GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_q1_C - NADH-Ubiquinone oxidoreductase (complex I) subunit C-terminus
Pfam: PF01010 (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: 242
Sequences: 1390
Seq/Len: 5.74
HH_delta: 0.892 (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
41_N44_F0.257182.503
103_L133_W0.218282.124
25_S89_F0.203261.978
104_I131_S0.200721.953
133_W189_A0.184411.795
24_S157_N0.182211.773
196_G199_K0.176631.719
19_S193_V0.171711.671
138_I174_F0.170391.658
80_I87_K0.170021.655
35_E103_L0.159771.555
93_H156_T0.158751.545
60_S189_A0.158681.544
3_Y7_F0.1571.528
199_K203_D0.156121.519
4_L7_F0.154121.500
149_V156_T0.148711.447
1_R5_L0.148331.444
199_K202_L0.146281.424
60_S133_W0.145451.416
147_E153_E0.145031.411
62_K68_E0.144831.410
3_Y6_T0.142521.387
12_R177_G0.142151.383
93_H157_N0.141861.381
21_K74_I0.141771.380
1_R4_L0.141251.375
129_I231_I0.141081.373
125_I159_I0.139741.360
179_V224_D0.139151.354
144_N224_D0.138141.344
136_P172_A0.136821.332
25_S93_H0.135521.319
103_L189_A0.133411.298
111_V132_K0.13291.293
12_R178_P0.132681.291
21_K26_F0.132111.286
179_V208_F0.130951.274
22_K81_T0.130841.273
12_R21_K0.129981.265
146_H197_P0.129931.265
108_I160_F0.129791.263
76_P178_P0.129781.263
81_T88_T0.129741.263
1_R7_F0.129571.261
200_I209_I0.129271.258
1_R6_T0.129011.256
20_G169_I0.128621.252
6_T10_H0.127891.245
25_S156_T0.127271.239
2_I138_I0.127021.236
125_I200_I0.12611.227
81_T217_G0.125611.222
84_G211_N0.124441.211
21_K191_S0.124011.207
19_S73_M0.123631.203
23_N197_P0.12361.203
210_Y213_S0.122811.195
81_T138_I0.122111.188
100_T103_L0.122071.188
23_N195_K0.121581.183
79_T147_E0.121511.183
24_S68_E0.120621.174
235_A239_S0.120491.173
58_F77_F0.120371.171
182_S235_A0.119961.167
133_W187_D0.119371.162
115_F133_W0.119341.161
111_V131_S0.118721.155
102_P198_K0.118371.152
159_I231_I0.118231.151
65_R171_I0.118011.149
164_I183_F0.117971.148
68_E156_T0.117941.148
151_W235_A0.117671.145
17_N170_F0.116921.138
75_R103_L0.116871.137
233_G238_T0.116731.136
144_N150_D0.116641.135
3_Y9_G0.116411.133
25_S31_L0.116271.132
218_Y223_Y0.116111.130
84_G173_Y0.11481.117
37_S85_N0.114431.114
31_L101_F0.114121.111
113_I239_S0.113851.108
22_K170_F0.113781.107
195_K230_G0.113691.106
66_I236_K0.112371.094
95_S136_P0.111361.084
228_V238_T0.110851.079
149_V191_S0.110541.076
5_L9_G0.110531.076
87_K138_I0.110241.073
152_Y160_F0.109771.068
21_K201_F0.109621.067
126_G145_S0.109591.067
62_K82_H0.109181.063
61_K79_T0.107921.050
200_I230_G0.107871.050
170_F191_S0.107341.045
139_N153_E0.107161.043
22_K217_G0.107141.043
43_N197_P0.107131.043
201_F209_I0.106781.039
40_I174_F0.106761.039
46_L101_F0.106561.037
220_D223_Y0.106491.036
201_F230_G0.106391.035
26_F201_F0.106371.035
51_N63_T0.105411.026
61_K198_K0.105351.025
105_V200_I0.105331.025
121_N167_F0.104951.021
115_F187_D0.104871.021
173_Y197_P0.104661.019
