GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3308 - Protein of unknown function (DUF3308)
Pfam: PF11751 (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: CL0193
Length: 274
Sequences: 1658
Seq/Len: 6.05
HH_delta: 0.534 (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
63_H86_Y0.365013.916
106_F136_F0.320353.437
98_L144_L0.250692.689
151_F183_A0.210942.263
152_Y184_G0.204622.195
100_F144_L0.20352.183
67_L84_L0.199252.138
36_Y50_Q0.195982.102
226_G250_G0.192682.067
98_L146_Y0.185781.993
218_R224_W0.180371.935
176_P182_S0.175121.879
103_S141_G0.172991.856
85_S103_S0.168871.812
101_G143_G0.163571.755
23_Y27_E0.161821.736
190_N193_F0.160791.725
236_S254_D0.157831.693
22_A145_Y0.15571.670
105_G141_G0.154821.661
229_Y233_D0.15121.622
69_F82_A0.14671.574
147_Y152_Y0.144411.549
141_G158_P0.14191.522
30_I54_A0.141261.515
54_A67_L0.140111.503
37_R49_T0.139171.493
151_F185_Y0.1381.480
50_Q71_N0.137641.477
69_F80_T0.136591.465
193_F217_F0.136421.463
17_Y68_S0.13621.461
214_G238_M0.134781.446
201_Y209_Q0.13451.443
112_D115_K0.133751.435
107_V163_P0.133431.431
67_L82_A0.132181.418
157_V177_R0.131871.415
102_L142_A0.13111.406
25_G64_G0.130961.405
93_S97_Y0.130751.403
157_V160_L0.130351.398
145_Y152_Y0.129851.393
94_E97_Y0.128661.380
195_L215_A0.127591.369
219_Y223_F0.126751.360
17_Y85_S0.126621.358
139_D159_H0.125011.341
224_W240_G0.122751.317
24_A27_E0.122481.314
104_A140_F0.122261.312
228_G238_M0.120881.297
222_R241_F0.120771.296
37_R40_W0.119811.285
244_K247_F0.119761.285
20_N154_G0.11881.274
144_L155_L0.11851.271
58_I65_L0.117681.262
228_G236_S0.117271.258
186_R194_K0.116361.248
22_A143_G0.115241.236
226_G238_M0.114531.229
227_L235_F0.114071.224
83_Y105_G0.113931.222
178_H182_S0.113531.218
216_M224_W0.113021.212
83_Y141_G0.112061.202
216_M240_G0.111671.198
23_Y145_Y0.110821.189
69_F249_I0.110541.186
40_W47_P0.110461.185
225_A239_L0.11031.183
56_A65_L0.109971.180
193_F219_Y0.10971.177
97_Y148_Y0.10881.167
25_G99_S0.107371.152
108_Q136_F0.105571.133
105_G139_D0.103421.109
33_N53_S0.10311.106
47_P180_Y0.102111.095
104_A138_P0.102081.095
66_G87_A0.10171.091
70_Y81_G0.101071.084
85_S141_G0.101011.084
66_G85_S0.100631.080
53_S66_G0.099821.071
243_L249_I0.099481.067
81_G240_G0.099441.067
210_Q230_R0.099321.065
213_I229_Y0.099141.064
79_Q111_I0.098861.061
162_Q165_F0.098711.059
214_G228_G0.098281.054
150_N188_D0.097991.051
21_P143_G0.097081.041
77_F113_G0.096821.039
94_E108_Q0.095821.028
97_Y146_Y0.095691.027
185_Y188_D0.095661.026
89_H99_S0.094921.018
17_Y55_D0.094851.018
198_S212_D0.093721.005
152_Y186_R0.093671.005
35_N51_S0.093651.005
230_R234_A0.09361.004
219_Y225_A0.093491.003
71_N78_S0.093120.999
216_M250_G0.092910.997
