GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GyrI-like - GyrI-like small molecule binding domain
Pfam: PF06445 (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: CL0319
Length: 155
Sequences: 2975
Seq/Len: 19.19
HH_delta: 0.09 (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
10_A89_T0.722553.329
100_H110_A0.674273.106
7_T94_K0.610012.810
12_R87_S0.554842.556
96_A118_W0.554242.553
111_Y150_I0.495912.285
6_V97_V0.488682.251
12_R89_T0.476962.197
96_A119_L0.471822.174
17_R68_R0.468152.157
53_G69_Y0.461372.125
10_A92_A0.45622.102
118_W122_S0.455342.098
99_E149_E0.424951.958
98_F114_L0.41351.905
94_K124_Y0.401911.851
124_Y154_I0.399331.840
97_V151_Y0.382621.763
7_T92_A0.379221.747
132_F151_Y0.359661.657
15_G70_D0.355671.638
70_D88_R0.354781.634
5_I94_K0.349571.610
98_F110_A0.345751.593
5_I96_A0.343711.583
10_A91_P0.34071.570
6_V149_E0.33891.561
13_V72_G0.332471.532
19_K68_R0.330221.521
6_V151_Y0.328411.513
11_F90_I0.318121.465
134_I149_E0.316261.457
101_K147_V0.315531.454
17_R70_D0.314221.448
14_A85_M0.312831.441
126_R155_K0.312381.439
57_D68_R0.303691.399
137_N146_Y0.301611.389
3_V98_F0.297151.369
104_Y148_T0.295351.361
17_R86_E0.294431.356
56_Y70_D0.294191.355
34_R84_G0.293741.353
106_D109_E0.290441.338
116_N121_E0.281861.298
15_G88_R0.281151.295
63_D66_E0.276881.276
102_G148_T0.271721.252
111_Y133_E0.267451.232
12_R78_D0.264471.218
55_Y69_Y0.263921.216
142_D145_E0.263081.212
5_I154_I0.258681.192
134_I151_Y0.258491.191
31_L71_I0.258421.190
38_W85_M0.252651.164
13_V88_R0.248781.146
100_H106_D0.247331.139
111_Y131_D0.245811.132
97_V149_E0.245541.131
19_K66_E0.243571.122
112_Q116_N0.24271.118
138_D146_Y0.242181.116
114_L152_I0.241111.111
129_G153_P0.240461.108
16_I34_R0.238631.099
82_P85_M0.237751.095
110_A150_I0.236131.088
118_W124_Y0.233951.078
119_L122_S0.226071.041
95_Y132_F0.225321.038
3_V118_W0.221381.020
99_E147_V0.217031.000
50_P134_I0.216760.999
30_E33_Q0.214890.990
16_I31_L0.214010.986
109_E112_Q0.213990.986
31_L35_L0.213780.985
36_M73_V0.212990.981
32_W71_I0.212680.980
38_W41_E0.208710.961
14_A75_V0.208170.959
5_I118_W0.207860.958
104_Y139_P0.206310.950
8_L11_F0.205450.946
52_I72_G0.205310.946
94_K154_I0.204170.941
18_R34_R0.20390.939
53_G133_E0.200580.924
93_G129_G0.199060.917
5_I124_Y0.198750.916
54_I72_G0.197790.911
114_L150_I0.196940.907
135_Y148_T0.195910.903
104_Y146_Y0.19390.893
8_L95_Y0.193850.893
93_G127_R0.193790.893
4_E97_V0.192580.887
101_K145_E0.190060.876
14_A58_N0.189010.871
96_A114_L0.188880.870
16_I35_L0.18850.868
52_I74_E0.188450.868
115_Y120_P0.188020.866
15_G86_E0.18750.864
38_W42_I0.186640.860
136_L149_E0.184450.850
3_V96_A0.182530.841
20_G58_N0.179120.825
