GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrom_D1 - Cytochrome D1 heme domain
Pfam: PF02239 (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: CL0186
Length: 369
Sequences: 29936
Seq/Len: 81.13
HH_delta: 0.104 (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
52_Y62_V1.277062.721
41_G54_A1.266932.699
64_D67_T1.246952.657
300_D303_T1.212072.583
284_W298_V1.157142.466
61_S70_V1.147362.445
53_V63_I1.144022.438
35_G53_V1.12572.399
52_Y85_V1.108852.363
106_D109_T1.091852.326
82_G95_A1.016392.166
103_S112_P1.007552.147
285_V299_I0.996562.123
255_D258_A0.964532.055
61_S73_T0.957892.041
156_D159_D0.948412.021
200_D203_T0.944442.012
284_W323_F0.936241.995
70_V73_T0.901731.921
43_K84_A0.888651.893
297_Q306_V0.879351.874
45_S85_V0.849541.810
320_H333_S0.848871.809
297_Q309_T0.841931.794
324_N328_K0.839051.788
273_F286_D0.83131.771
96_N99_P0.828181.765
93_Y104_V0.813051.732
252_S261_V0.800471.706
176_D190_A0.797851.700
60_V94_V0.79681.698
282_Y298_V0.795331.695
94_V105_I0.794591.693
244_P254_H0.783721.670
50_Y62_V0.782381.667
252_S264_T0.772141.645
275_K322_E0.765631.631
103_S115_T0.759521.618
187_L198_V0.750591.599
59_T73_T0.740511.578
45_S49_R0.732621.561
306_V309_T0.731641.559
197_A206_L0.710911.515
331_W343_V0.705021.502
86_S135_A0.70431.501
112_P115_T0.701521.495
134_V178_G0.698631.489
93_Y135_A0.698111.487
136_S179_F0.696521.484
332_V344_Y0.686651.463
170_V174_P0.68621.462
50_Y71_V0.675781.440
35_G39_H0.662471.412
295_T309_T0.659451.405
334_V337_G0.656821.399
53_V61_S0.654221.394
105_I112_P0.64471.374
299_I306_V0.643441.371
64_D71_V0.642151.368
268_Q285_V0.638481.360
40_A56_R0.637971.359
254_H261_V0.636631.356
277_H281_R0.636431.356
101_T115_T0.635121.353
185_Y198_V0.628371.339
324_N329_E0.619471.320
333_S337_G0.615481.311
91_Y104_V0.61341.307
277_H323_F0.60831.296
136_S140_P0.607311.294
196_I244_P0.605631.290
206_L209_L0.603181.285
275_K321_M0.598531.275
52_Y92_V0.595931.270
90_K108_E0.59441.266
313_G332_V0.593381.264
150_G153_W0.593141.264
291_P297_Q0.591691.261
84_A134_V0.590381.258
180_D183_G0.589871.257
51_L65_L0.589231.255
237_G240_Y0.589071.255
77_G94_V0.588011.253
55_N59_T0.584651.246
49_R66_A0.579991.236
282_Y285_V0.573571.222
329_E343_V0.572981.221
197_A209_L0.5721.219
180_D184_R0.570891.216
278_P323_F0.570371.215
251_V285_V0.566941.208
332_V336_D0.566081.206
63_I70_V0.561881.197
296_V332_V0.560121.193
45_S48_G0.555131.183
261_V264_T0.55511.183
282_Y307_V0.554531.182
91_Y94_V0.552391.177
277_H282_Y0.552221.177
291_P295_T0.546891.165
132_A146_L0.544981.161
44_F51_L0.541461.154
180_D185_Y0.538841.148
45_S50_Y0.534031.138
136_S139_R0.531911.133
132_A145_N0.531861.133
278_P327_G0.531081.132
300_D307_V0.530491.130
35_G55_N0.530341.130
284_W330_V0.528941.127
277_H280_S0.527211.123
42_L53_V0.525821.120
273_F320_H0.52411.117
49_R64_D0.521151.110
324_N327_G0.520831.110
250_P264_T0.520311.109
245_L249_D0.520121.108
102_V145_N0.519121.106
52_Y83_I0.517681.103
44_F65_L0.515691.099
91_Y113_V0.511781.090
285_V291_P0.509251.085
267_T299_I0.508721.084
263_K304_L0.506371.079
55_N61_S0.50521.076
86_S89_G0.503031.072
96_N101_T0.502371.070
42_L51_L0.501841.069
255_D262_V0.501421.068
54_A83_I0.499181.064
64_D69_K0.495891.057
286_D318_V0.495891.057
106_D113_V0.49531.055
285_V297_Q0.494511.054
86_S90_K0.493261.051
