GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3552 - Domain of unknown function (DUF3552)
Pfam: PF12072 (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: 201
Sequences: 930
Seq/Len: 4.63
HH_delta: 0.902 (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
139_E142_E0.534165.042
167_A174_I0.313962.963
163_A167_A0.289782.735
177_E181_E0.276692.611
178_A182_A0.266062.511
41_E44_E0.248052.341
163_A174_I0.229722.168
159_L167_A0.219222.069
9_A13_G0.210141.983
63_Q66_R0.205771.942
21_R26_R0.203111.917
36_A39_I0.201011.897
164_R174_I0.199941.887
157_E160_E0.195541.846
131_E135_E0.187541.770
10_L13_G0.182191.720
157_E161_E0.181251.711
153_E157_E0.181081.709
65_L69_L0.178621.686
17_G21_R0.175851.660
134_E138_Q0.175721.658
175_E185_K0.173891.641
35_E38_Q0.172471.628
69_L73_L0.170131.606
159_L163_A0.16821.588
52_K56_L0.16611.568
185_K188_R0.165861.565
155_L159_L0.163651.545
62_A65_L0.159671.507
15_G19_L0.156571.478
128_E131_E0.15471.460
51_K55_E0.150881.424
190_I194_I0.149441.410
178_A190_I0.148531.402
176_E180_E0.147571.393
50_I54_A0.145281.371
38_Q42_E0.144971.368
134_E137_Q0.143681.356
80_L87_L0.142561.346
86_R95_D0.141761.338
55_E61_E0.141721.338
39_I43_A0.140621.327
62_A69_L0.140231.324
146_L154_I0.13991.320
135_E138_Q0.139481.316
156_L163_A0.139261.314
122_L125_R0.138851.311
169_A187_R0.136711.290
13_G17_G0.136291.286
146_L155_L0.134811.272
127_E131_E0.132111.247
191_A201_H0.13061.233
34_K37_E0.129841.225
183_D187_R0.129421.222
107_E110_K0.129181.219
53_E59_K0.129081.218
164_R167_A0.128851.216
32_A39_I0.128571.213
18_Y21_R0.128431.212
61_E64_K0.12541.184
95_D98_L0.125151.181
78_K82_R0.124751.177
137_Q158_K0.124171.172
22_K26_R0.123451.165
130_E133_I0.12181.150
66_R70_E0.120991.142
160_E170_L0.11971.130
181_E185_K0.119151.125
133_I136_Q0.11791.113
103_K107_E0.117121.105
150_E153_E0.116521.100
89_Q97_R0.114241.078
60_E63_Q0.11391.075
52_K63_Q0.113571.072
125_R128_E0.11351.071
131_E134_E0.113331.070
124_E127_E0.113241.069
188_R194_I0.111541.053
109_E180_E0.111021.048
173_R177_E0.109941.038
190_I197_Y0.109411.033
55_E62_A0.10891.028
122_L126_E0.10871.026
188_R192_T0.108531.024
25_N125_R0.107961.019
85_K89_Q0.10791.018
60_E80_L0.107721.017
6_A9_A0.106251.003
51_K66_R0.106221.003
197_Y201_H0.106181.002
14_I17_G0.105890.999
56_L59_K0.105120.992
57_E64_K0.105060.992
63_Q67_Q0.102230.965
46_E51_K0.102070.963
36_A43_A0.101940.962
21_R25_N0.101210.955
80_L84_E0.100980.953
136_Q171_I0.100180.946
82_R85_K0.100050.944
106_E152_K0.100020.944
5_I11_I0.099390.938
136_Q143_I0.099070.935
3_I137_Q0.09840.929
142_E154_I0.098370.928
51_K57_E0.09790.924
172_R201_H0.097730.922
125_R130_E0.097710.922
129_L132_L0.097570.921
166_E193_A0.096450.910
129_L136_Q0.096290.909
175_E179_K0.095850.905
143_I151_A0.095840.905
97_R105_E0.09530.899
29_L65_L0.095290.899
14_I20_V0.095240.899
112_E200_E0.095210.899
168_A198_A0.094980.896
137_Q163_A0.094960.896
145_G150_E0.094490.892
16_I44_E0.094220.889
161_E164_R0.094090.888
138_Q141_E0.094080.888
76_R91_E0.093840.886
168_A172_R0.093760.885
163_A200_E0.093740.885
98_L101_L0.093720.885
4_I50_I0.093660.884
152_K158_K0.093230.880
50_I71_R0.093020.878
132_L136_Q0.092770.876
93_Q96_R0.092190.870
148_A156_L0.091960.868
7_I131_E0.091920.868
122_L172_R0.091880.867
4_I101_L0.091860.867
57_E89_Q0.091490.864
11_I14_I0.091430.863
63_Q76_R0.091260.861
59_K162_E0.091050.859
77_R81_Q0.091020.859
135_E139_E0.090970.859
163_A171_I0.090920.858
123_E127_E0.090910.858
54_A144_A0.090750.857
