GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glycos_transf_1 - Glycosyl transferases group 1
Pfam: PF00534 (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: CL0113
Length: 172
Sequences: 40066
Seq/Len: 232.94
HH_delta: -0.034 (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
19_L93_S4.59153.684
49_K76_I3.558042.855
96_F112_A3.395932.725
39_K149_A2.969812.383
17_I51_V2.951832.368
59_K63_K2.938062.357
51_V78_L2.704652.170
20_F30_I2.51762.020
15_K49_K2.505192.010
151_A154_K2.248051.804
29_G32_L2.152231.727
158_D161_L2.140631.717
41_K74_N2.10631.690
154_K161_L2.104471.688
17_I92_S2.075191.665
35_E65_L2.073321.663
35_E145_I2.064191.656
154_K158_D2.059711.653
51_V76_I2.04291.639
123_D128_N2.006181.610
162_R166_G1.990171.597
16_K156_L1.94721.562
17_I49_K1.936721.554
96_F117_C1.904141.528
138_F151_A1.880621.509
65_L69_L1.868821.499
153_E157_N1.849111.484
53_V89_L1.830421.469
39_K146_E1.829551.468
45_N153_E1.81791.459
87_D115_C1.802161.446
37_F50_L1.80091.445
16_K94_D1.791161.437
58_Y61_E1.779121.427
147_E151_A1.759261.411
132_N135_V1.730511.388
123_D141_D1.729261.387
27_E102_N1.712311.374
105_F110_L1.64341.319
21_I86_L1.64021.316
18_I95_I1.638951.315
144_D147_E1.612281.294
161_L164_K1.607461.290
81_V85_E1.604091.287
164_K168_N1.603731.287
17_I94_D1.597231.281
32_L101_R1.582111.269
145_I149_A1.578781.267
51_V89_L1.567621.258
138_F154_K1.560771.252
132_N136_N1.560391.252
29_G101_R1.552381.245
39_K145_I1.545511.240
91_K115_C1.536431.233
85_E88_E1.52931.227
51_V93_S1.490631.196
163_Q167_K1.482151.189
93_S117_C1.475771.184
33_L50_L1.472221.181
141_D147_E1.467231.177
55_D59_K1.41861.138
67_E72_K1.399261.123
53_V78_L1.360391.091
166_G169_A1.350871.084
38_K69_L1.341461.076
40_L153_E1.337331.073
149_A153_E1.331931.069
140_F151_A1.319691.059
131_I137_G1.307021.049
100_S103_E1.295011.039
98_S108_S1.282221.029
161_L165_L1.282051.029
31_D101_R1.281841.028
86_L90_Y1.277841.025
125_G128_N1.275431.023
31_D65_L1.275061.023
30_I52_I1.271971.021
37_F48_Y1.269471.018
36_A148_L1.268631.018
87_D91_K1.265721.015
81_V89_L1.259371.010
121_A127_N1.24861.002
98_S109_L1.238630.994
147_E150_D1.237470.993
135_V168_N1.233330.990
82_P85_E1.233120.989
33_L97_V1.231750.988
23_R27_E1.20610.968
32_L145_I1.198440.962
122_S140_F1.187820.953
90_Y115_C1.180160.947
64_N68_K1.179720.946
65_L68_K1.175980.943
124_I127_N1.170650.939
121_A139_L1.169270.938
51_V92_S1.157560.929
18_I97_V1.154850.927
18_I152_I1.148530.921
45_N157_N1.138710.914
78_L81_V1.130810.907
159_P162_R1.116260.896
31_D35_E1.116160.895
60_K63_K1.115580.895
159_P163_Q1.100370.883
20_F33_L1.10010.883
140_F148_L1.094540.878
60_K64_N1.08760.873
109_L127_N1.086070.871
117_C166_G1.083910.870
150_D154_K1.080340.867
113_M169_A1.060570.851
116_G167_K1.057640.849
63_K67_E1.056960.848
16_K48_Y1.056060.847