133_S167_F0.092470.992
76_P116_L0.092280.990
141_G146_Y0.091820.985
211_L229_Y0.091120.978
23_Y26_S0.091030.977
172_N213_I0.090650.972
164_S172_N0.090430.970
151_F155_L0.089390.959
82_A108_Q0.088920.954
33_N51_S0.088880.953
184_G194_K0.088770.952
198_S214_G0.088490.949
94_E192_D0.088450.949
155_L179_Y0.087680.941
88_Y146_Y0.087650.940
226_G240_G0.08760.940
199_V211_L0.087170.935
77_F159_H0.087050.934
176_P193_F0.086940.933
64_G240_G0.086660.930
92_L100_F0.086530.928
65_L86_Y0.086440.927
192_D220_N0.086330.926
186_R196_S0.086190.925
148_Y153_V0.085960.922
141_G159_H0.08530.915
212_D230_R0.085210.914
48_N144_L0.085110.913
220_N223_F0.084910.911
16_P23_Y0.084570.907
43_I75_G0.084020.901
152_Y226_G0.083880.900
24_A55_D0.083690.898
87_A224_W0.083690.898
240_G250_G0.083680.898
25_G87_A0.083620.897
59_N63_H0.083530.896
153_V181_L0.083530.896
109_Y238_M0.083430.895
182_S200_L0.083220.893
79_Q109_Y0.083110.892
49_T72_D0.0830.890
75_G101_G0.082910.889
78_S102_L0.08220.882
88_Y253_Y0.082060.880
159_H163_P0.081890.879
25_G143_G0.081620.876
65_L84_L0.081190.871
23_Y74_I0.081130.870
215_A227_L0.0810.869
243_L246_N0.0810.869
37_R230_R0.08090.868
81_G111_I0.080750.866
26_S31_R0.080640.865
159_H178_H0.080330.862
40_W43_I0.080260.861
142_A248_R0.080240.861
106_F249_I0.080210.860
97_Y147_Y0.07980.856
58_I86_Y0.079570.854
88_Y93_S0.079410.852
16_P55_D0.079260.850
25_G89_H0.079250.850
64_G87_A0.079230.850
16_P182_S0.079090.848
143_G254_D0.078880.846
216_M238_M0.07870.844
43_I202_R0.078450.842
155_L183_A0.078170.839
194_K221_D0.077960.836
22_A57_P0.077860.835
39_Q230_R0.077850.835
32_I82_A0.077720.834
81_G105_G0.077370.830
217_F239_L0.077360.830
56_A106_F0.077270.829
109_Y178_H0.077230.829
233_D256_N0.077110.827
224_W236_S0.077050.827
135_S175_L0.076820.824
187_F197_P0.076750.823
155_L168_S0.07640.820
146_Y229_Y0.07630.819
133_S165_F0.076030.816
18_L61_K0.075470.810
111_I129_N0.075450.809
176_P187_F0.07530.808
153_V214_G0.075260.807
140_F159_H0.075140.806
111_I191_E0.075090.806
22_A234_A0.074990.804
54_A65_L0.074970.804
72_D76_P0.074870.803
89_H97_Y0.074730.802
242_N246_N0.074670.801
199_V209_Q0.074660.801
47_P184_G0.074450.799
221_D242_N0.074450.799
167_F170_N0.074380.798
19_L252_S0.074330.797
29_G252_S0.074330.797
207_S253_Y0.07430.797
170_N192_D0.074150.795
180_Y196_S0.07410.795
68_S85_S0.074040.794
53_S70_Y0.073820.792
198_S205_G0.073720.791
148_Y183_A0.073650.790
99_S153_V0.073580.789
85_S105_G0.073560.789
150_N185_Y0.073520.789
86_Y251_Y0.073510.789
176_P204_Q0.073510.789
37_R254_D0.073450.788
31_R55_D0.073390.787
93_S173_N0.073340.787
140_F157_V0.073330.787
98_L155_L0.073290.786
141_G156_S0.073180.785
139_D161_N0.073020.783
237_F249_I0.072960.783
