GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrom_B561 - Eukaryotic cytochrome b561
Pfam: PF03188 (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: 137
Sequences: 1161
Seq/Len: 8.47
HH_delta: 0.862 (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
79_T125_T0.482913.781
77_L81_V0.38743.033
113_W116_Y0.353012.764
6_M52_G0.317732.488
5_L48_F0.295542.314
74_I78_A0.287592.252
75_L125_T0.286422.242
17_G42_Q0.242741.900
46_L84_L0.23721.857
53_F80_F0.226271.772
17_G41_L0.210311.647
56_I59_N0.206531.617
21_A34_W0.203911.596
34_W108_N0.19811.551
61_N67_H0.188321.474
11_V126_I0.187311.467
75_L121_L0.186921.463
13_L45_A0.183971.440
18_I119_Y0.177681.391
104_R108_N0.170811.337
7_T12_F0.168231.317
9_G45_A0.15851.241
54_V58_I0.156851.228
10_F49_A0.154641.211
60_K69_K0.152041.190
2_H5_L0.149851.173
21_A35_F0.148481.163
11_V15_P0.146531.147
60_K73_S0.146321.146
123_I127_F0.14471.133
50_I84_L0.141831.110
79_T129_G0.141481.108
98_G101_R0.141421.107
22_R86_Q0.137951.080
48_F78_A0.137781.079
93_R108_N0.137711.078
15_P42_Q0.137251.075
107_W110_W0.136441.068
114_L118_I0.135561.061
113_W117_L0.134531.053
37_I40_I0.134291.051
112_R116_Y0.133541.046
86_Q115_G0.131811.032
6_M80_F0.13151.030
93_R107_W0.130061.018
8_I12_F0.129781.016
33_W47_V0.129011.010
8_I13_L0.128841.009
19_L88_L0.128721.008
13_L102_K0.128321.005
35_F104_R0.127540.999
51_I82_L0.125590.983
4_I21_A0.12540.982
2_H6_M0.125380.982
108_N112_R0.123850.970
39_W95_F0.123740.969
79_T121_L0.123620.968
47_V51_I0.123520.967
8_I98_G0.123360.966
6_M53_F0.122890.962
22_R34_W0.122890.962
90_G94_F0.122720.961
60_K67_H0.122030.955
22_R35_F0.121720.953
46_L50_I0.121390.950
57_F77_L0.121110.948
68_F77_L0.121090.948
9_G49_A0.120480.943
20_A41_L0.12040.943
120_V126_I0.119910.939
9_G122_A0.119460.935
12_F88_L0.119430.935
48_F70_S0.119410.935
10_F34_W0.119380.935
12_F80_F0.118570.928
105_P110_W0.1180.924
2_H9_G0.117770.922
20_A29_K0.117690.921
52_G62_R0.117640.921
71_W87_P0.117220.918
79_T118_I0.115880.907
46_L80_F0.115860.907
29_K33_W0.115360.903
114_L117_L0.114240.894
113_W124_A0.113920.892
14_M45_A0.113760.891
5_L51_I0.113480.888
117_L121_L0.11290.884
87_P123_I0.112670.882
15_P45_A0.111740.875
4_I8_I0.111730.875
58_I61_N0.111690.874
60_K70_S0.111140.870
43_V78_A0.110810.868
43_V84_L0.110490.865
76_G86_Q0.110290.863
70_S73_S0.110050.862
50_I80_F0.109540.858
44_L47_V0.109320.856
86_Q90_G0.108850.852
39_W124_A0.108770.852
49_A80_F0.108610.850
3_P60_K0.108530.850
9_G13_L0.108140.847
105_P112_R0.108110.846
96_M99_L0.108040.846
51_I117_L0.107050.838
54_V57_F0.106820.836
11_V129_G0.106780.836
85_L121_L0.106410.833
70_S74_I0.106140.831
120_V124_A0.106050.830
11_V107_W0.104920.821
111_H115_G0.104440.818
30_S42_Q0.104030.814
56_I60_K0.103360.809
104_R109_K0.103360.809
3_P21_A0.103210.808
19_L22_R0.103190.808
32_K36_R0.103040.807
21_A104_R0.10260.803
88_L92_F0.101860.797
6_M130_L0.101780.797
70_S77_L0.101490.795
10_F83_A0.100660.788
14_M42_Q0.100630.788
15_P119_Y0.099670.780
118_I130_L0.099630.780
91_F117_L0.099560.779
49_A77_L0.09950.779
22_R112_R0.099310.778
42_Q86_Q0.098850.774
13_L50_I0.098390.770
123_I130_L0.098260.769
23_Y124_A0.09820.769
99_L102_K0.097360.762
117_L124_A0.097360.762
71_W74_I0.097240.761
80_F126_I0.097180.761
78_A87_P0.097150.761
20_A44_L0.097130.760
30_S103_R0.096960.759
94_F108_N0.096440.755
39_W98_G0.096440.755
69_K73_S0.096380.755
76_G81_V0.096240.753
43_V124_A0.096140.753
110_W114_L0.096120.753
21_A109_K0.096060.752
75_L128_L0.095930.751
76_G123_I0.095890.751
14_M47_V0.095870.751
10_F122_A0.095210.745
119_Y123_I0.094980.744
68_F74_I0.09460.741
55_A123_I0.094520.740
82_L88_L0.094460.740
82_L120_V0.094450.739
85_L106_I0.09440.739
57_F69_K0.093990.736
14_M17_G0.093970.736
103_R106_I0.093960.736
53_F57_F0.093690.734
49_A122_A0.093280.730
30_S33_W0.09290.727
57_F61_N0.092740.726
12_F120_V0.092290.723
19_L86_Q0.092270.722
29_K32_K0.092180.722
57_F68_F0.092050.721
61_N70_S0.091880.719
56_I125_T0.091690.718
102_K110_W0.09160.717
37_I61_N0.091250.714
14_M49_A0.091150.714
57_F67_H0.09090.712
57_F60_K0.090880.712
40_I78_A0.090830.711
5_L16_E0.090810.711
44_L89_L0.090680.710
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
1kqfC0.846783.10.862
4gd3A0.8832650.88
3j1zP0.948918.20.912
3cx5C0.671512.90.917
4h44A0.78839.20.922
3h90A0.93436.90.926
2lomA0.47456.60.926
2vpzC0.86866.40.927
2lonA0.51094.40.932
2bs2C0.40884.30.932
If you are interested in a protein containing this domain,
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