164_K167_K1.054870.846
24_L52_I1.052840.845
78_L89_L1.046510.840
32_L35_E1.045440.839
18_I37_F1.045360.839
99_P148_L1.044610.838
88_E92_S1.042990.837
19_L53_V1.040580.835
17_I93_S1.03990.834
126_G129_E1.039570.834
32_L143_N1.039310.834
96_F108_S1.038710.833
53_V81_V1.037250.832
66_I71_L1.035290.831
165_L168_N1.031550.828
97_V152_I1.029270.826
138_F161_L1.027540.824
133_D151_A1.022680.820
113_M119_V1.016940.816
121_A131_I1.005580.807
101_R143_N1.004570.806
120_I151_A0.993430.797
133_D136_N0.985010.790
28_K108_S0.979970.786
32_L122_S0.976420.783
66_I77_F0.969840.778
88_E91_K0.958370.769
16_K95_I0.95590.767
49_K74_N0.949130.761
28_K103_E0.948930.761
21_I53_V0.945780.759
103_E106_G0.941690.756
15_K47_N0.941460.755
163_Q166_G0.936460.751
56_G59_K0.936320.751
81_V86_L0.93560.751
89_L92_S0.935210.750
35_E69_L0.920490.739
109_L130_I0.918090.737
112_A117_C0.917770.736
106_G127_N0.917410.736
113_M136_N0.912120.732
155_L165_L0.907020.728
19_L89_L0.90350.725
138_F165_L0.903070.725
120_I140_F0.902390.724
40_L48_Y0.901580.723
113_M166_G0.892390.716
118_P155_L0.891470.715
150_D153_E0.880760.707
34_I66_I0.875030.702
32_L148_L0.874530.702
41_K45_N0.873690.701
146_E150_D0.868010.696
154_K157_N0.865210.694
35_E38_K0.862130.692
98_S127_N0.859740.690
33_L99_P0.857070.688
112_A119_V0.856370.687
36_A149_A0.849490.682
131_I135_V0.849050.681
38_K71_L0.848070.680
38_K41_K0.845560.678
131_I139_L0.838510.673
95_I155_L0.829860.666
120_I155_L0.827560.664
48_Y156_L0.825710.662
21_I90_Y0.825140.662
146_E149_A0.818650.657
109_L119_V0.817920.656
35_E39_K0.812840.652
108_S112_A0.812540.652
109_L121_A0.811630.651
94_D162_R0.80980.650
128_N139_L0.803730.645
110_L130_I0.803560.645
116_G166_G0.803170.644
160_E164_K0.800330.642
25_D57_E0.800210.642
64_N67_E0.799650.642
45_N48_Y0.798550.641
20_F99_P0.79830.640
61_E64_N0.796070.639
40_L152_I0.795670.638
90_Y117_C0.793610.637
23_R28_K0.791870.635
61_E65_L0.789320.633
95_I152_I0.789260.633
100_S104_G0.789050.633
16_K47_N0.788830.633
22_G28_K0.787760.632
107_L111_E0.783340.628
100_S108_S0.778980.625
40_L156_L0.777950.624
37_F74_N0.777690.624
95_I120_I0.777560.624
165_L169_A0.776550.623
58_Y62_L0.776120.623
160_E163_Q0.769760.618
36_A40_L0.768760.617
123_D139_L0.767930.616
138_F155_L0.763320.612
118_P166_G0.752280.604
20_F52_I0.749130.601
158_D162_R0.743950.597
136_N169_A0.743020.596
122_S148_L0.731250.587
40_L45_N0.728040.584
90_Y108_S0.723620.581
20_F50_L0.722550.580
27_E104_G0.722470.580
149_A152_I0.722070.579
63_K66_I0.719160.577
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
3s28A0.994299.9-0.034
3c48A0.994299.9-0.021
3okpA0.976799.9-0.012
2r60A199.9-0.012
2x6qA0.982699.9-0.006
3oy2A0.988499.9-0.004
3froA0.970999.9-0.003
2jjmA0.976799.90.012
2iw1A0.982699.90.016
2qzsA0.965199.90.039

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