GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4066 - Putative amidotransferase
Pfam: PF13278 (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: CL0014
Length: 166
Sequences: 7266
Seq/Len: 43.77
HH_delta: 0.019 (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
115_R146_G1.28232.892
33_R62_F1.174672.650
115_R145_D1.059192.389
17_V165_I1.051912.373
41_P51_Q0.956952.159
116_R135_N0.943492.128
33_R54_G0.936252.112
112_L117_A0.926192.089
124_A128_R0.91972.075
113_D133_N0.897532.025
116_R137_V0.844411.905
36_S39_G0.802011.809
115_R148_I0.795081.793
127_L136_V0.77241.742
126_A129_E0.77141.740
6_F44_S0.763281.722
15_L19_R0.729471.645
90_H96_I0.728331.643
57_D81_A0.715451.614
144_D163_Y0.712961.608
89_Q94_T0.705231.591
90_H147_N0.689551.555
88_Q92_Q0.685311.546
8_L12_A0.67751.528
55_S58_D0.674391.521
6_F11_L0.667561.506
37_P79_D0.666951.504
84_D87_R0.661221.491
115_R147_N0.660651.490
98_A150_T0.655111.478
144_D149_I0.653671.474
116_R145_D0.653291.474
117_A134_V0.647411.460
4_P43_T0.646531.458
21_A165_I0.646241.458
116_R133_N0.63631.435
64_I95_Y0.633891.430
126_A130_R0.629341.420
140_Q159_D0.626651.414
151_A156_A0.626311.413
80_P84_D0.62471.409
84_D88_Q0.62451.409
108_E130_R0.61751.393
83_L87_R0.610281.377
90_H148_I0.599051.351
81_A84_D0.593881.340
93_G147_N0.59381.339
127_L132_P0.584631.319
98_A106_L0.569781.285
9_L13_G0.566151.277
87_R91_A0.560871.265
85_W89_Q0.551061.243
103_A119_T0.550271.241
18_L161_A0.543921.227
43_T49_R0.541261.221
2_L34_L0.540421.219
107_A134_V0.538991.216
63_D94_T0.53861.215
90_H111_L0.536121.209
97_A164_L0.528321.192
93_G96_I0.528271.192
13_G16_D0.527061.189
11_L34_L0.526691.188
41_P49_R0.522771.179
15_L34_L0.522741.179
16_D20_A0.521981.177
97_A160_L0.521841.177
41_P52_P0.508861.148
116_R140_Q0.508181.146
54_G58_D0.506941.143
2_L11_L0.50621.142
6_F50_I0.503191.135
118_T143_V0.500291.128
116_R143_V0.499621.127
83_L109_A0.498091.124
149_I160_L0.495421.117
49_R53_D0.477211.076
8_L48_L0.475161.072
65_L89_Q0.468441.057
108_E131_F0.467051.054
83_L108_E0.46331.045
110_G113_D0.463071.045
131_F134_V0.462561.043
15_L32_V0.458841.035
16_D19_R0.455581.028
142_F163_Y0.454511.025
66_V97_A0.454441.025
104_L126_A0.453781.024
67_V105_L0.451991.020
101_T123_L0.450871.017
120_H153_G0.438650.989
13_G158_I0.438210.988
88_Q91_A0.42990.970
95_Y149_I0.427660.965
2_L6_F0.427230.964
36_S52_P0.426130.961
37_P81_A0.424010.956
67_V86_L0.422960.954
62_F89_Q0.422180.952
144_D147_N0.420330.948
14_P66_V0.420020.947
39_G55_S0.419750.947
125_E129_E0.417250.941
149_I164_L0.416330.939
90_H93_G0.413470.933
127_L131_F0.412620.931
37_P56_L0.412170.930
137_V140_Q0.408910.922
98_A103_A0.406270.916
59_A89_Q0.405040.914
95_Y147_N0.403070.909
158_I162_L0.393110.887
35_V54_G0.392580.886
30_F64_I0.3910.882
141_L159_D0.388990.877
67_V102_G0.387340.874
14_P157_A0.383420.865
