GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CN_hydrolase - Carbon-nitrogen hydrolase
Pfam: PF00795 (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. )
Length: 186
Sequences: 8146
Seq/Len: 43.8
HH_delta: 0.128 (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
3_A35_A1.287462.724
102_S117_R1.223952.590
93_E117_R1.203742.547
145_E155_R1.199442.538
23_I44_A1.084832.295
15_D18_E1.065892.255
91_I104_V1.029112.177
159_L170_V1.009132.135
28_E82_E1.00272.122
24_L79_L0.92991.968
39_V182_I0.920891.948
156_I180_I0.919911.946
29_E33_Q0.918861.944
146_T154_G0.912581.931
157_G173_L0.910991.927
38_V85_I0.888011.879
28_E83_N0.876531.855
24_L75_R0.876331.854
100_Y117_R0.872121.845
80_A87_I0.854471.808
86_T105_V0.839391.776
86_T108_P0.829471.755
107_D113_L0.813081.720
5_V40_F0.805641.705
76_L89_A0.801321.695
103_A184_P0.800411.694
21_K25_S0.784951.661
88_V105_V0.782531.656
155_R179_D0.77711.644
102_S115_R0.776381.643
22_K25_S0.759871.608
77_A106_I0.756781.601
78_E82_E0.746281.579
103_A158_V0.743741.574
5_V38_V0.736881.559
159_L183_N0.735511.556
26_L29_E0.714331.511
162_Y166_F0.698391.478
105_V158_V0.693551.467
24_L28_E0.688981.458
88_V103_A0.672181.422
170_V181_L0.665151.407
23_I40_F0.663211.403
107_D111_E0.657361.391
37_L182_I0.647851.371
84_G108_P0.63971.353
25_S29_E0.635181.344
93_E102_S0.620211.312
22_K26_L0.614241.300
159_L169_L0.611321.293
88_V182_I0.61061.292
100_Y135_S0.609061.289
27_I38_V0.605271.281
86_T113_L0.592751.254
88_V158_V0.587631.243
154_G179_D0.585451.239
78_E81_K0.580161.228
29_E32_R0.569141.204
42_E161_C0.56621.198
168_E171_R0.564811.195
73_L104_V0.561291.188
17_E21_K0.560441.186
7_L26_L0.556141.177
106_I112_I0.550571.165
91_I115_R0.54191.147
27_I87_I0.539911.142
79_L83_N0.53951.141
120_H163_D0.535891.134
170_V183_N0.535771.134
28_E79_L0.535481.133
157_G178_A0.53451.131
66_E70_G0.527171.115
35_A38_V0.525621.112
73_L106_I0.522181.105
98_G135_S0.519271.099
118_K161_C0.514791.089
7_L23_I0.51071.081
178_A181_L0.510651.080
21_K75_R0.507361.073
20_L75_R0.506971.073
74_E78_E0.50591.070
164_L183_N0.504121.067
36_D108_P0.496711.051
45_L72_Y0.495271.048
20_L24_L0.493071.043
156_I182_I0.48151.019
27_I85_I0.480091.016
18_E21_K0.478761.013
172_E176_Q0.475051.005
162_Y165_R0.470450.995
86_T107_D0.464710.983
68_L73_L0.463760.981
24_L82_E0.463450.981
28_E32_R0.457670.968
74_E77_A0.454050.961
27_I40_F0.452760.958
43_M134_F0.4510.954
154_G180_I0.449790.952
171_R175_K0.448470.949
104_V115_R0.439910.931
93_E115_R0.439790.931
128_I132_R0.431770.914
101_N118_K0.430870.912
44_A89_A0.430450.911
23_I27_I0.427470.904
66_E72_Y0.425270.900
43_M48_Y0.424270.898
75_R78_E0.42280.895
1_R33_Q0.422590.894
18_E22_K0.421290.891
60_D63_E0.418520.886
37_L88_V0.415090.878
31_A83_N0.413040.874
70_G74_E0.412260.872
73_L112_I0.411590.871
16_P20_L0.408110.863
75_R79_L0.408020.863
77_A111_E0.404710.856
16_P19_N0.403830.854
12_S18_E0.401010.848
