GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_tran_28_C - Glycosyltransferase family 28 C-terminal domain
Pfam: PF04101 (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: 167
Sequences: 36972
Seq/Len: 221.39
HH_delta: 0.104 (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
4_V73_A3.574943.139
76_V88_A3.37632.965
33_Q58_K3.270112.871
35_I60_F2.848932.502
24_L135_A2.778792.440
43_Y47_K2.550462.239
137_A140_E2.437132.140
28_K139_E2.382972.092
35_I58_K2.244891.971
5_T15_N2.148071.886
20_K131_P2.077331.824
140_E147_K2.02941.782
148_L152_A2.027791.781
144_D147_K2.018831.773
140_E144_D1.987961.746
139_E143_S1.925721.691
26_A56_N1.890151.660
67_A91_L1.869051.641
76_V93_K1.864921.637
133_E137_A1.814671.593
20_K49_K1.813851.593
122_I137_A1.770821.555
35_I69_L1.765121.550
14_L17_L1.760691.546
150_E154_A1.752191.539
24_L132_E1.729791.519
71_A91_L1.705691.498
147_K150_E1.700121.493
135_A139_E1.658131.456
37_Q69_L1.63181.433
99_P125_D1.631361.432
131_P135_A1.619181.422
22_L34_V1.598781.404
49_K53_F1.586161.393
35_I73_A1.579741.387
149_K153_K1.541671.354
122_I140_E1.524761.339
35_I72_A1.48321.302
99_P112_A1.482321.302
42_N45_E1.464371.286
24_L131_P1.458821.281
116_A119_G1.456281.279
39_G43_Y1.453071.276
73_A93_K1.427461.253
152_A155_A1.395291.225
65_N68_E1.375031.207
78_S84_T1.351041.186
68_E71_A1.328521.167
133_E136_E1.310441.151
23_E53_F1.294611.137
6_G66_M1.28251.126
147_K151_M1.27621.121
125_D133_E1.268281.114
68_E72_A1.264481.110
60_F63_V1.257961.105
122_I125_D1.244971.093
81_G86_A1.237571.087
115_L121_A1.237181.086
145_P149_K1.235351.085
22_L32_I1.228171.078
67_A71_A1.217641.069
25_L139_E1.210381.063
124_L137_A1.199341.053
3_L75_L1.192381.047
89_L155_A1.189921.045
93_K152_A1.18741.043
128_E133_E1.155611.015
145_P148_L1.155551.015
151_M154_A1.151091.011
66_M70_M1.146761.007
96_I137_A1.144841.005
92_G153_K1.141161.002
63_V69_L1.138751.000
8_S12_R1.132270.994
60_F69_L1.129580.992
37_Q63_V1.12570.988
75_L141_L1.125370.988
49_K52_N1.119360.983
136_E140_E1.116040.980
18_V34_V1.107050.972
23_E27_E1.092510.959
50_V53_F1.092160.959
37_Q60_F1.085090.953
70_M91_L1.084450.952
21_I134_L1.055460.927
69_L72_A1.054630.926
119_G154_A1.046560.919
116_A120_A1.046150.919
24_L27_E1.037050.911
24_L28_K1.032860.907
141_L151_M1.032850.907
50_V59_V1.025770.901
150_E153_K1.023970.899
77_I138_I1.023390.899
122_I147_K1.023120.898
44_E48_I1.022350.898
85_I111_N1.010910.888
13_D84_T1.008960.886
44_E47_K1.001670.880
89_L95_A1.000430.878
94_P141_L0.995980.875
17_L131_P0.995040.874
136_E139_E0.995030.874
76_V84_T0.993940.873
88_A95_A0.984060.864
48_I52_N0.982690.863
96_I141_L0.980180.861
23_E26_A0.974880.856
16_R20_K0.969620.851
122_I151_M0.965290.848
117_K120_A0.96520.847
98_I124_L0.955920.839
3_L77_I0.947740.832
78_S85_I0.947170.832
125_D128_E0.945310.830
111_N114_E0.932380.819
13_D16_R0.930620.817
89_L152_A0.930340.817
3_L138_I0.926020.813
39_G62_F0.925950.813
151_M155_A0.920270.808
21_I25_L0.91680.805
88_A93_K0.909220.798
84_T88_A0.909060.798
94_P152_A0.908440.798
15_N36_V0.902230.792
149_K152_A0.901090.791
32_I142_L0.900220.790
121_A125_D0.894220.785
45_E49_K0.892190.783
25_L32_I0.884060.776
124_L134_L0.880430.773
132_E136_E0.879240.772
79_H134_L0.872810.766
20_K23_E0.869470.763
28_K135_A0.867610.762
74_D148_L0.865440.760
47_K51_E0.863840.758
34_V38_T0.86060.756
18_V77_I0.858550.754
83_G87_E0.856360.752
25_L138_I0.846690.743
89_L120_A0.843430.741
92_G152_A0.841440.739
17_L127_S0.841390.739
45_E48_I0.835530.734
75_L96_I0.834870.733
28_K143_S0.83450.733
97_V111_N0.829870.729
63_V66_M0.829370.728
66_M69_L0.829180.728
48_I51_E0.827340.726
22_L56_N0.826170.725
20_K53_F0.819770.720
75_L138_I0.817920.718
132_E135_A0.817530.718
10_G41_N0.816020.717
140_E143_S0.81460.715
16_R49_K0.810940.712
69_L73_A0.810150.711
146_E150_E0.809420.711
144_D148_L0.806120.708
83_G86_A0.796970.700
19_L50_V0.795280.698
99_P123_M0.790750.694
75_L148_L0.789680.693
97_V123_M0.788640.692
17_L20_K0.785340.690
85_I95_A0.782350.687
146_E149_K0.775290.681
33_Q56_N0.770490.677
70_M93_K0.766180.673
6_G70_M0.759320.667
25_L135_A0.753330.661
82_A85_I0.749880.658
3_L22_L0.748720.657
58_K72_A0.744910.654
46_L49_K0.744720.654
98_I134_L0.734450.645
78_S111_N0.726170.638
33_Q74_D0.723490.635
116_A121_A0.721630.634
40_K43_Y0.719440.632
22_L25_L0.717140.630
85_I89_L0.71710.630
94_P148_L0.716090.629
135_A138_I0.715950.629
19_L49_K0.710050.623
85_I97_V0.706590.620
14_L19_L0.706440.620
102_G113_K0.705270.619
8_S13_D0.702860.617
27_E135_A0.702640.617
102_G111_N0.702590.617
36_V57_V0.697920.613
5_T18_V0.697280.612
66_M87_E0.691040.607
100_L111_N0.690440.606
17_L134_L0.69010.606
6_G9_Q0.689630.606
76_V95_A0.686950.603
9_Q36_V0.685310.602
120_A154_A0.685190.602
13_D19_L0.685030.601
50_V54_N0.683290.600
122_I141_L0.682520.599
70_M88_A0.676040.594
19_L23_E0.67390.592
21_I135_A0.673390.591
47_K50_V0.669290.588
20_K24_L0.666310.585
5_T79_H0.664060.583
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
3s28A0.940199.80.104
3okpA0.934199.80.104
2gekA0.934199.80.106
2x6qA0.928199.80.11
3c48A0.940199.80.111
2iw1A0.934199.80.115
2jjmA0.934199.80.119
3s2uA0.99499.80.133
3oy2A0.934199.80.133
3froA0.934199.80.137

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