63_H88_Y0.072910.782
32_I38_N0.072880.782
88_Y133_S0.072580.779
137_Y228_G0.072520.778
71_N247_F0.072410.777
178_H204_Q0.072410.777
178_H202_R0.072330.776
163_P167_F0.072250.775
107_V137_Y0.072030.773
24_A92_L0.071990.772
94_E191_E0.071990.772
63_H67_L0.07190.771
69_F221_D0.071890.771
33_N255_F0.071870.771
65_L247_F0.071850.771
42_G171_S0.071780.770
50_Q54_A0.071730.770
108_Q247_F0.071440.766
53_S232_N0.07140.766
42_G47_P0.071330.765
100_F117_T0.071270.765
65_L168_S0.071260.764
174_K179_Y0.070960.761
77_F248_R0.070940.761
18_L136_F0.070920.761
82_A128_N0.07080.760
34_L52_L0.070560.757
155_L164_S0.070490.756
143_G154_G0.07030.754
52_L69_F0.070290.754
178_H185_Y0.070270.754
187_F198_S0.070270.754
33_N251_Y0.070230.753
136_F240_G0.070230.753
58_I190_N0.070210.753
87_A147_Y0.070210.753
148_Y180_Y0.070180.753
109_Y229_Y0.070130.752
192_D219_Y0.070120.752
82_A155_L0.069990.751
166_S198_S0.069710.748
210_Q234_A0.06960.747
212_D226_G0.069590.747
204_Q207_S0.069560.746
112_D128_N0.069530.746
67_L89_H0.069430.745
81_G137_Y0.069420.745
235_F239_L0.069240.743
112_D195_L0.069210.742
16_P165_F0.069130.742
66_G83_Y0.069110.741
143_G156_S0.069030.741
202_R212_D0.0690.740
39_Q87_A0.068890.739
220_N241_F0.068890.739
25_G55_D0.068810.738
108_Q234_A0.06880.738
84_L106_F0.068790.738
139_D175_L0.068790.738
113_G116_L0.068740.737
32_I78_S0.068650.736
220_N239_L0.068650.736
69_F208_P0.068620.736
180_Y200_L0.068510.735
237_F255_F0.068490.735
99_S217_F0.068450.734
93_S190_N0.068330.733
233_D254_D0.068330.733
157_V179_Y0.068320.733
141_G240_G0.068210.732
94_E244_K0.068180.731
59_N235_F0.068150.731
226_G254_D0.068080.730
48_N223_F0.0680.729
18_L51_S0.067990.729
57_P61_K0.067960.729
27_E202_R0.067920.729
201_Y204_Q0.067910.729
150_N153_V0.06790.728
241_F249_I0.067850.728
182_S238_M0.06780.727
43_I52_L0.067770.727
17_Y155_L0.067680.726
28_D55_D0.067540.725
198_S228_G0.06750.724
29_G54_A0.067450.724
146_Y161_N0.067450.724
129_N133_S0.067410.723
103_S158_P0.067370.723
109_Y163_P0.067340.722
38_N48_N0.067310.722
107_V161_N0.067230.721
38_N206_G0.067210.721
18_L151_F0.067170.721
64_G111_I0.067150.720
68_S83_Y0.067130.720
53_S68_S0.066940.718
84_L203_Y0.066890.718
25_G61_K0.066740.716
52_L67_L0.06670.716
25_G44_P0.066680.715
234_A254_D0.066540.714
30_I59_N0.066460.713
216_M226_G0.06640.712
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
3pguA0.959999.90.534
3bs0A0.959999.90.536
3bryA0.959999.90.538
3dwoX0.959999.90.551
3pguA0.883296.80.88
1ormA0.474596.70.881
3qraA0.510996.20.889
2k0lA0.6679960.891
3dwoX0.9161960.891
1qjpA0.551195.70.893
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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