17_E71_P0.400130.847
116_Y163_D0.395770.837
93_E100_Y0.394350.834
26_L30_A0.393550.833
173_L178_A0.387940.821
1_R36_D0.385880.816
5_V26_L0.385830.816
27_I79_L0.384910.814
43_M92_P0.384130.813
37_L86_T0.37960.803
73_L77_A0.377110.798
159_L173_L0.375870.795
120_H166_F0.375650.795
119_I169_L0.374020.791
28_E31_A0.373780.791
72_Y75_R0.3730.789
40_F44_A0.372590.788
158_V184_P0.36980.782
116_Y142_P0.369060.781
25_S28_E0.365860.774
119_I172_E0.36330.769
12_S15_D0.363030.768
105_V144_F0.362150.766
70_G73_L0.361520.765
172_E175_K0.360260.762
21_K24_L0.359210.760
79_L82_E0.35870.759
46_P64_F0.357460.756
168_E172_E0.356710.755
3_A38_V0.356580.754
143_V176_Q0.355890.753
48_Y161_C0.348550.737
31_A35_A0.348210.737
17_E75_R0.347910.736
143_V155_R0.345950.732
23_I89_A0.343420.727
80_A83_N0.342450.725
114_G142_P0.341370.722
95_D100_Y0.34090.721
30_A38_V0.339630.719
39_V88_V0.338880.717
35_A85_I0.332570.704
23_I76_L0.330520.699
101_N161_C0.329450.697
165_R185_S0.328070.694
31_A34_G0.327570.693
141_F144_F0.326270.690
95_D98_G0.325630.689
160_I163_D0.324910.687
27_I30_A0.324450.686
7_L44_A0.322410.682
86_T146_T0.32210.682
30_A35_A0.321810.681
76_L87_I0.321570.680
16_P66_E0.317270.671
77_A81_K0.317080.671
20_L76_L0.31250.661
105_V156_I0.31190.660
130_E134_F0.311730.660
76_L79_L0.31110.658
43_M101_N0.30780.651
27_I83_N0.304830.645
32_R83_N0.304560.644
62_D94_R0.30310.641
58_F61_L0.296250.627
42_E101_N0.294430.623
169_L173_L0.293630.621
116_Y166_F0.293410.621
23_I26_L0.292690.619
157_G181_L0.288890.611
3_A30_A0.288670.611
101_N160_I0.288480.610
71_P74_E0.287740.609
16_P72_Y0.286050.605
58_F62_D0.285140.603
143_V178_A0.282320.597
61_L64_F0.282270.597
15_D19_N0.282170.597
30_A33_Q0.281260.595
104_V112_I0.280990.595
173_L181_L0.279060.590
7_L22_K0.278260.589
121_L134_F0.276030.584
2_V5_V0.274630.581
68_L104_V0.274560.581
95_D117_R0.273160.578
130_E137_G0.272740.577
81_K110_G0.27270.577
89_A106_I0.272330.576
43_M46_P0.271960.575
59_A63_E0.270380.572
114_G144_F0.269930.571
8_N22_K0.269880.571
24_L27_I0.269480.570
114_G158_V0.268810.569
20_L79_L0.268030.567
31_A85_I0.263260.557
60_D64_F0.263230.557
19_N47_G0.262940.556
45_L89_A0.262780.556
40_F89_A0.26150.553
93_E104_V0.261410.553
174_A178_A0.260920.552
73_L91_I0.260920.552
19_N23_I0.260450.551
171_R177_G0.256970.544
160_I166_F0.256890.544
42_E118_K0.256090.542
116_Y119_I0.252790.535
37_L105_V0.25130.532
62_D65_A0.250310.530
130_E133_Y0.24940.528
92_P134_F0.249320.528
140_P143_V0.24930.527
23_I45_L0.247780.524
77_A112_I0.247740.524
8_N12_S0.246840.522
8_N13_W0.246360.521
45_L91_I0.246090.521
174_A181_L0.245830.520
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
3ilvA0.93011000.128
3sdbA0.94621000.13
2vhhA0.95161000.137
3hkxA0.89781000.155
3n05A0.89781000.157
3p8kA0.90321000.159
4f4hA0.9141000.159
2w1vA0.90861000.159
3ivzA0.90321000.162
2e11A0.88171000.18

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