GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Chorismate_bind - chorismate binding enzyme
Pfam: PF00425 (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: 257
Sequences: 3832
Seq/Len: 14.91
HH_delta: -0.011 (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
181_V205_A0.967243.539
91_R106_E0.791092.894
2_R6_K0.75892.776
15_H20_E0.753672.757
81_R159_S0.747782.736
246_D249_A0.73442.687
5_Y239_A0.721292.639
140_P159_S0.718922.630
188_R191_E0.683882.502
147_R152_Q0.664712.432
90_T151_V0.636972.330
209_G219_F0.632252.313
31_E232_R0.625482.288
15_H195_E0.613232.243
141_D144_E0.593052.170
6_K248_E0.590972.162
110_S113_E0.58672.146
31_E234_R0.583592.135
138_E159_S0.565252.068
84_T124_I0.561542.054
12_A24_V0.561392.054
21_L189_A0.556272.035
93_R100_D0.555132.031
71_R218_E0.550262.013
14_E18_A0.546752.000
101_A105_E0.540151.976
2_R248_E0.538311.969
57_F66_G0.535751.960
1_S4_D0.530011.939
105_E109_W0.528871.935
28_R254_T0.522351.911
178_T221_V0.508381.860
163_K166_V0.499251.826
104_A147_R0.497591.820
78_G161_R0.491171.797
33_P232_R0.489311.790
7_Q10_R0.489241.790
12_A26_L0.480381.757
9_V247_P0.466911.708
23_K240_G0.464591.700
85_E146_E0.463641.696
81_R161_R0.459521.681
29_R234_R0.458261.677
64_F203_W0.457681.674
94_G99_E0.443821.624
228_I233_A0.442811.620
40_P63_A0.441191.614
87_L155_V0.440221.611
104_A145_I0.438261.603
60_Q63_A0.436851.598
21_L24_V0.433631.586
57_F208_V0.432761.583
24_V193_I0.428871.569
252_E256_L0.426851.562
2_R251_W0.417791.528
192_F196_L0.416751.525
99_E102_E0.415511.520
166_V170_D0.413131.511
248_E252_E0.410551.502
131_I174_A0.403391.476
39_D42_A0.403211.475
251_W255_E0.402821.474
101_A104_A0.401731.470
11_K15_H0.394161.442
15_H192_F0.392161.435
76_D216_D0.390771.430
97_P101_A0.382881.401
14_E17_R0.37881.386
102_E106_E0.378511.385
212_D216_D0.378141.383
21_L192_F0.372741.364
83_E157_D0.36941.351
226_A233_A0.359951.317
44_F48_R0.359781.316
11_K14_E0.356841.305
10_R247_P0.353541.293
4_D198_P0.352191.288
146_E155_V0.352121.288
6_K247_P0.350671.283
129_S135_G0.348761.276
94_G103_L0.345271.263
4_D7_Q0.345221.263
108_L154_L0.343831.258
113_E249_A0.34361.257
6_K10_R0.343051.255
118_R143_P0.34011.244
99_E103_L0.338591.239
26_L241_I0.338431.238
10_R13_Q0.336321.230
20_E188_R0.334961.225
82_L160_G0.334661.224
249_A252_E0.331421.212
40_P228_I0.33061.209
13_Q17_R0.329091.204
27_A236_Y0.3281.200
33_P231_G0.326811.196
203_W222_A0.325031.189
95_A99_E0.323211.182
74_R83_E0.319741.170
32_L233_A0.31541.154
145_I154_L0.315121.153
96_D99_E0.314381.150
2_R252_E0.312431.143
10_R14_E0.312271.142
82_L128_L0.308851.130
65_V228_I0.308191.127
77_G216_D0.307751.126
16_I243_A0.306031.120
58_Y63_A0.303951.112
43_L228_I0.303251.109
25_V238_G0.29921.095
123_L179_P0.298961.094
82_L171_L0.298021.090
4_D8_A0.297991.090
115_A119_M0.295591.081
9_V13_Q0.295081.080
66_G220_A0.295041.079
91_R113_E0.294551.078
15_H188_R0.292141.069
203_W227_Q0.291811.068
41_L58_Y0.291791.067
172_L219_F0.285171.043
208_V222_A0.283481.037