29_L33_E0.090740.856
160_E167_A0.090730.856
25_N33_E0.090620.855
52_K104_R0.090280.852
104_R173_R0.090.849
145_G159_L0.090.849
170_L178_A0.089760.847
27_K137_Q0.089720.847
51_K54_A0.088890.839
162_E165_R0.088860.839
110_K113_E0.088850.839
175_E189_I0.088530.836
170_L173_R0.08820.832
131_E189_I0.087960.830
54_A57_E0.087570.827
58_A162_E0.087350.824
149_E153_E0.087270.824
174_I178_A0.086970.821
37_E41_E0.086850.820
163_A197_Y0.086720.818
152_K163_A0.086520.817
102_E106_E0.08640.815
186_A190_I0.086170.813
44_E128_E0.085980.812
54_A193_A0.085650.808
90_R144_A0.085570.808
12_V30_E0.085020.802
46_E67_Q0.084810.800
128_E133_I0.084750.800
164_R177_E0.084650.799
150_E189_I0.084640.799
133_I137_Q0.084320.796
44_E50_I0.084120.794
7_I11_I0.084030.793
181_E184_K0.083590.789
3_I124_E0.083520.788
51_K60_E0.08290.782
59_K103_K0.082850.782
181_E193_A0.082280.777
53_E123_E0.08220.776
136_Q139_E0.082190.776
3_I7_I0.081630.770
47_A51_K0.081470.769
63_Q199_S0.081150.766
98_L102_E0.081140.766
156_L159_L0.081060.765
7_I15_G0.080950.764
90_R98_L0.080940.764
147_T198_A0.080850.763
54_A79_E0.080710.762
143_I152_K0.080660.761
192_T196_R0.080650.761
60_E70_E0.080610.761
61_E66_R0.080610.761
96_R101_L0.080220.757
97_R100_Q0.080060.756
107_E112_E0.080020.755
104_R124_E0.079710.752
90_R174_I0.079670.752
17_G25_N0.07950.750
82_R106_E0.079450.750
30_E33_E0.07920.748
18_Y24_I0.079160.747
47_A54_A0.079030.746
40_L65_L0.078680.743
138_Q147_T0.078530.741
182_A189_I0.078110.737
40_L44_E0.077950.736
37_E44_E0.077940.736
156_L170_L0.077920.735
15_G135_E0.077850.735
147_T155_L0.077750.734
7_I109_E0.077650.733
122_L129_L0.077640.733
37_E52_K0.077620.733
148_A163_A0.07740.731
124_E155_L0.077220.729
41_E87_L0.077210.729
97_R102_E0.077170.728
99_E110_K0.077060.727
24_I27_K0.077010.727
167_A171_I0.076990.727
86_R90_R0.076980.727
132_L200_E0.076870.726
51_K61_E0.076840.725
129_L177_E0.076830.725
58_A84_E0.076790.725
171_I186_A0.076760.724
42_E188_R0.076730.724
167_A197_Y0.07670.724
148_A167_A0.076650.723
103_K172_R0.07640.721
186_A189_I0.076310.720
56_L99_E0.07590.716
21_R24_I0.075860.716
145_G152_K0.07580.715
27_K149_E0.075780.715
95_D184_K0.075750.715
28_K31_Q0.075270.710
145_G157_E0.075190.710
3_I113_E0.075130.709
158_K162_E0.074990.708
53_E102_E0.074970.708
5_I153_E0.074950.707
90_R164_R0.074930.707
164_R191_A0.074810.706
54_A58_A0.074690.705
132_L135_E0.07430.701
186_A196_R0.074090.699
185_K191_A0.074040.699
11_I114_E0.073950.698
154_I158_K0.073890.697
114_E137_Q0.073750.696
23_K27_K0.073670.695
143_I154_I0.073620.695
13_G177_E0.07360.695
64_K68_E0.073570.694
89_Q93_Q0.073510.694
83_L87_L0.07340.693
55_E65_L0.073380.693
6_A153_E0.073330.692
13_G189_I0.073090.690
106_E124_E0.072990.689
84_E103_K0.072950.689
59_K63_Q0.072910.688
8_V12_V0.072870.688
71_R80_L0.072850.688
68_E107_E0.072790.687
33_E38_Q0.072780.687
7_I106_E0.072740.687
40_L43_A0.072670.686
184_K187_R0.072510.684
187_R201_H0.072510.684
137_Q141_E0.07250.684
68_E74_K0.072480.684
35_E166_E0.072440.684
53_E99_E0.072360.683
152_K159_L0.072330.683
82_R108_L0.072320.683
27_K128_E0.072190.681
106_E110_K0.072170.681
36_A108_L0.07190.679
49_A56_L0.07150.675
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
2j69A0.636870.20.902
1s7qA0.303564.30.906
1l2pA0.303563.50.906
2i1jA0.910454.60.911
4efaE0.308549.10.914
2kk7A0.2587290.924
2jwaA0.1443250.926
2ks1B0.1493210.928
1iijA0.119417.30.931
2ls4A0.129416.50.931
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