GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glycos_transf_2 - Glycosyl transferase family 2
Pfam: PF00535 (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: CL0110
Length: 169
Sequences: 26392
Seq/Len: 156.17
HH_delta: -0.021 (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
162_R166_E2.954263.137
10_A40_E2.742632.912
9_E87_D2.543982.701
34_D59_R2.262182.402
60_N72_R2.164612.298
81_Y103_L2.099852.229
29_E56_R2.077412.206
1_S79_G2.053572.180
42_E46_E1.994212.117
3_V73_G1.983872.106
42_E59_R1.978552.101
33_V73_G1.941212.061
72_R76_H1.895412.012
1_S29_E1.872571.988
6_T41_T1.851.964
14_E18_E1.821751.934
40_E43_E1.805041.916
66_F70_R1.803391.915
18_E48_Y1.798911.910
83_L159_L1.74671.855
14_E44_I1.702221.807
10_A44_I1.648091.750
70_R86_D1.647841.750
99_L159_L1.643841.745
34_D37_S1.6311.732
24_T97_E1.618981.719
81_Y159_L1.549411.645
4_I30_I1.520191.614
8_N38_T1.512831.606
15_R90_I1.501991.595
103_L159_L1.495861.588
91_I95_W1.481961.573
70_R84_F1.478441.570
4_I16_T1.470561.561
58_I76_H1.442031.531
42_E57_Y1.403141.490
14_E48_Y1.390211.476
60_N64_L1.386391.472
64_L68_A1.376591.462
14_E47_E1.371941.457
72_R75_K1.363021.447
46_E59_R1.357531.441
7_Y63_N1.348481.432
74_I165_F1.33791.420
85_L91_I1.336791.419
56_R76_H1.295271.375
98_E101_E1.26881.347
102_A106_N1.252761.330
8_N37_S1.246281.323
6_T87_D1.212721.288
58_I72_R1.211591.286
1_S77_A1.208031.283
29_E79_G1.207621.282
83_L95_W1.202641.277
163_S167_E1.202451.277
32_V45_L1.200531.275
95_W99_L1.188091.261
102_A105_K1.173751.246
45_L57_Y1.171131.243
6_T32_V1.165191.237
25_D100_V1.16251.234
44_I47_E1.153591.225
33_V69_A1.15241.224
109_D161_R1.152131.223
101_E105_K1.135921.206
83_L96_L1.131291.201
94_D98_E1.130991.201
97_E101_E1.127081.197
82_I162_R1.121781.191
9_E12_Y1.119871.189
66_F86_D1.116961.186
43_E47_E1.115311.184
81_Y100_V1.106861.175
67_S71_N1.100641.169
6_T9_E1.100261.168
19_S91_I1.090321.158
60_N68_A1.075611.142
44_I48_Y1.074911.141
74_I84_F1.068921.135
163_S166_E1.05721.122
17_L48_Y1.049121.114
29_E78_K1.047471.112
60_N69_A1.045491.110
34_D42_E1.035881.100
66_F155_G1.035441.099
161_R164_V1.034411.098
18_E22_K1.031381.095
19_S90_I1.023971.087
5_P69_A1.018481.081
17_L32_V1.012181.075
106_N109_D1.001251.063
74_I82_I0.997291.059
25_D28_F0.986421.047
21_L52_D0.983191.044
1_S31_I0.980791.041
100_V104_E0.967211.027
43_E46_E0.963211.023
103_L161_R0.941981.000
40_E44_I0.940970.999
81_Y161_R0.923680.981
71_N75_K0.916440.973
35_D60_N0.8890.944
17_L30_I0.882250.937
77_A162_R0.877970.932
83_L91_I0.867320.921
7_Y35_D0.858340.911
2_V20_L0.852560.905
35_D63_N0.851520.904
21_L54_N0.84430.896
2_V83_L0.826520.878
99_L103_L0.821640.872
16_T19_S0.815440.866
164_V168_I0.814460.865
15_R18_E0.798420.848
18_E21_L0.794450.843
10_A14_E0.780750.829
20_L85_L0.780750.829
35_D69_A0.780050.828
22_K93_P0.772290.820
24_T27_D0.770330.818
30_I55_I0.767680.815
101_E104_E0.764460.812
