GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ring_hydroxyl_B - Ring hydroxylating beta subunit
Pfam: PF00866 (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: CL0051
Length: 145
Sequences: 1584
Seq/Len: 10.92
HH_delta: 0.135 (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_R13_E1.257985.759
119_D133_R0.840913.850
124_T127_G0.725473.321
4_R83_R0.708833.245
95_V121_L0.690953.163
122_R131_A0.580342.657
99_F115_G0.577992.646
20_E51_R0.517142.368
23_H132_R0.480462.200
120_V132_R0.477412.186
97_S119_D0.437142.001
93_I128_L0.435131.992
18_F22_C0.431291.974
7_D77_H0.42281.936
123_R128_L0.395911.813
5_L13_E0.389391.783
19_T131_A0.387491.774
86_E93_I0.357441.636
25_W134_R0.354571.623
96_R116_R0.352831.615
92_E122_R0.351921.611
13_E16_A0.351481.609
21_D131_A0.35061.605
91_G123_R0.347131.589
121_L130_I0.338171.548
92_E120_V0.337781.546
120_V131_A0.334671.532
89_D92_E0.325421.490
5_L17_L0.312541.431
82_V97_S0.312141.429
50_D53_M0.31.373
12_D62_R0.293961.346
94_E120_V0.28891.323
6_L14_W0.275051.259
124_T129_K0.274681.258
4_R96_R0.271811.244
19_T129_K0.266631.221
92_E131_A0.264941.213
22_C54_L0.263481.206
4_R8_E0.262471.202
19_T122_R0.262021.200
5_L10_R0.26021.191
78_F100_L0.256511.174
56_D59_E0.232451.064
15_L55_E0.231341.059
85_E94_E0.223731.024
26_V135_V0.222441.018
25_W132_R0.221811.015
3_A79_V0.218481.000
94_E118_E0.210840.965
5_L16_A0.204760.937
84_V93_I0.201740.924
79_V97_S0.197110.902
19_T124_T0.196360.899
115_G135_V0.194680.891
102_Y114_A0.194180.889
97_S117_R0.193990.888
96_R118_E0.193670.887
15_L54_L0.192470.881
78_F98_N0.190620.873
14_W58_V0.189880.869
103_R111_D0.189580.868
121_L128_L0.188870.865
18_F130_I0.185190.848
12_D55_E0.18030.825
123_R127_G0.179180.820
104_S114_A0.179020.820
118_E134_R0.178030.815
14_W57_R0.177830.814
75_T103_R0.174920.801
51_R55_E0.174480.799
95_V133_R0.171390.785
52_G55_E0.170770.782
52_G56_D0.17040.780
8_E96_R0.168810.773
18_F30_E0.168780.773
100_L112_L0.166350.762
8_E76_R0.164720.754
95_V130_I0.164080.751
125_D129_K0.163230.747
76_R101_V0.163060.747
15_L51_R0.162710.745
55_E59_E0.159130.729
49_D53_M0.159050.728
20_E125_D0.158670.726
71_P105_R0.155910.714
16_A51_R0.155770.713
56_D61_L0.15560.712
14_W80_S0.154820.709
97_S133_R0.154050.705
56_D62_R0.153970.705
27_P60_R0.152640.699
8_E116_R0.152390.698
116_R136_V0.152330.697
14_W99_F0.150140.687
106_L113_F0.149330.684
99_F103_R0.148320.679
100_L115_G0.146370.670
102_Y112_L0.143690.658
4_R75_T0.143570.657
13_E124_T0.143160.655
20_E124_T0.142590.653
49_D128_L0.142260.651
82_V93_I0.14050.643
84_V95_V0.140.641
81_N98_N0.139930.641
10_R16_A0.13980.640
91_G126_G0.137890.631
53_M56_D0.137350.629
7_D75_T0.136410.624
24_Y135_V0.136110.623
21_D129_K0.135920.622
11_Y15_L0.135870.622
12_D90_G0.134550.616
51_R59_E0.133990.613
25_W130_I0.13320.610
21_D132_R0.132760.608
118_E136_V0.13230.606
18_F54_L0.132050.605
108_G111_D0.131640.603
17_L130_I0.130990.600
6_L75_T0.130530.598
17_L129_K0.129540.593
99_F135_V0.129450.593
99_F117_R0.129270.592
14_W24_Y0.128510.588
79_V82_V0.127720.585
24_Y57_R0.126020.577
26_V77_H0.125690.575
82_V95_V0.123630.566
9_R110_Q0.122720.562
89_D94_E0.12250.561
12_D16_A0.122430.560
86_E89_D0.122370.560
96_R108_G0.121430.556
52_G136_V0.121270.555
9_R75_T0.120550.552
59_E63_T0.120010.549
23_H49_D0.119470.547
24_Y101_V0.11940.547
56_D60_R0.119270.546
19_T22_C0.118920.544
9_R134_R0.11890.544
86_E126_G0.118220.541
18_F77_H0.117830.539
89_D123_R0.116920.535
9_R72_P0.116860.535
16_A129_K0.116820.535
89_D112_L0.116360.533
119_D130_I0.116250.532
3_A96_R0.115990.531
86_E123_R0.115450.529
82_V121_L0.115420.528
104_S112_L0.115070.527
103_R133_R0.11430.523
59_E62_R0.114020.522
7_D101_V0.113610.520
102_Y110_Q0.113610.520
124_T131_A0.113250.518
100_L104_S0.113170.518
100_L114_A0.112910.517
86_E128_L0.112360.514
82_V86_E0.1120.513
54_L57_R0.111430.510
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
3e99A0.986299.90.135
3gzxB0.986299.90.142
3ebyA0.937999.90.148
2gbwB0.993199.90.148
2b1xB0.986299.90.153
1uliB0.986299.90.164
1wqlB0.993199.90.165
2bmoB0.986299.90.166
3ef8A0.827699.80.292
4gb5A0.848399.80.296

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