GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrom_C_asm - Cytochrome C assembly protein
Pfam: PF01578 (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: CL0328
Length: 214
Sequences: 1804
Seq/Len: 8.43
HH_delta: 0.947 (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
137_T168_W0.41473.370
86_F171_Y0.398623.239
79_A139_G0.345152.805
170_V195_G0.323972.632
153_S156_S0.286182.325
90_A193_I0.252242.050
89_A129_I0.249292.026
133_F172_G0.245821.997
78_L138_I0.213571.735
151_W157_W0.210241.708
70_P74_I0.205291.668
133_F168_W0.196411.596
87_A196_F0.194051.577
202_S205_G0.193581.573
86_F195_G0.189911.543
182_G186_R0.189321.538
83_Y136_L0.188341.530
161_E176_H0.188321.530
183_W187_R0.181621.476
122_E178_R0.181251.473
170_V198_L0.181151.472
151_W161_E0.177441.442
181_K184_R0.176351.433
151_W155_W0.175191.424
85_A132_G0.173311.408
155_W176_H0.171241.391
205_G208_L0.17111.390
80_L84_A0.169591.378
147_A151_W0.167641.362
70_P73_Y0.167491.361
167_T199_L0.166511.353
182_G185_G0.16611.350
157_W176_H0.164811.339
177_L188_A0.163511.329
157_W161_E0.159721.298
100_E118_L0.158071.284
155_W161_E0.157661.281
86_F132_G0.156851.274
171_Y195_G0.156021.268
37_F95_L0.155781.266
10_F49_A0.152151.236
41_S87_A0.152051.235
147_A155_W0.151421.230
16_A42_V0.150371.222
46_L50_L0.149121.212
140_L164_S0.147671.200
130_L175_L0.145921.186
146_W176_H0.141141.147
203_Y208_L0.140541.142
12_A45_L0.139771.136
93_A192_S0.138811.128
67_L146_W0.138091.122
16_A20_L0.138021.121
202_S208_L0.137911.121
67_L176_H0.136821.112
190_Y194_I0.136621.110
39_L42_V0.134771.095
174_Y192_S0.133631.086
63_L163_W0.133531.085
174_Y195_G0.133361.084
96_Y118_L0.133021.081
90_A196_F0.13281.079
144_A150_S0.131811.071
13_W17_L0.131061.065
173_A177_L0.130571.061
48_F55_P0.130491.060
154_Y157_W0.130311.059
82_G94_L0.13031.059
147_A161_E0.130171.058
5_Y76_V0.129681.054
93_A125_S0.129281.050
144_A152_G0.128921.048
7_S139_G0.12871.046
152_G161_E0.127271.034
146_W157_W0.127231.034
44_I191_L0.126931.031
12_A38_S0.126551.028
152_G176_H0.126351.027
122_E125_S0.126051.024
14_L84_A0.125711.021
93_A188_A0.125661.021
63_L67_L0.125581.020
39_L43_L0.125171.017
122_E183_W0.125121.017
190_Y193_I0.124411.011
160_K207_N0.124111.008
24_Y88_I0.123191.001
19_Y35_G0.122740.997
3_N72_L0.122730.997
92_A121_L0.122470.995
10_F14_L0.121820.990
135_L175_L0.12040.978
67_L151_W0.120220.977
83_Y160_K0.119210.969
120_T194_I0.118380.962
87_A200_L0.117910.958
196_F204_F0.117580.955
125_S179_S0.117280.953
150_S160_K0.116180.944
188_A192_S0.115580.939
7_S203_Y0.115180.936
21_F32_R0.114970.934
146_W161_E0.114960.934
94_L119_E0.114690.932
69_S163_W0.113830.925
154_Y203_Y0.113340.921
146_W155_W0.11310.919
67_L158_D0.112910.917
166_I170_V0.112760.916
169_L173_A0.112580.915
163_W206_V0.112420.913
84_A187_R0.112240.912
158_D161_E0.112050.910
142_T145_I0.111930.909
6_E163_W0.111620.907
122_E189_A0.111590.907
87_A90_A0.111540.906
15_L87_A0.111320.905
21_F25_L0.111310.904
151_W176_H0.11110.903
36_A40_P0.111050.902
10_F139_G0.111020.902
147_A152_G0.110920.901
155_W158_D0.11070.899
101_R186_R0.110350.897
24_Y170_V0.110140.895
67_L147_A0.110070.894
167_T202_S0.109950.893
36_A200_L0.109830.892
74_I141_I0.109710.891
125_S192_S0.109630.891
174_Y202_S0.109480.890
64_N69_S0.109240.888
151_W158_D0.109130.887
139_G164_S0.108980.886
122_E185_G0.108950.885
131_I135_L0.108630.883