230_G236_K0.104511.017
16_Q156_T0.104411.016
205_I208_F0.103841.011
214_Y231_I0.103521.007
55_K202_L0.103421.007
153_E191_S0.103361.006
77_F165_A0.103321.006
46_L175_L0.102831.001
6_T9_G0.102650.999
19_S145_S0.102490.997
216_R220_D0.102330.996
68_E116_I0.102290.996
48_T203_D0.101950.992
113_I174_F0.10170.990
92_P95_S0.101680.990
105_V127_L0.101650.989
8_E178_P0.10090.982
66_I102_P0.100820.981
155_L195_K0.100460.978
135_T186_L0.100280.976
184_Q230_G0.100130.975
16_Q235_A0.099950.973
169_I206_I0.099950.973
156_T193_V0.099910.972
4_L9_G0.099590.969
220_D232_R0.099470.968
86_K123_G0.099450.968
98_T152_Y0.099030.964
172_A201_F0.0990.964
80_I90_H0.098790.961
27_Y58_F0.098710.961
122_Q140_L0.098640.960
96_P171_I0.098630.960
17_N72_N0.098530.959
65_R143_E0.098340.957
24_S41_N0.098340.957
43_N207_N0.098190.956
54_E197_P0.098150.955
103_L187_D0.098120.955
40_I103_L0.097980.954
169_I229_K0.097920.953
212_W215_N0.097890.953
221_E225_I0.097840.952
188_L192_F0.097810.952
24_S156_T0.097690.951
2_I8_E0.097590.950
25_S88_T0.097370.948
89_F156_T0.097240.946
73_M209_I0.097020.944
48_T60_S0.096940.943
107_A228_V0.096740.942
68_E157_N0.096590.940
212_W220_D0.096470.939
91_Y100_T0.096120.935
65_R202_L0.095890.933
90_H137_S0.095630.931
13_V236_K0.095520.930
30_S158_A0.095510.930
133_W145_S0.095010.925
123_G195_K0.094930.924
85_N103_L0.094780.922
56_V66_I0.094680.921
149_V229_K0.094550.920
195_K233_G0.09440.919
209_I212_W0.094290.918
23_N37_S0.094150.916
2_I116_I0.094140.916
90_H177_G0.094050.915
1_R9_G0.0940.915
80_I111_V0.093920.914
15_F26_F0.093670.912
29_I107_A0.093640.911
39_S79_T0.093550.910
10_H162_V0.093520.910
19_S88_T0.093510.910
228_V239_S0.09340.909
14_H55_K0.093210.907
35_E93_H0.093060.906
227_F236_K0.092990.905
84_G217_G0.092980.905
10_H47_S0.092790.903
20_G81_T0.092660.902
145_S174_F0.092410.899
47_S82_H0.092350.899
166_L173_Y0.092350.899
237_F242_D0.09230.898
137_S142_H0.092260.898
119_P122_Q0.092130.897
48_T183_F0.0920.895
103_L202_L0.091890.894
16_Q24_S0.091790.893
51_N200_I0.091620.892
72_N125_I0.09160.891
2_I7_F0.091580.891
66_I125_I0.091490.890
37_S156_T0.091230.888
166_L169_I0.091220.888
148_S235_A0.091110.887
2_I5_L0.091010.886
60_S103_L0.090720.883
158_A161_S0.090710.883
110_T240_F0.09070.883
159_I183_F0.090690.883
5_L8_E0.090620.882
202_L206_I0.090510.881
113_I138_I0.090470.880
182_S191_S0.090330.879
175_L207_N0.090310.879
88_T145_S0.09030.879
48_T66_I0.090240.878
121_N178_P0.090180.878
133_W225_I0.090160.877
24_S174_F0.089650.873
157_N162_V0.089390.870
63_T107_A0.089370.870
135_T159_I0.089270.869
69_N120_F0.0890.866
217_G220_D0.088910.865
81_T144_N0.08890.865
18_Y164_I0.088810.864
76_P90_H0.088780.864
121_N177_G0.088640.863
89_F159_I0.088580.862
44_F68_E0.088480.861
74_I146_H0.088430.861
10_H139_N0.088370.860
183_F195_K0.088280.859
43_N192_F0.088230.859
101_F177_G0.088130.858