142_F149_I0.380860.859
35_V85_W0.376270.849
11_L15_L0.375960.848
98_A102_G0.375170.846
123_L126_A0.374220.844
59_A88_Q0.373290.842
90_H115_R0.36720.828
59_A85_W0.36690.828
35_V62_F0.36590.825
78_K108_E0.364450.822
119_T134_V0.362490.818
59_A62_F0.360910.814
83_L86_L0.360520.813
33_R53_D0.356940.805
60_P88_Q0.35670.805
77_A108_E0.356650.804
64_I164_L0.352230.795
67_V82_L0.349930.789
159_D162_L0.348850.787
80_P87_R0.345830.780
7_S16_D0.344590.777
117_A127_L0.343410.775
13_G157_A0.340550.768
6_F68_P0.339220.765
74_D126_A0.338110.763
10_E154_P0.335380.756
10_E14_P0.335330.756
30_F63_D0.330760.746
64_I97_A0.330760.746
99_I157_A0.329250.743
106_L150_T0.328820.742
62_F65_L0.326850.737
61_D92_Q0.326820.737
14_P18_L0.326710.737
8_L44_S0.325530.734
125_E128_R0.322770.728
76_A79_D0.321310.725
66_V160_L0.317950.717
15_L48_L0.317390.716
17_V20_A0.316980.715
10_E69_G0.316780.715
8_L46_S0.316710.714
30_F165_I0.315930.713
87_R109_A0.315540.712
120_H123_L0.312330.705
96_I147_N0.310930.701
151_A160_L0.310680.701
104_L131_F0.309510.698
95_Y164_L0.309110.697
8_L45_S0.308430.696
142_F160_L0.307920.695
89_Q92_Q0.30780.694
149_I163_Y0.306010.690
18_L164_L0.303960.686
86_L109_A0.303270.684
86_L96_I0.303080.684
3_F72_G0.301930.681
111_L148_I0.299780.676
39_G52_P0.298580.673
4_P38_T0.296530.669
60_P92_Q0.294570.664
106_L109_A0.294530.664
141_L144_D0.291850.658
152_G156_A0.290380.655
97_A149_I0.289560.653
14_P154_P0.28890.652
107_A110_G0.288410.651
69_G154_P0.288040.650
121_W134_V0.287680.649
117_A132_P0.286960.647
94_T147_N0.286580.646
18_L30_F0.286290.646
13_G161_A0.285720.644
67_V98_A0.28330.639
67_V109_A0.28220.637
11_L68_P0.280340.632
141_L152_G0.279410.630
21_A30_F0.276940.625
47_G50_I0.27690.625
107_A127_L0.27670.624
114_G133_N0.276470.624
7_S100_C0.273880.618
40_G51_Q0.273720.617
18_L32_V0.272820.615
34_L37_P0.271880.613
113_D131_F0.27180.613
107_A112_L0.271330.612
52_P55_S0.271020.611
107_A132_P0.269830.609
157_A161_A0.269720.608
86_L111_L0.269480.608
85_W88_Q0.269350.608
17_V162_L0.268230.605
79_D82_L0.267060.602
96_I148_I0.266730.602
141_L156_A0.26470.597
99_I154_P0.262220.591
5_G43_T0.26220.591
22_N30_F0.260140.587
121_W153_G0.258860.584
13_G17_V0.256940.580
7_S45_S0.256930.580
87_R111_L0.256760.579
9_L157_A0.254970.575
9_L16_D0.253980.573
124_A136_V0.253610.572
56_L82_L0.253440.572
65_L86_L0.252830.570
10_E99_I0.252580.570
10_E100_C0.252120.569
8_L11_L0.251920.568
74_D77_A0.251820.568
14_P161_A0.249810.563
74_D78_K0.24970.563
104_L123_L0.247620.559
36_S42_V0.246250.555
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
3er6A11000.019
3graA0.96991000.044
3mgkA0.96991000.06
3efeA0.9881000.084
4hcjA0.93981000.087
3fseA0.93981000.089
3noqA0.94581000.091
3l18A0.93981000.108
3ewnA0.94581000.109
2rk3A0.94581000.114

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