177_L184_R0.108540.882
160_K171_Y0.108240.880
67_L161_E0.108140.879
67_L155_W0.107980.877
147_A176_H0.107720.875
60_P165_L0.107680.875
6_E207_N0.107660.875
65_P155_W0.107370.872
37_F44_I0.107290.872
76_V160_K0.107150.871
175_L178_R0.107070.870
66_A150_S0.107010.870
94_L193_I0.106940.869
120_T123_R0.106890.869
7_S10_F0.106710.867
122_E134_I0.10660.866
12_A16_A0.106370.864
67_L157_W0.106310.864
17_L20_L0.106270.864
159_P176_H0.106170.863
138_I142_T0.105980.861
76_V162_V0.10570.859
136_L140_L0.105540.858
119_E186_R0.10540.856
147_A157_W0.105370.856
44_I182_G0.105310.856
22_L34_L0.10530.856
87_A91_L0.104720.851
14_L34_L0.10460.850
122_E182_G0.104450.849
123_R198_L0.10440.848
77_P82_G0.10420.847
154_Y161_E0.103920.844
175_L191_L0.103890.844
66_A70_P0.103880.844
130_L178_R0.103840.844
45_L49_A0.103660.842
156_S161_E0.103640.842
141_I175_L0.103560.841
91_L191_L0.10350.841
69_S76_V0.103320.840
160_K178_R0.10330.839
120_T124_L0.103010.837
22_L92_A0.102860.836
14_L22_L0.102740.835
42_V45_L0.10270.834
34_L99_Q0.102680.834
32_R177_L0.102190.830
86_F144_A0.102140.830
149_D153_S0.10170.826
63_L165_L0.101510.825
19_Y32_R0.101490.825
173_A191_L0.10130.823
4_L208_L0.101290.823
120_T178_R0.101280.823
11_L87_A0.101260.823
64_N93_A0.10120.822
131_I134_I0.101170.822
203_Y207_N0.101170.822
44_I100_E0.100830.819
178_R183_W0.100790.819
133_F137_T0.100770.819
65_P147_A0.100560.817
158_D176_H0.100370.816
20_L23_E0.100270.815
13_W142_T0.10.813
7_S83_Y0.099850.811
78_L124_L0.099820.811
32_R35_G0.098950.804
157_W165_L0.098650.802
81_L175_L0.098210.798
180_W183_W0.09820.798
51_F93_A0.098110.797
157_W163_W0.098110.797
16_A98_I0.097880.795
31_L58_P0.097870.795
8_L22_L0.09770.794
140_L168_W0.097390.791
145_I199_L0.097110.789
16_A200_L0.097090.789
14_L135_L0.097040.789
146_W151_W0.097010.788
34_L41_S0.096970.788
24_Y61_A0.096960.788
12_A46_L0.096870.787
83_Y143_G0.096780.786
8_L56_F0.09660.785
161_E207_N0.096570.785
95_L121_L0.096540.784
199_L203_Y0.096340.783
40_P142_T0.096170.781
10_F68_Q0.096170.781
99_Q131_I0.096070.781
90_A94_L0.096020.780
180_W187_R0.095340.775
34_L125_S0.095240.774
65_P144_A0.095240.774
146_W159_P0.095230.774
123_R127_R0.095210.774
65_P157_W0.095210.774
98_I119_E0.095060.772
126_Y174_Y0.094870.771
63_L69_S0.094770.770
3_N207_N0.094660.769
89_A134_I0.094520.768
38_S89_A0.094510.768
37_F87_A0.094480.768
64_N76_V0.094310.766
136_L167_T0.094210.766
164_S205_G0.094180.765
20_L36_A0.094160.765
63_L157_W0.094060.764
20_L182_G0.093970.764
46_L59_P0.093960.763
136_L142_T0.093950.763
95_L101_R0.093950.763
84_A126_Y0.09390.763
96_Y189_A0.09380.762
76_V147_A0.093790.762
150_S157_W0.093790.762
196_F200_L0.093450.759
152_G155_W0.093430.759
122_E201_L0.093260.758
25_L80_L0.09320.757
99_Q118_L0.093140.757
34_L179_S0.0930.756
84_A87_A0.092890.755
9_L82_G0.092760.754
178_R182_G0.092730.753
3_N73_Y0.092550.752
155_W162_V0.092530.752
60_P140_L0.092440.751
78_L201_L0.092420.751
65_P176_H0.092140.749
18_I41_S0.092060.748
179_S182_G0.091970.747
125_S174_Y0.091870.746
93_A132_G0.091780.746
72_L155_W0.091770.746
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
2gsmA0.929930.20.947
3giaA0.476628.70.948
4he8M0.789727.80.948
2yevA0.9439210.95
1fftA0.934619.60.951
3ayfA0.929918.40.952
2jwaA0.205613.70.954
2ks1B0.205610.60.956
3l1lA0.42998.50.958
3s8fA0.87857.80.959
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