140_P157_D0.282161.032
55_Y71_R0.279291.022
3_E7_Q0.279171.021
114_R143_P0.278741.020
13_Q243_A0.276621.012
59_F208_V0.276241.011
103_L106_E0.276091.010
3_E6_K0.274231.003
145_I152_Q0.273651.001
43_L65_V0.273641.001
28_R255_E0.272750.998
7_Q11_K0.268230.981
172_L211_I0.266750.976
29_R199_F0.265480.971
141_D157_D0.265150.970
105_E108_L0.263320.963
74_R218_E0.263020.962
239_A254_T0.2630.962
144_E157_D0.262780.961
72_L175_L0.259910.951
73_F217_G0.259680.950
121_V142_L0.259430.949
12_A21_L0.258820.947
88_A117_H0.257880.943
8_A198_P0.257820.943
88_A180_A0.257770.943
11_K195_E0.255460.935
75_V78_G0.253140.926
26_L239_A0.252890.925
210_W218_E0.252370.923
102_E105_E0.252160.923
194_R200_P0.252150.922
77_G81_R0.250590.917
188_R195_E0.250370.916
181_V223_I0.249580.913
25_V205_A0.247680.906
85_E157_D0.246540.902
113_E242_V0.243490.891
75_V82_L0.242410.887
75_V171_L0.241560.884
98_E102_E0.241160.882
47_L67_A0.24030.879
83_E159_S0.239380.876
91_R103_L0.239130.875
104_A152_Q0.238540.873
85_E155_V0.238270.872
72_L88_A0.238070.871
169_L211_I0.237920.870
120_V180_A0.236930.867
123_L127_D0.236530.865
182_T190_L0.23570.862
118_R142_L0.234150.857
136_S161_R0.233910.856
192_F195_E0.233910.856
13_Q244_D0.233090.853
51_N150_N0.232410.850
66_G208_V0.231150.846
9_V241_I0.231150.846
162_L171_L0.229680.840
25_V181_V0.226950.830
92_P256_L0.226670.829
117_H156_S0.226110.827
56_V67_A0.226060.827
75_V168_L0.225560.825
40_P58_Y0.223280.817
8_A12_A0.223240.817
17_R243_A0.223210.817
92_P103_L0.223140.816
124_I178_T0.222870.815
134_C160_G0.22230.813
253_E257_K0.221190.809
72_L84_T0.21920.802
78_G164_P0.218760.800
9_V26_L0.218570.800
117_H121_V0.218440.799
28_R251_W0.218130.798
250_E253_E0.216710.793
88_A120_V0.216320.791
245_S250_E0.213680.782
161_R164_P0.213320.780
207_P219_F0.213310.780
73_F175_L0.213010.779
64_F208_V0.212820.779
85_E141_D0.211770.775
252_E255_E0.211630.774
6_K9_V0.210430.770
27_A199_F0.208590.763
199_F236_Y0.208510.763
108_L145_I0.208440.763
42_A46_R0.207560.759
250_E257_K0.20520.751
143_P154_L0.204880.750
98_E101_A0.203810.746
75_V162_L0.203650.745
8_A26_L0.203310.744
117_H120_V0.201570.737
12_A241_I0.200790.735
38_I43_L0.19980.731
111_E115_A0.199360.729
117_H205_A0.19880.727
187_E191_E0.198590.727
57_F64_F0.196170.718
12_A192_F0.1960.717
227_Q234_R0.195390.715
15_H18_A0.195090.714
10_R17_R0.194090.710
57_F225_S0.1940.710
73_F219_F0.193890.709
94_G100_D0.193350.707
167_S170_D0.19270.705
10_R248_E0.192210.703
71_R85_E0.192070.703
114_R118_R0.191720.701
71_R74_R0.191630.701
84_T175_L0.191350.700
124_I221_V0.191310.700
30_F237_A0.191150.699
36_S228_I0.18960.694
229_D234_R0.189390.693
127_D186_K0.188710.690
187_E190_L0.187810.687
229_D232_R0.187570.686
103_L152_Q0.18750.686
120_V179_P0.186940.684
44_F65_V0.186810.683
25_V189_A0.185930.680
24_V192_F0.185380.678
129_S137_V0.185210.678
43_L226_A0.185150.677
114_R142_L0.184170.674
6_K251_W0.183940.673
226_A235_L0.182830.669
13_Q247_P0.181610.664
92_P95_A0.180750.661
82_L162_L0.180670.661