272_L292_D0.490841.046
145_N155_V0.489941.044
142_F145_N0.489621.043
276_T283_V0.487711.039
86_S91_Y0.485611.035
334_V338_N0.483361.030
47_D50_Y0.482361.028
184_R202_K0.481621.026
65_L68_G0.48141.026
34_T63_I0.480751.024
43_K52_Y0.479461.022
295_T311_T0.478881.020
283_V301_K0.478071.019
191_N197_A0.474631.011
167_T170_V0.474451.011
246_I252_S0.474071.010
43_K83_I0.473251.008
175_H192_G0.469971.001
293_A297_Q0.469871.001
87_P135_A0.469561.000
60_V83_I0.468050.997
45_S52_Y0.467970.997
236_S240_Y0.467390.996
246_I250_P0.464350.989
332_V337_G0.462240.985
149_T153_W0.461740.984
273_F321_M0.461260.983
43_K85_V0.455090.970
256_D259_W0.451970.963
180_D187_L0.45120.961
268_Q291_P0.451030.961
81_R98_E0.450560.960
50_Y53_V0.449580.958
246_I249_D0.449160.957
50_Y91_Y0.447040.953
284_W321_M0.447030.952
300_D305_K0.444940.948
170_V188_V0.443940.946
193_S197_A0.442790.943
94_V103_S0.442780.943
174_P177_G0.442470.943
190_A194_N0.442080.942
248_T252_S0.439230.936
236_S239_G0.439220.936
268_Q271_G0.438970.935
185_Y188_V0.438940.935
150_G154_V0.438490.934
281_R302_K0.438330.934
191_N194_N0.437580.932
143_V179_F0.432840.922
291_P294_D0.432350.921
244_P248_T0.431910.920
46_P89_G0.431240.919
199_I206_L0.430560.917
88_D91_Y0.428130.912
276_T301_K0.425810.907
137_P179_F0.424580.905
329_E332_V0.424030.903
46_P85_V0.421820.899
134_V177_G0.420920.897
144_V154_V0.42080.897
170_V191_N0.419280.893
191_N195_K0.419070.893
312_P344_Y0.417660.890
152_I188_V0.415760.886
332_V335_W0.415670.886
188_V199_I0.414830.884
296_V321_M0.413860.882
268_Q297_Q0.411890.878
313_G334_V0.411420.877
267_T271_G0.409960.874
62_V72_A0.409040.872
157_Y160_P0.409020.872
251_V255_D0.407790.869
182_D185_Y0.407240.868
76_V105_I0.407040.867
102_V144_V0.406560.866
244_P252_S0.405760.865
102_V133_I0.403840.860
64_D68_G0.400480.853
92_V95_A0.400180.853
59_T75_K0.398910.850
116_I119_G0.397860.848
84_A133_I0.396720.845
62_V85_V0.396630.845
326_D329_E0.396530.845
35_G57_D0.396230.844
41_G83_I0.395810.843
140_P158_S0.395220.842
170_V193_S0.393920.839
106_D111_E0.392350.836
235_T239_G0.391940.835
275_K323_F0.391410.834
332_V338_N0.386690.824
253_V276_T0.386630.824
200_D205_K0.386440.823
76_V94_V0.384660.820
153_W162_N0.384610.819
319_V335_W0.383540.817
334_V342_V0.381260.812
80_P83_I0.380970.812
301_K304_L0.379870.809
50_Y64_D0.37960.809
41_G82_G0.379220.808
338_N342_V0.379150.808
34_T61_S0.378550.807
87_P139_R0.378270.806
298_V323_F0.377680.805
104_V114_K0.377610.805
318_V321_M0.377370.804
44_F276_T0.375290.800
235_T238_L0.374790.799
321_M332_V0.373080.795
279_D282_Y0.373020.795
39_H42_L0.372470.794
142_F146_L0.372440.794
85_V107_A0.369820.788
52_Y107_A0.368570.785
101_T117_P0.368450.785
91_Y95_A0.368260.785
253_V265_I0.36790.784
198_V208_A0.367520.783
147_K151_E0.366560.781
281_R300_D0.366240.780
40_A81_R0.36530.778
86_S93_Y0.364710.777
99_P103_S0.363430.774
96_N103_S0.362740.773
245_L248_T0.362740.773
236_S242_A0.362270.772
179_F186_F0.36090.769
150_G155_V0.360630.768
324_N331_W0.360250.768
241_F253_V0.359980.767
235_T240_Y0.358030.763
195_K209_L0.357760.762
131_A148_D0.357310.761
253_V263_K0.356710.760
54_A80_P0.355660.758
90_K106_D0.35450.755
31_R34_T0.354490.755
186_F201_T0.353760.754
83_I94_V0.353410.753
255_D260_K0.352150.750
184_R200_D0.35120.748
119_G122_P0.350790.747
