GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glu_cyclase_2 - Glutamine cyclotransferase
Pfam: PF05096 (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: CL0186
Length: 264
Sequences: 27365
Seq/Len: 103.66
HH_delta: 0.149 (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
143_I153_F1.325892.773
49_G62_T1.271792.659
51_E94_G1.139732.383
112_G144_M1.035632.166
74_D77_T1.03382.162
201_D204_T1.006652.105
116_D119_T0.972412.033
113_F125_T0.97162.032
60_E72_K0.971472.031
144_M154_L0.936661.959
152_Y164_T0.913611.910
71_R80_V0.912091.907
113_F122_K0.90911.901
141_R153_F0.900931.884
151_L190_N0.891091.863
235_G249_G0.88641.854
90_Y93_E0.876391.833
42_D61_S0.842631.762
198_V210_W0.840561.758
71_R83_S0.831211.738
61_S73_V0.824161.723
48_Q64_L0.822871.721
161_E164_T0.820571.716
152_Y161_E0.819681.714
155_D158_T0.804521.682
197_I248_T0.803521.680
70_L105_L0.77381.618
198_V207_V0.773481.617
69_S83_S0.773321.617
94_G134_G0.75371.576
247_V257_E0.742061.552
190_N200_I0.741011.550
244_R257_E0.740761.549
60_E103_Y0.73451.536
200_I207_V0.720041.506
101_K114_V0.716761.499
173_P177_L0.713461.492
53_L95_I0.709661.484
248_T258_V0.708431.481
234_N251_L0.707781.480
92_G106_T0.704091.472
80_V83_S0.701371.467
96_T135_L0.69911.462
122_K125_T0.697331.458
53_L57_T0.695171.454
103_Y114_V0.691141.445
105_L115_Y0.682391.427
189_A238_Y0.667691.396
239_D244_R0.664271.389
115_Y122_K0.663921.388
141_R144_M0.652441.364
207_V210_W0.648281.356
104_Q115_Y0.645741.350
57_T74_D0.62121.299
146_D150_R0.616441.289
60_E95_I0.616311.289
143_I188_Y0.608171.272
96_T99_G0.607351.270
186_K199_R0.605651.266
136_T140_K0.605221.266
73_V80_V0.603381.262
111_T125_T0.598891.252
154_L161_E0.595371.245
249_G252_W0.590141.234
63_G69_S0.584121.221
51_E95_I0.573171.199
53_L56_G0.570481.193
65_Y69_S0.566011.184
188_Y199_R0.565971.184
196_R210_W0.563231.178
189_A199_R0.562041.175
146_D152_Y0.560251.172
104_Q107_W0.559991.171
53_L58_L0.556211.163
63_G66_G0.55381.158
173_P176_N0.55181.154
101_K104_Q0.549511.149
52_F75_L0.549171.148
106_T109_E0.545121.140
246_F257_E0.541561.132
104_Q142_L0.540311.130
150_R164_T0.537461.124
93_E97_I0.53081.110
91_F108_K0.52791.104
239_D243_D0.524531.097
104_Q114_V0.524071.096
107_W111_T0.51981.087
180_L183_I0.518331.084
191_V233_L0.517791.083
194_T198_V0.51491.077
86_L89_R0.512891.073
174_V177_L0.512231.071
47_T50_L0.503851.054
250_K254_K0.503741.053
132_G145_S0.497381.040
148_S152_Y0.497131.040
90_Y97_I0.496021.037
140_K157_E0.494131.033
62_T90_Y0.49381.033
138_D141_R0.493381.032
190_N198_V0.488631.022
86_L90_Y0.487761.020
239_D242_T0.487131.019
214_S248_T0.484081.012
153_F165_I0.482211.008
192_W196_R0.480931.006
51_E93_E0.480081.004
86_L105_L0.479741.003
94_G97_I0.47871.001
252_W256_Y0.478691.001
213_L258_V0.474410.992
74_D79_K0.472450.988
199_R211_I0.469990.983
43_P61_S0.469880.983
250_K253_P0.469670.982
241_E244_R0.468160.979
74_D81_L0.464330.971
50_L61_S0.460510.963
129_P146_D0.459660.961
132_G135_L0.459380.961
60_E93_E0.458910.960
90_Y95_I0.458180.958
165_I168_T0.457620.957
238_Y245_L0.45720.956
199_R238_Y0.45570.953
93_E96_T0.449570.940
197_I236_I0.445710.932
49_G92_G0.444860.930
244_R259_K0.442210.925
169_D173_P0.442130.925
52_F59_Y0.440640.921
233_L236_I0.44050.921
69_S85_P0.439350.919
72_K81_L0.438350.917
186_K201_D0.438060.916
128_Y154_L0.436730.913
239_D246_F0.43630.912
41_H61_S0.434910.909
191_V194_T0.428630.896
57_T76_E0.425250.889
144_M152_Y0.424070.887
199_R208_V0.422750.884
72_K95_I0.420750.880
111_T127_P0.418890.876
201_D208_V0.417610.873
182_Y238_Y0.416070.870
57_T72_K0.41550.869
62_T65_Y0.415260.868
49_G93_E0.415080.868
131_E147_G0.414420.867
231_D251_L0.413510.865