63_A228_I0.180330.660
204_Y239_A0.180150.659
12_A196_L0.180140.659
191_E195_E0.180050.659
73_F171_L0.179960.658
130_R187_E0.179880.658
12_A25_V0.179870.658
84_T128_L0.179860.658
87_L223_I0.179510.657
119_M126_N0.179440.656
128_L175_L0.17920.656
57_F220_A0.178840.654
168_L217_G0.178670.654
245_S257_K0.178380.653
106_E110_S0.177240.648
28_R189_A0.177220.648
71_R83_E0.176540.646
245_S253_E0.176170.645
27_A238_G0.175920.644
22_Y122_D0.175910.644
76_D81_R0.175740.643
33_P36_S0.175610.642
205_A220_A0.175540.642
93_R152_Q0.175160.641
36_S233_A0.175010.640
91_R256_L0.174120.637
53_S56_V0.173190.634
88_A240_G0.173150.633
115_A244_D0.172910.633
122_D125_R0.172520.631
72_L117_H0.171490.627
73_F178_T0.169140.619
25_V88_A0.169080.619
7_Q164_P0.168920.618
119_M123_L0.168570.617
108_L114_R0.168430.616
88_A153_H0.168320.616
88_A242_V0.168270.616
117_H124_I0.168260.616
33_P37_P0.168040.615
110_S249_A0.167830.614
68_S86_P0.167140.611
28_R153_H0.167040.611
125_R139_V0.163950.600
148_L155_V0.163920.600
65_V226_A0.163780.599
176_H182_T0.162630.595
22_Y126_N0.162360.594
122_D126_N0.161570.591
6_K246_D0.161180.590
64_F222_A0.161140.590
27_A254_T0.160860.588
126_N130_R0.160830.588
19_G125_R0.160350.587
178_T220_A0.160230.586
72_L124_I0.15940.583
107_L154_L0.15930.583
171_L223_I0.158810.581
3_E10_R0.157950.578
188_R192_F0.157840.577
130_R174_A0.15720.575
251_W254_T0.156750.573
222_A225_S0.156560.573
117_H143_P0.156550.573
128_L160_G0.156120.571
25_V66_G0.155930.570
119_M127_D0.155880.570
119_M125_R0.155850.570
75_V217_G0.155810.570
171_L175_L0.155270.568
117_H221_V0.155110.567
23_K120_V0.155050.567
170_D173_R0.155040.567
29_R236_Y0.154880.567
124_I180_A0.154860.567
119_M184_A0.154360.565
181_V221_V0.154170.564
93_R147_R0.153540.562
111_E244_D0.153370.561
74_R216_D0.153350.561
66_G222_A0.153260.561
197_E201_R0.153110.560
124_I205_A0.151750.555
153_H189_A0.15130.554
111_E114_R0.15070.551
13_Q246_D0.150.549
239_A245_S0.149950.549
207_P222_A0.149880.548
119_M122_D0.149770.548
7_Q14_E0.149720.548
78_G81_R0.149390.547
2_R247_P0.149130.546
87_L153_H0.148650.544
75_V216_D0.148530.543
87_L222_A0.148530.543
118_R226_A0.148130.542
120_V124_I0.148120.542
23_K242_V0.148060.542
127_D184_A0.147160.538
36_S42_A0.146920.537
202_G227_Q0.146680.537
38_I233_A0.146260.535
3_E18_A0.146230.535
40_P60_Q0.144640.529
52_P67_A0.14460.529
138_E161_R0.144540.529
25_V28_R0.144470.529
91_R152_Q0.144250.528
22_Y119_M0.143990.527
241_I246_D0.143780.526
12_A193_I0.143760.526
5_Y254_T0.143550.525
13_Q242_V0.143460.525
117_H180_A0.143420.525
72_L180_A0.143210.524
176_H221_V0.142670.522
100_D152_Q0.142370.521
151_V256_L0.142360.521
9_V16_I0.142320.521
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
1qdlA0.9844100-0.011
4grhA0.9883100-0.011
3h9mA0.9844100-0.008
1k0eA0.9844100-0.008
1i1qA0.98051000.002
2fn0A0.98051000.003
3os6A0.98441000.008
3hwoA0.98441000.008
3logA0.98441000.01
3gseA0.97281000.026

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