GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sod_Cu - Copperzinc superoxide dismutase (SODC)
Pfam: PF00080 (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: 142
Sequences: 1682
Seq/Len: 11.85
HH_delta: 0.013 (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
126_T129_P0.620652.820
32_S95_S0.611622.778
31_V96_F0.586142.663
44_H62_H0.513412.332
69_P128_Q0.502872.284
27_V104_S0.482452.192
68_V77_N0.412821.875
89_D93_S0.412121.872
40_Q87_Y0.402531.829
18_F116_I0.395861.798
59_A115_S0.392081.781
126_T132_N0.391671.779
40_Q122_P0.378981.722
16_V31_V0.373251.696
28_Q97_T0.370861.685
37_P137_L0.370081.681
111_I114_R0.368451.674
44_H119_H0.367761.671
127_S130_T0.365021.658
22_S25_D0.359251.632
120_S135_A0.358641.629
49_G141_V0.350371.592
69_P77_N0.347921.581
62_H79_H0.346971.576
18_F111_I0.338081.536
51_C115_S0.330741.503
41_H88_V0.313011.422
56_C139_C0.312571.420
18_F142_I0.312111.418
18_F29_V0.304041.381
28_Q99_T0.30161.370
46_H119_H0.298341.355
31_V97_T0.295461.342
50_D58_S0.27911.268
53_S58_S0.279051.268
26_G99_T0.275021.249
27_V103_L0.274651.248
62_H119_H0.273641.243
70_H79_H0.273591.243
46_H62_H0.271711.234
59_A117_V0.270321.228
20_Q105_L0.265681.207
17_T30_T0.264841.203
45_I142_I0.262541.193
63_Y80_A0.253951.154
73_P77_N0.251571.143
30_T97_T0.250851.140
136_R139_C0.250781.139
85_N125_F0.249221.132
38_P92_G0.248811.130
21_V28_Q0.247521.124
48_N60_G0.24351.106
78_C100_D0.238241.082
50_D55_N0.237181.077
85_N124_D0.235381.069
39_G88_V0.233341.060
14_G20_Q0.230911.049
16_V96_F0.230831.049
19_T30_T0.230691.048
131_G134_G0.230681.048
119_H136_R0.230211.046
66_T80_A0.230021.045
89_D92_G0.225121.023
47_E67_N0.223431.015
34_N93_S0.223341.015
79_H123_D0.220481.002
86_K94_A0.218130.991
62_H82_D0.217440.988
31_V98_F0.217140.986
50_D53_S0.216860.985
105_L110_S0.215180.978
15_T30_T0.212690.966
29_V103_L0.211010.959
68_V127_S0.210910.958
47_E61_G0.210790.958
20_Q26_G0.209020.950
30_T95_S0.206730.939
16_V116_I0.205370.933
62_H136_R0.204580.929
83_L103_L0.204390.929
129_P132_N0.20020.909
37_P88_V0.199780.908
49_G115_S0.198350.901
37_P41_H0.198330.901
80_A102_N0.197770.898
42_G123_D0.197510.897
130_T133_A0.197030.895
33_L86_K0.195450.888
126_T130_T0.193920.881
119_H139_C0.192940.876
72_G125_F0.191910.872
78_C84_G0.190110.864
70_H123_D0.189670.862
38_P90_A0.188280.855
19_T28_Q0.186740.848
29_V98_F0.185720.844
38_P94_A0.183470.833
49_G58_S0.183040.832
54_N57_S0.181960.827
20_Q27_V0.181270.823
125_F128_Q0.180970.822
45_I116_I0.179290.814
49_G113_G0.178760.812
83_L86_K0.178650.812
104_S110_S0.178430.811
13_K34_N0.178120.809
22_S26_G0.177790.808
59_A136_R0.177670.807
65_P79_H0.177670.807
40_Q125_F0.177270.805
63_Y114_R0.177120.805
44_H79_H0.176820.803
88_V91_D0.176610.802
73_P114_R0.176460.802
36_L39_G0.176420.801
64_N69_P0.175720.798
123_D131_G0.174150.791
127_S133_A0.172810.785
127_S131_G0.172210.782
56_C114_R0.172080.782
13_K138_A0.171690.780
15_T32_S0.171360.778
89_D94_A0.170560.775
27_V111_I0.169970.772
42_G133_A0.168370.765
124_D133_A0.16730.760
61_G115_S0.167110.759
65_P80_A0.16630.755
83_L100_D0.16630.755
88_V94_A0.166040.754
78_C86_K0.165870.754
47_E115_S0.16540.751
50_D141_V0.165240.751
124_D132_N0.164920.749
74_S77_N0.163680.744
124_D127_S0.162490.738
127_S132_N0.161590.734
32_S93_S0.160.727
71_G78_C0.15990.726
119_H133_A0.158120.718
51_C59_A0.157220.714
55_N58_S0.1570.713
64_N132_N0.155480.706
10_G13_K0.155130.705
38_P137_L0.155090.705
51_C141_V0.154950.704
35_G115_S0.154330.701
43_Y79_H0.153770.699
84_G125_F0.153220.696
71_G85_N0.152530.693
56_C100_D0.151850.690
19_T32_S0.151590.689
121_G137_L0.151470.688
87_Y95_S0.151090.686
130_T135_A0.149940.681
21_V26_G0.149910.681
72_G78_C0.14850.675
34_N95_S0.148430.674
125_F132_N0.146220.664
48_N114_R0.146190.664
48_N115_S0.145510.661
79_H82_D0.144470.656
36_L41_H0.142640.648
65_P111_I0.142420.647
105_L117_V0.142270.646
110_S114_R0.142080.645
73_P83_L0.141780.644
70_H73_P0.14140.642
76_D90_A0.141360.642
58_S136_R0.141350.642
27_V110_S0.140540.638
42_G62_H0.139890.635
49_G114_R0.137830.626
51_C139_C0.137470.625
65_P82_D0.137340.624
14_G33_L0.137270.624
36_L94_A0.136890.622
25_D99_T0.136810.622
51_C84_G0.136790.621
50_D84_G0.136160.619
56_C128_Q0.135640.616
123_D134_G0.134840.613
27_V51_C0.134290.610
34_N91_D0.133140.605
16_V29_V0.13280.603
45_I110_S0.132690.603
11_K135_A0.132340.601
17_T93_S0.132270.601
63_Y110_S0.131820.599
31_V86_K0.131790.599
31_V36_L0.13150.597
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
4a7uA0.98591000.013
3f7lA0.97181000.023
3pu7A0.97891000.026
3l9yA0.97181000.026
3kbeA0.97891000.029
1to4A0.98591000.031
2q2lA0.97891000.033
2wytA0.98591000.034
1f1gA0.98591000.039
3ce1A0.98591000.039

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