860
13_V17_V0.126160.859
73_L77_L0.125950.857
99_D163_S0.12590.857
294_I303_L0.125690.856
63_P66_S0.125590.855
201_D281_R0.125520.855
95_F185_I0.125340.853
155_V159_T0.125330.853
169_N266_L0.125290.853
186_A298_L0.12420.846
206_E209_L0.124110.845
201_D208_E0.123770.843
156_A159_T0.123710.842
22_L45_I0.123660.842
270_F274_W0.123480.841
241_S268_V0.123310.839
185_I189_I0.123240.839
43_M166_E0.122940.837
26_K36_G0.122580.835
80_I163_S0.122510.834
104_L167_I0.122340.833
240_F245_L0.1220.831
107_F164_L0.121930.830
27_I274_W0.121760.829
43_M303_L0.121320.826
19_F23_I0.121260.826
151_I190_A0.121160.825
43_M84_L0.121010.824
93_P96_I0.120750.822
25_R36_G0.120640.821
194_E197_R0.120490.820
37_P54_K0.120240.819
24_E276_R0.120170.818
281_R284_Y0.120010.817
93_P247_G0.119870.816
219_G223_A0.119640.814
158_L299_S0.119510.814
84_L100_F0.11940.813
19_F49_F0.119350.813
171_Q176_F0.119350.813
107_F111_L0.119170.811
125_S217_Y0.119070.811
186_A189_I0.119020.810
56_F146_V0.118970.810
168_V248_W0.118660.808
29_A34_R0.11850.807
75_P217_Y0.118480.807
47_Q54_K0.11840.806
12_F16_S0.118320.805
163_S169_N0.118320.805
140_Q144_Y0.118210.805
21_T52_L0.118080.804
18_A227_L0.117420.799
202_I209_L0.117320.799
120_L303_L0.117060.797
201_D209_L0.116990.796
205_A281_R0.116950.796
220_P228_A0.116730.795
193_A200_F0.11650.793
291_C303_L0.116230.791
86_W235_F0.115860.789
17_V29_A0.115430.786
248_W260_W0.115280.785
168_V247_G0.115090.784
247_G264_K0.115090.784
37_P47_Q0.115020.783
87_A96_I0.11490.782
262_L301_I0.11490.782
24_E197_R0.114890.782
140_Q143_S0.114850.782
282_F286_Q0.114710.781
46_L50_Y0.114540.780
89_I242_V0.113940.776
78_A118_I0.113690.774
89_I235_F0.113610.773
276_R285_D0.11360.773
246_G264_K0.113550.773
94_N186_A0.113290.771
167_I243_L0.113250.771
42_P160_G0.113140.770
28_L276_R0.113030.769
172_S176_F0.112950.769
127_S210_V0.112840.768
100_F225_F0.112530.766
155_V248_W0.112370.765
80_I239_L0.112320.765
10_I17_V0.112230.764
69_W110_L0.111240.757
41_G47_Q0.111140.757
26_K30_R0.1110.756
159_T266_L0.110820.754
123_W135_S0.110580.753
16_S266_L0.110360.751
272_F284_Y0.110350.751
91_F262_L0.110320.751
10_I262_L0.110190.750
12_F19_F0.110190.750
135_S203_P0.10970.747
16_S234_F0.109030.742
214_N226_F0.108940.742
263_I270_F0.108570.739
267_I270_F0.108550.739
173_P259_L0.108440.738
226_F234_F0.108270.737
114_S232_K0.108160.736
169_N270_F0.108030.735
18_A21_T0.107970.735
88_F107_F0.107850.734
34_R37_P0.107760.734
43_M165_S0.107760.734
25_R32_Q0.107740.733
32_Q37_P0.107540.732
117_G134_A0.107520.732
141_M149_M0.107490.732
13_V16_S0.107320.731
185_I271_I0.107110.729
229_E233_L0.107110.729
130_S211_S0.107070.729
107_F180_M0.107060.729
81_L113_L0.1070.728
48_P86_W0.106930.728
261_F265_V0.106870.728
25_R206_E0.106730.727
26_K45_I0.106450.725
114_S235_F0.106440.725
76_I80_I0.106420.724
119_I138_L0.106340.724
23_I39_K0.106320.724
116_Y148_L0.106230.723
170_Y173_P0.106230.723
78_A225_F0.10620.723
62_I271_I0.106050.722
25_R204_E0.105840.721
28_L273_V0.10580.720
169_N181_P0.10560.719
30_R228_A0.105380.717
211_S226_F0.105380.717
52_L223_A0.105320.717
32_Q36_G0.105250.717
111_L114_S0.105120.716
51_D281_R0.104970.715
87_A165_S0.104940.714
53_I57_S0.104930.714
31_I218_S0.10480.713
24_E28_L0.104790.713
15_L249_F0.104770.713
51_D54_K0.104770.713
104_L152_L0.104720.713
287_L296_L0.104630.712
144_Y193_A0.104180.709
65_S282_F0.104160.709
154_A302_N0.103820.707
27_I150_L0.103730.706
78_A85_A0.10340.704
281_R292_W0.103180.702
192_L272_F0.103150.702
19_F45_I0.103070.702
213_F275_I0.103040.701
155_V260_W0.102920.701
135_S295_L0.102820.700
10_I168_V0.102750.700
153_F303_L0.102740.699
118_I137_E0.102670.699
10_I83_L0.102460.698
80_I173_P0.102340.697
15_L53_I0.102330.697
84_L93_P0.102310.697
64_N219_G0.102160.695
15_L291_C0.102150.695
16_S269_M0.102090.695
71_F217_Y0.101970.694
23_I27_I0.10180.693
67_N126_N0.10170.692
61_I65_S0.101410.690
155_V304_I0.101290.690
39_K43_M0.101280.689
74_A124_S0.101250.689
105_L284_Y0.10120.689
16_S76_I0.101180.689
204_E208_E0.101050.688
104_L165_S0.101030.688
17_V157_L0.100910.687
197_R201_D0.100850.687
70_L77_L0.100820.686
196_N229_E0.100780.686
135_S227_L0.100420.684
93_P298_L0.100360.683
173_P260_W0.100210.682
132_I165_S0.10020.682
43_M152_L0.100170.682
237_S241_S0.100150.682
238_A262_L0.100020.681
77_L84_L0.099820.680
58_K229_E0.099810.679
43_M178_F0.099780.679
153_F156_A0.099460.677
290_F293_K0.099290.676
24_E32_Q0.099280.676
30_R43_M0.099250.676
53_I169_N0.099210.675
69_W272_F0.099110.675
213_F226_F0.099070.674
223_A228_A0.0990.674
24_E34_R0.098990.674
226_F276_R0.098960.674
118_I141_M0.098890.673
235_F242_V0.098820.673
35_K39_K0.098790.673
32_Q216_E0.098650.672
52_L121_A0.098630.671
14_L17_V0.09840.670
118_I282_F0.098160.668
67_N70_L0.098150.668
168_V171_Q0.09810.668
85_A95_F0.098060.668
193_A287_L0.098020.667
79_F215_T0.097930.667
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
4he8H0.99681000.044
2jpkA0.11259.10.972
1vryA0.18655.30.975
3dacP0.06754.40.976
2jwaA0.10294.10.976
2ll2A0.083640.976
4he8L0.874630.977
1xkmA0.08362.60.978
1l4tA0.09322.30.979
1qleD0.13832.20.979

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