GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cupin_6 - Cupin
Pfam: PF12852 (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: CL0029
Length: 186
Sequences: 1313
Seq/Len: 7.06
HH_delta: 0.567 (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
157_E182_R0.472854.481
39_H114_C0.336653.190
171_R174_E0.294072.787
39_H73_H0.286722.717
45_S58_R0.252092.389
38_F115_G0.241812.292
45_S60_E0.22922.172
47_W58_R0.223922.122
48_L65_V0.195341.851
148_A152_A0.186221.765
154_L169_L0.186011.763
47_W56_P0.17911.697
40_V151_L0.175351.662
77_S81_S0.168541.597
168_V175_L0.167781.590
164_G182_R0.166131.574
63_D138_R0.156541.483
43_R111_R0.15441.463
47_W76_S0.154061.460
12_L177_L0.151171.433
161_P165_S0.150911.430
171_R175_L0.150321.425
64_I180_A0.150111.423
20_C114_C0.149411.416
41_V44_G0.148821.410
46_C59_L0.144611.370
151_L176_L0.142081.346
79_P82_P0.138711.315
40_V64_I0.137151.300
73_H114_C0.136691.295
49_R76_S0.134341.273
171_R178_V0.134171.271
13_R118_E0.133931.269
18_F22_L0.133321.263
147_L151_L0.129121.224
157_E168_V0.12881.221
30_F37_S0.128471.217
50_V54_G0.128461.217
174_E184_W0.128141.214
82_P137_I0.126611.200
36_A69_R0.12621.196
6_L9_S0.125791.192
41_V46_C0.123591.171
36_A119_F0.121531.152
48_L75_L0.12081.145
147_L176_L0.120461.142
165_S169_L0.119961.137
156_S161_P0.119951.137
59_L63_D0.119651.134
9_S12_L0.119331.131
49_R74_V0.119241.130
17_F20_C0.118651.124
29_R51_P0.118031.119
60_E138_R0.117631.115
14_G184_W0.116841.107
29_R74_V0.116081.100
7_L173_A0.115671.096
164_G178_V0.115461.094
38_F46_C0.114551.086
54_G133_P0.114091.081
4_S168_V0.112091.062
4_S166_D0.11111.053
16_L154_L0.11111.053
28_L41_V0.111071.053
10_L119_F0.110921.051
46_C75_L0.109071.034
52_G55_E0.108611.029
63_D136_H0.106941.013
26_W46_C0.106451.009
65_V133_P0.106321.008
32_G72_A0.106041.005
47_W79_P0.10350.981
51_P54_G0.102520.972
20_C23_C0.1020.967
40_V158_S0.101370.961
33_S37_S0.101360.961
61_A118_E0.101080.958
11_R137_I0.100410.952
41_V62_G0.100040.948
125_H129_A0.09980.946
59_L65_V0.099420.942
175_L178_V0.099220.940
31_P38_F0.099170.940
178_V182_R0.098880.937
130_A181_L0.098720.936
55_E83_P0.09840.933
9_S150_L0.098280.931
13_R23_C0.09820.931
58_R66_L0.098110.930
48_L57_I0.0970.919
156_S160_Q0.096730.917
84_V106_G0.09670.916
65_V69_R0.096670.916
173_A177_L0.096410.914
150_L176_L0.096070.910
20_C39_H0.095880.909
117_F173_A0.095840.908
146_W156_S0.095810.908
145_P166_D0.095740.907
157_E169_L0.095650.906
47_W78_D0.095430.904
7_L12_L0.095020.900
156_S162_R0.095010.900
48_L67_L0.094910.899
106_G156_S0.094510.896
158_S164_G0.094410.895
68_P73_H0.093970.891
16_L20_C0.093690.888
13_R170_D0.093280.884
55_E120_D0.093240.884
9_S126_P0.092830.880
28_L180_A0.092560.877
84_V103_D0.092240.874
12_L18_F0.092150.873
62_G132_P0.092060.872
42_L111_R0.091530.867
127_L157_E0.091460.867
39_H68_P0.091340.866
173_A184_W0.09130.865