87_K174_F0.087970.856
35_E228_V0.087920.856
7_F11_L0.087890.855
156_T229_K0.08780.855
84_G227_F0.087680.853
68_E172_A0.087650.853
44_F74_I0.08760.853
14_H143_E0.087490.851
74_I183_F0.087290.850
63_T208_F0.087180.848
139_N180_Y0.087170.848
22_K88_T0.086920.846
69_N187_D0.086920.846
6_T19_S0.086840.845
231_I238_T0.086780.845
184_Q201_F0.086770.844
202_L231_I0.08670.844
71_R84_G0.086640.843
149_V153_E0.086450.841
129_I138_I0.086430.841
41_N175_L0.086410.841
2_I235_A0.086380.841
147_E207_N0.086380.841
21_K178_P0.086360.840
170_F196_G0.086350.840
82_H217_G0.086290.840
182_S238_T0.086280.840
8_E169_I0.08610.838
40_I202_L0.086090.838
30_S77_F0.086090.838
127_L231_I0.086090.838
227_F232_R0.086040.837
85_N189_A0.0860.837
55_K93_H0.085910.836
25_S120_F0.085820.835
87_K167_F0.085740.834
8_E20_G0.08570.834
37_S103_L0.085680.834
43_N173_Y0.085640.833
105_V231_I0.085460.832
113_I195_K0.085460.832
165_A181_S0.085440.832
37_S133_W0.085320.830
15_F71_R0.0850.827
46_L83_F0.084940.827
14_H51_N0.084830.826
177_G226_V0.084740.825
206_I229_K0.08470.824
36_E178_P0.084630.824
146_H159_I0.084570.823
173_Y224_D0.084510.822
3_Y8_E0.08450.822
105_V171_I0.08450.822
8_E229_K0.084370.821
40_I87_K0.084360.821
51_N226_V0.084190.819
138_I145_S0.084160.819
30_S71_R0.084050.818
170_F221_E0.08390.817
46_L52_N0.083860.816
179_V192_F0.08370.815
181_S185_N0.083560.813
115_F189_A0.083550.813
72_N152_Y0.083540.813
57_S224_D0.083490.813
169_I239_S0.083450.812
119_P204_K0.083270.810
105_V109_F0.083210.810
238_T242_D0.083140.809
17_N20_G0.083060.808
123_G150_D0.083040.808
135_T217_G0.082850.806
88_T113_I0.08280.806
18_Y182_S0.082530.803
152_Y215_N0.082410.802
26_F105_V0.082370.802
62_K169_I0.082330.801
142_H150_D0.08230.801
34_K155_L0.082210.800
15_F234_L0.082210.800
104_I184_Q0.082120.799
183_F226_V0.082090.799
212_W216_R0.082080.799
151_W173_Y0.0820.798
53_N172_A0.081970.798
95_S151_W0.081930.797
128_D151_W0.081740.796
35_E64_Y0.08170.795
53_N107_A0.081590.794
126_G207_N0.081560.794
187_D239_S0.081530.793
74_I179_V0.081520.793
50_M217_G0.081410.792
21_K147_E0.081410.792
61_K70_V0.081350.792
146_H165_A0.081330.792
15_F155_L0.081280.791
51_N144_N0.081270.791
116_I185_N0.081190.790
134_L214_Y0.081190.790
18_Y100_T0.081160.790
35_E144_N0.081130.790
224_D228_V0.081080.789
2_I174_F0.081020.789
13_V106_L0.081020.789
74_I209_I0.080930.788
25_S69_N0.08080.786
43_N67_D0.080750.786
144_N200_I0.080690.785
210_Y214_Y0.080570.784
140_L205_I0.080520.784
48_T159_I0.080430.783
89_F149_V0.080420.783
155_L224_D0.080250.781
66_I209_I0.080160.780
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
4he8L0.706698.90.892
3rkoL0.681898.50.909
1jb0I0.1573.40.982
2ls2A0.107430.983
2lsjB0.10742.60.983
4hdjA0.24792.50.984
1yzwA0.260320.984
1eoqA0.15720.984
2wscI0.16531.80.985
3lw5I0.1241.80.985
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0186 seconds.