114_V124_G0.412160.862
117_P120_L0.411870.861
150_R166_Q0.411470.860
52_F238_Y0.411040.860
114_V126_F0.410160.858
176_N182_Y0.408490.854
91_F107_W0.407240.852
124_G159_F0.407040.851
248_T252_W0.406180.849
116_D123_I0.40310.843
182_Y185_G0.40290.843
103_Y135_L0.402130.841
153_F163_R0.400790.838
189_A236_I0.39940.835
174_V180_L0.398250.833
42_D47_T0.393930.824
75_L78_G0.392460.821
96_T101_K0.392330.820
214_S250_K0.391150.818
142_L156_P0.39080.817
129_P144_M0.390610.817
61_S71_R0.389990.816
181_E238_Y0.38980.815
183_I186_K0.386740.809
163_R205_G0.386180.808
41_H73_V0.386110.807
126_F129_P0.383780.803
94_G135_L0.382030.799
249_G254_K0.381750.798
86_L115_Y0.380440.796
53_L59_Y0.379820.794
129_P148_S0.379090.793
141_R162_V0.378780.792
59_Y72_K0.377390.789
50_L59_Y0.376680.788
248_T256_Y0.375160.785
141_R155_D0.374560.783
119_T123_I0.374210.783
193_Q232_V0.372570.779
151_L188_Y0.371380.777
112_G126_F0.371010.776
186_K189_A0.370750.775
93_E105_L0.370370.774
48_Q234_N0.369760.773
86_L113_F0.369690.773
192_W198_V0.368820.771
166_Q169_D0.36880.771
119_T122_K0.36560.765
65_Y71_R0.365350.764
191_V236_I0.364860.763
95_I117_P0.364640.763
62_T93_E0.364540.762
168_T174_V0.362010.757
124_G127_P0.359160.751
109_E113_F0.359010.751
177_L182_Y0.358080.749
84_V87_P0.356550.746
188_Y238_Y0.355950.744
99_G102_L0.355760.744
142_L145_S0.35550.743
189_A246_F0.352970.738
55_D58_L0.351560.735
90_Y94_G0.350520.733
86_L104_Q0.350450.733
41_H71_R0.349710.731
72_K82_Q0.347530.727
162_V166_Q0.346750.725
192_W195_D0.345580.723
41_H47_T0.34520.722
156_P159_F0.345080.722
155_D162_V0.344260.720
39_Y42_D0.342960.717
136_T139_G0.341560.714
48_Q91_F0.338440.708
59_Y75_L0.33620.703
196_R212_D0.33590.702
61_S65_Y0.334830.700
70_L93_E0.334340.699
189_A192_W0.332960.696
54_D95_I0.331880.694
177_L180_L0.331470.693
37_E40_P0.330990.692
116_D121_K0.330440.691
188_Y192_W0.330020.690
81_L84_V0.327770.685
186_K203_E0.327520.685
232_V251_L0.327510.685
114_V123_I0.327170.684
189_A200_I0.326460.683
42_D63_G0.326420.683
135_L142_L0.32460.679
155_D160_K0.324320.678
141_R202_P0.32420.678
250_K256_Y0.324110.678
112_G142_L0.322870.675
58_L72_K0.322790.675
51_E60_E0.321940.673
202_P205_G0.321210.672
247_V258_V0.320830.671
143_I180_L0.320720.671
199_R209_G0.318250.666
187_I190_N0.317850.665
143_I151_L0.317570.664
250_K258_V0.316240.661
104_Q133_W0.316230.661
140_K143_I0.315530.660
132_G136_T0.315230.659
215_G231_D0.314630.658
103_Y142_L0.314610.658
243_D259_K0.314360.657
70_L104_Q0.313340.655
188_Y246_F0.31120.651
136_T141_R0.311160.651
70_L255_L0.309530.647
92_G105_L0.309360.647
172_R177_L0.309030.646
163_R167_V0.308680.645
40_P43_P0.307530.643
96_T100_D0.307290.643
209_G213_L0.30670.641
37_E78_G0.306670.641
92_G96_T0.305940.640
181_E184_N0.304970.638
191_V196_R0.304110.636
66_G69_S0.303510.635
173_P180_L0.303040.634
172_R176_N0.302770.633
190_N194_T0.30260.633
213_L256_Y0.300650.629
86_L109_E0.298690.625
82_Q85_P0.297590.622
208_V213_L0.294560.616
168_T190_N0.293920.615
47_T62_T0.293830.614
42_D65_Y0.293380.613
42_D71_R0.291970.611
168_T192_W0.29160.610
172_R175_S0.291520.610
53_L72_K0.291490.610
141_R145_S0.290470.607
72_K84_V0.289630.606
128_Y152_Y0.289520.605
101_K118_N0.289510.605
102_L105_L0.28940.605
92_G97_I0.289390.605
146_D154_L0.289220.605
214_S231_D0.288460.603
102_L106_T0.287340.601
191_V198_V0.286510.599
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
4gqbB0.91671000.149
1vyhC0.912999.90.193
4gqbB0.916799.90.194
2ynnA0.916799.90.216
4j73A0.916799.90.219
2oajA0.871299.90.221
1vyhC0.897799.90.221
3ow8A0.901599.90.229
4j0xA0.965999.90.236
3ow8A0.909199.90.24

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