133_P138_R0.091130.864
26_W77_S0.090980.862
12_L17_F0.090940.862
41_V110_T0.090790.860
17_F151_L0.090570.858
5_D13_R0.090330.856
43_R152_A0.090330.856
119_F175_L0.090280.856
133_P136_H0.090230.855
29_R72_A0.090040.853
12_L173_A0.089590.849
136_H179_E0.089350.847
132_P164_G0.089220.846
34_P128_L0.088820.842
67_L75_L0.088350.837
10_L125_H0.088040.834
51_P136_H0.088010.834
68_P162_R0.088010.834
5_D8_S0.087880.833
67_L71_T0.087290.827
75_L78_D0.087160.826
36_A66_L0.087130.826
67_L114_C0.0870.824
103_D145_P0.086830.823
23_C40_V0.086770.822
25_P77_S0.086690.822
77_S172_L0.086540.820
36_A65_V0.086480.820
13_R133_P0.086240.817
137_I183_H0.086180.817
64_I73_H0.085360.809
46_C110_T0.085210.808
11_R185_L0.085070.806
81_S84_V0.084990.805
30_F73_H0.084730.803
62_G164_G0.084410.800
109_S159_A0.084360.799
4_S164_G0.084320.799
54_G159_A0.084030.796
54_G129_A0.083680.793
10_L14_G0.083460.791
15_S18_F0.083390.790
60_E152_A0.083350.790
20_C154_L0.083250.789
76_S79_P0.0830.787
149_A156_S0.082820.785
45_S129_A0.08280.785
21_E66_L0.082740.784
137_I147_L0.082680.784
36_A181_L0.082130.778
117_F174_E0.082120.778
42_L115_G0.082110.778
7_L33_S0.08210.778
147_L179_E0.0820.777
20_C37_S0.081590.773
5_D9_S0.081460.772
33_S73_H0.081390.771
8_S72_A0.081350.771
18_F23_C0.081340.771
6_L18_F0.081130.769
156_S180_A0.081120.769
27_G49_R0.081110.769
133_P169_L0.081030.768
42_L113_L0.080890.767
153_L172_L0.080880.766
22_L43_R0.080680.765
177_L181_L0.080640.764
38_F179_E0.080510.763
14_G64_I0.08050.763
10_L17_F0.080340.761
64_I77_S0.080170.760
59_L110_T0.079970.758
11_R15_S0.079940.758
162_R179_E0.079740.756
10_L13_R0.079430.753
5_D10_L0.079270.751
32_G70_G0.079230.751
55_E183_H0.07910.750
56_P78_D0.079040.749
70_G175_L0.0790.749
61_A79_P0.078980.748
64_I151_L0.078740.746
8_S16_L0.078320.742
54_G57_I0.078310.742
21_E43_R0.078280.742
157_E164_G0.078230.741
59_L175_L0.078220.741
39_H48_L0.078080.740
84_V184_W0.077910.738
13_R16_L0.077720.737
9_S17_F0.077540.735
22_L105_G0.07750.734
67_L117_F0.077440.734
64_I121_P0.077420.734
127_L172_L0.077030.730
172_L175_L0.0770.730
32_G35_G0.076590.726
7_L123_A0.076540.725
30_F116_R0.076370.724
64_I152_A0.076180.722
137_I144_A0.076130.721
38_F173_A0.076090.721
74_V113_L0.076010.720
6_L179_E0.075950.720
6_L21_E0.075880.719
63_D117_F0.075740.718
55_E148_A0.075720.718
103_D106_G0.07560.716
82_P133_P0.075520.716
175_L179_E0.075450.715
22_L39_H0.075380.714
8_S110_T0.075350.714
124_A144_A0.075270.713
58_R78_D0.075220.713
19_R153_L0.075070.711
46_C175_L0.074980.711
70_G73_H0.074920.710
55_E143_A0.074630.707
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
2arcA0.833399.20.567
3gbgA0.838798.80.635
1vj2A0.598.40.686
4i4aA0.580698.40.688
2xlgA0.854898.40.69
1o4tA0.483998.30.695
2b8mA0.559198.30.698
3fjsA0.598.30.698
3es1A0.580698.30.701
2gu9A0.54398.20.703
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