185_Y207_V0.350540.747
200_D207_V0.350310.746
74_I105_I0.350150.746
146_L149_T0.348830.743
84_A135_A0.34580.737
162_N165_V0.345420.736
30_A68_G0.344510.734
277_H284_W0.343580.732
286_D321_M0.342020.729
92_V107_A0.33960.724
179_F201_T0.339210.723
282_Y300_D0.339080.722
136_S143_V0.338770.722
44_F323_F0.337660.719
333_S338_N0.337610.719
62_V71_V0.337120.718
145_N149_T0.336790.718
55_N63_I0.335290.714
251_V274_I0.334830.713
85_V135_A0.334670.713
245_L274_I0.332030.707
143_V154_V0.330770.705
35_G61_S0.33070.705
74_I77_G0.330240.704
321_M330_V0.33020.704
175_H319_V0.330170.703
93_Y143_V0.329140.701
259_W262_V0.328950.701
274_I285_V0.328870.701
245_L251_V0.328570.700
282_Y286_D0.328540.700
268_Q293_A0.328490.700
261_V306_V0.328320.700
236_S241_F0.328250.699
104_V135_A0.328230.699
336_D342_V0.327650.698
330_V333_S0.32740.698
238_L241_F0.326720.696
72_A110_L0.326710.696
133_I144_V0.326630.696
323_F330_V0.324520.691
151_E154_V0.322510.687
283_V286_D0.322510.687
132_A177_G0.322250.687
298_V308_K0.322240.687
313_G318_V0.322030.686
202_K257_Y0.321360.685
154_V179_F0.319970.682
323_F327_G0.319970.682
322_E331_W0.319860.682
187_L242_A0.319610.681
144_V179_F0.319360.680
52_Y60_V0.319250.680
134_V179_F0.318450.679
85_V92_V0.317930.677
57_D61_S0.317250.676
203_T207_V0.316380.674
240_Y257_Y0.314670.670
107_A110_L0.314040.669
51_L63_I0.313950.669
135_A138_G0.312210.665
82_G132_A0.312080.665
185_Y200_D0.310690.662
200_D204_G0.310510.662
135_A142_F0.310350.661
38_P56_R0.309820.660
54_A58_G0.309510.659
135_A157_Y0.309470.659
179_F276_T0.309260.659
286_D296_V0.308490.657
147_K150_G0.307180.655
274_I283_V0.303120.646
235_T242_A0.30230.644
190_A193_S0.300180.640
143_V146_L0.299760.639
53_V57_D0.299580.638
144_V147_K0.299130.637
70_V206_L0.298450.636
44_F331_W0.29760.634
155_V162_N0.297330.634
40_A131_A0.297140.633
170_V197_A0.297040.633
169_K199_I0.296990.633
298_V310_I0.296840.632
156_D161_K0.296380.631
333_S341_I0.296350.631
267_T297_Q0.296340.631
50_Y185_Y0.296210.631
212_T217_H0.29610.631
313_G344_Y0.296080.631
66_A108_E0.295330.629
309_T312_P0.294970.628
32_I63_I0.294780.628
134_V137_P0.294210.627
131_A147_K0.294090.627
137_P183_G0.293920.626
151_E167_T0.292890.624
270_G292_D0.292810.624
312_P332_V0.292710.624
166_T169_K0.292450.623
337_G342_V0.291380.621
174_P191_N0.290950.620
76_V80_P0.29080.620
109_T113_V0.290480.619
82_G133_I0.29020.618
267_T270_G0.289640.617
166_T170_V0.289090.616
312_P342_V0.288460.615
109_T112_P0.288420.615
67_T71_V0.28830.614
135_A179_F0.288260.614
30_A72_A0.287160.612
282_Y329_E0.2870.612
331_W341_I0.28680.611
333_S336_D0.284660.607
217_H244_P0.284550.606
106_D110_L0.284030.605
95_A133_I0.282970.603
91_Y106_D0.282910.603
119_G145_N0.282840.603
147_K153_W0.281540.600
114_K160_P0.281290.599
44_F85_V0.280590.598
77_G96_N0.28010.597
236_S276_T0.279650.596
241_F262_V0.279150.595
153_W166_T0.278770.594
149_T155_V0.278670.594
257_Y302_K0.277430.591
275_K284_W0.277030.590
177_G188_V0.277010.590
131_A135_A0.276580.589
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
1nr0A0.94851000.104
1nr0A0.96751000.111
3sfzA0.91061000.115
3sfzA0.90511000.124
1nirA0.96481000.145
2ymuA0.89431000.157
2oajA0.96211000.162
2ymuA0.83471000.166
1vyhC0.79671000.171
3mkqA0.91871000.175

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