119_D123_R0.759260.806
31_I56_R0.754040.801
95_W98_E0.750670.797
77_A82_I0.750260.797
94_D97_E0.750210.797
99_L102_A0.749690.796
33_V72_R0.737910.783
31_I73_G0.724690.769
13_L87_D0.720940.765
56_R78_K0.718410.763
16_T85_L0.692860.736
23_Q97_E0.691950.735
164_V167_E0.683370.726
98_E102_A0.675010.717
15_R19_S0.673510.715
82_I165_F0.672920.714
68_A72_R0.671570.713
33_V60_N0.670610.712
4_I20_L0.670340.712
155_G158_A0.667010.708
100_V159_L0.663320.704
84_F160_F0.663280.704
80_E161_R0.661310.702
35_D65_G0.661170.702
95_W157_C0.660750.702
41_T45_L0.654430.695
19_S94_D0.6540.694
66_F69_A0.652380.693
126_D129_L0.64380.684
6_T13_L0.637820.677
92_S95_W0.637020.676
5_P70_R0.635460.675
52_D55_I0.634370.674
20_L30_I0.633170.672
81_Y104_E0.632330.671
99_L157_C0.627320.666
21_L48_Y0.626560.665
118_I122_N0.622230.661
60_N63_N0.622110.661
13_L45_L0.620850.659
16_T20_L0.620430.659
160_F165_F0.618970.657
86_D155_G0.61740.656
17_L21_L0.616080.654
74_I77_A0.615390.653
3_V33_V0.613870.652
6_T45_L0.610580.648
66_F84_F0.607940.645
46_E57_Y0.605190.643
1_S162_R0.603620.641
31_I76_H0.603530.641
4_I87_D0.602340.640
36_G63_N0.601850.639
28_F96_L0.59370.630
16_T87_D0.593470.630
89_D157_C0.592960.630
70_R74_I0.591590.628
108_P112_I0.586180.622
17_L52_D0.584380.620
83_L157_C0.581590.617
65_G69_A0.581390.617
9_E13_L0.577950.614
21_L55_I0.575760.611
2_V28_F0.574770.610
123_R126_D0.573290.609
4_I32_V0.570460.606
111_V114_S0.567850.603
10_A39_D0.567630.603
31_I77_A0.567180.602
3_V77_A0.566590.602
25_D97_E0.566450.601
1_S78_K0.564990.600
12_Y15_R0.564520.599
140_K144_N0.562350.597
12_Y16_T0.56180.596
80_E163_S0.558940.593
19_S22_K0.558150.593
105_K108_P0.548310.582
153_F158_A0.548210.582
123_R127_R0.541190.575
9_E86_D0.540390.574
20_L91_I0.539770.573
5_P87_D0.534610.568
24_T28_F0.534320.567
5_P35_D0.531890.565
61_P64_L0.52390.556
35_D64_L0.523840.556
7_Y36_G0.522740.555
110_V114_S0.522180.554
71_N165_F0.52210.554
75_K166_E0.521750.554
2_V96_L0.518510.551
85_L89_D0.518060.550
13_L44_I0.515420.547
124_Y129_L0.515240.547
10_A13_L0.514710.546
28_F54_N0.513650.545
137_F140_K0.513540.545
79_G162_R0.513480.545
122_N125_P0.511950.544
76_H80_E0.511160.543
91_I157_C0.509720.541
45_L55_I0.507910.539
119_D126_D0.507080.538
56_R59_R0.506790.538
6_T34_D0.506460.538
41_T44_I0.506040.537
64_L72_R0.50540.537
10_A43_E0.505330.537
151_S154_I0.504080.535
89_D156_S0.502120.533
83_L99_L0.501950.533
103_L111_V0.50150.532
69_A86_D0.499690.531
122_N126_D0.496620.527
84_F158_A0.49450.525
36_G60_N0.492260.523
59_R62_E0.492130.523
69_A72_R0.491840.522
89_D155_G0.491510.522
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
3l7iA0.964599.9-0.021
3bcvA0.994199.90.019
2d7iA199.90.021
1qg8A0.934999.90.026
1xhbA199.90.028
2z86A0.940899.90.055
2ffuA0.982299.90.067
4fixA0.994199.90.069
3ckjA0.994199.90.098
4hg6A0.994199.90.101

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