95_Y129_G0.175930.810
136_L147_V0.175810.810
81_N84_G0.174990.806
143_E146_Y0.174630.804
22_Y67_F0.172730.796
95_Y151_Y0.171470.790
115_Y126_R0.16940.780
91_P94_K0.16790.773
111_Y152_I0.166270.766
56_Y68_R0.165750.764
107_L131_D0.165620.763
20_G28_I0.165610.763
33_Q37_S0.164340.757
9_P92_A0.164090.756
137_N147_V0.16210.747
16_I85_M0.161870.746
115_Y119_L0.160130.738
9_P77_E0.159830.736
8_L132_F0.159450.735
40_K43_G0.158710.731
34_R37_S0.158410.730
50_P74_E0.158160.729
139_P146_Y0.158160.729
115_Y152_I0.15780.727
35_L52_I0.156620.722
102_G107_L0.156230.720
58_N62_T0.155780.718
21_P64_D0.155310.715
100_H148_T0.154530.712
20_G68_R0.153560.707
116_N120_P0.152650.703
126_R131_D0.152270.701
109_E113_K0.152240.701
39_L73_V0.15110.696
34_R38_W0.1510.696
126_R129_G0.150030.691
3_V113_K0.149620.689
119_L128_D0.148550.684
104_Y135_Y0.147470.679
69_Y133_E0.146660.676
22_Y107_L0.146180.673
78_D87_S0.143640.662
103_P143_E0.143410.661
13_V70_D0.141970.654
127_R155_K0.141120.650
32_W53_G0.140830.649
55_Y133_E0.140750.648
67_F115_Y0.140330.646
144_E148_T0.139870.644
51_I55_Y0.139530.643
94_K155_K0.138920.640
106_D110_A0.138870.640
96_A122_S0.137710.634
3_V122_S0.137650.634
110_A113_K0.137080.631
28_I135_Y0.136020.627
94_K122_S0.135680.625
15_G72_G0.13520.623
35_L39_L0.135120.622
139_P143_E0.134710.621
70_D75_V0.134670.620
53_G135_Y0.134020.617
110_A152_I0.133640.616
21_P24_E0.133520.615
16_I84_G0.133390.614
103_P144_E0.133260.614
93_G132_F0.13310.613
21_P92_A0.132730.611
100_H107_L0.132730.611
113_K116_N0.132640.611
24_E66_E0.132260.609
51_I74_E0.132020.608
33_Q140_D0.131770.607
29_P133_E0.13170.607
100_H111_Y0.130920.603
45_S84_G0.130050.599
74_E122_S0.129810.598
3_V114_L0.129340.596
11_F93_G0.128780.593
56_Y130_P0.127760.589
80_P87_S0.127630.588
90_I95_Y0.127590.588
55_Y111_Y0.12740.587
36_M40_K0.126770.584
8_L151_Y0.126350.582
105_D109_E0.126350.582
31_L34_R0.126180.581
53_G107_L0.126170.581
20_G69_Y0.126020.581
77_E80_P0.126010.580
98_F108_Q0.12530.577
107_L118_W0.12490.575
30_E142_D0.123430.569
30_E56_Y0.123390.568
107_L110_A0.122550.565
135_Y150_I0.122250.563
7_T10_A0.122030.562
8_L93_G0.121930.562
70_D86_E0.121140.558
52_I134_I0.120810.557
115_Y128_D0.120660.556
122_S127_R0.120270.554
111_Y148_T0.120140.553
34_R40_K0.119830.552
32_W36_M0.119670.551
133_E150_I0.119220.549
99_E136_L0.118820.547
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
3e0hA0.954899.90.09
1jyhA0.967799.90.094
1d5yA0.967799.90.114
3lurA0.961399.80.138
3gk6A0.922699.80.144
3b49A0.980699.80.174
1r8eA0.948499.80.207
2govA0.967797.40.717
3r8jA0.967797.30.719
4b0yA0.967797.30.72

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