GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CopD - Copper resistance protein D
Pfam: PF05425 (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: CL0430
Length: 105
Sequences: 1071
Seq/Len: 10.2
HH_delta: 0.808 (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
54_M95_G0.437012.772
45_L49_A0.346472.198
15_V55_L0.342492.172
58_A91_E0.314561.995
50_L98_V0.28551.811
8_S62_R0.271061.719
42_R45_L0.267231.695
57_L103_A0.265851.686
53_L94_L0.257761.635
40_Y91_E0.252361.601
11_A58_A0.252061.599
42_R46_V0.247911.573
60_Y64_R0.233191.479
44_L51_V0.225621.431
59_A63_F0.223331.417
31_G34_A0.221261.403
4_L84_L0.220011.396
58_A62_R0.213651.355
50_L101_L0.213391.354
39_P42_R0.212621.349
25_M28_L0.210521.335
21_T58_A0.208491.322
66_I69_L0.205081.301
46_V101_L0.202351.284
3_V6_R0.198791.261
15_V18_L0.197181.251
30_L40_Y0.192641.222
11_A54_M0.191841.217
8_S58_A0.186371.182
92_L95_G0.182411.157
19_V51_V0.178831.134
43_L101_L0.177221.124
25_M29_R0.176891.122
61_N67_P0.174061.104
21_T54_M0.173271.099
7_F11_A0.17061.082
69_L84_L0.170151.079
7_F84_L0.171.078
64_R68_R0.169891.078
5_R9_W0.168931.072
50_L94_L0.167411.062
38_T41_G0.166331.055
47_K91_E0.162011.028
11_A102_A0.161591.025
33_D53_L0.160081.015
8_S91_E0.160081.015
62_R100_A0.159141.009
98_V102_A0.159131.009
40_Y47_K0.158831.007
61_N91_E0.155990.989
31_G39_P0.154960.983
8_S11_A0.151860.963
86_R89_R0.151540.961
57_L94_L0.151250.959
20_V23_L0.151090.958
11_A61_N0.150630.955
55_L58_A0.149680.949
21_T83_R0.149520.948
27_W31_G0.147320.934
23_L27_W0.1470.932
14_A87_L0.146130.927
17_V90_I0.14390.913
27_W30_L0.143340.909
38_T45_L0.142360.903
42_R99_L0.142340.903
59_A90_I0.142010.901
26_A38_T0.141120.895
19_V38_T0.140920.894
35_L41_G0.140090.889
3_V33_D0.13930.884
54_M94_L0.137740.874
49_A53_L0.137410.872
2_A46_V0.136790.868
4_L92_L0.136760.867
29_R100_A0.13670.867
40_Y58_A0.136420.865
29_R50_L0.135310.858
58_A61_N0.135050.857
84_L91_E0.134860.855
43_L62_R0.13290.843
35_L39_P0.132830.843
29_R102_A0.132810.842
84_L87_L0.13270.842
56_A70_R0.131740.836
45_L52_L0.13140.833
21_T25_M0.131220.832
5_R56_A0.130430.827
100_A104_V0.129220.820
89_R100_A0.129150.819
100_A103_A0.129050.819
35_L38_T0.128790.817
54_M88_V0.128310.814
7_F61_N0.127840.811
24_V29_R0.127460.808
46_V49_A0.12720.807
13_A90_I0.127120.806
57_L61_N0.12710.806
20_V79_A0.126420.802
15_V85_R0.126090.800
7_F54_M0.126040.799
4_L10_I0.125630.797
89_R93_I0.125510.796
23_L48_L0.124980.793
92_L101_L0.124780.791
8_S88_V0.12420.788
68_R83_R0.12420.788
11_A91_E0.124190.788
16_A20_V0.122720.778
7_F95_G0.122540.777
97_A101_L0.122540.777
93_I97_A0.122350.776
85_R88_V0.12220.775
47_K58_A0.122060.774
20_V64_R0.121840.773
25_M102_A0.121830.773
4_L65_L0.121590.771
25_M103_A0.120670.765
12_W88_V0.120610.765
60_Y63_F0.119440.758
49_A104_V0.118290.750
51_V102_A0.118190.750
48_L90_I0.118060.749
17_V42_R0.117730.747
4_L19_V0.117360.744
58_A87_L0.117130.743
77_A80_A0.116920.742
62_R66_I0.11630.738
22_G44_L0.116040.736
54_M92_L0.115860.735
68_R90_I0.115710.734
15_V87_L0.115650.734
39_P99_L0.115290.731
49_A52_L0.114840.728
18_L85_R0.114750.728
90_I94_L0.114460.726
51_V92_L0.114080.724
3_V85_R0.113980.723
48_L60_Y0.11350.720
51_V63_F0.113340.719
47_K51_V0.112880.716
47_K61_N0.112440.713
9_W86_R0.11230.712
36_F52_L0.112260.712
12_W43_L0.11210.711
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
4ev6A0.678.30.808
4i0uA0.609576.60.81
2iubA0.674.50.814
3cx5C0.876213.40.878
2qjyA0.876212.50.88
2wdqC0.933310.40.884
2f93B0.76198.90.887
4h44A0.87627.60.89
1kqfC0.99057.50.89
1zoyC0.94297.10.891
If you are interested in a protein containing this domain,
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