GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GFO_IDH_MocA_C - Oxidoreductase family C-terminal alphabeta domain
Pfam: PF02894 (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: CL0218
Length: 115
Sequences: 6555
Seq/Len: 57
HH_delta: 0.182 (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
1_K5_E1.644983.753
2_E6_E1.467623.349
3_L8_E1.215192.773
64_V91_E1.215142.773
92_F98_A1.132.578
58_F96_A0.961752.194
49_H52_D0.903492.062
63_T91_E0.892672.037
55_R61_P0.865031.974
3_L6_E0.817981.866
63_T93_G0.791261.805
1_K56_W0.773351.765
62_P93_G0.771891.761
62_P65_V0.744951.700
16_Q101_T0.720311.644
2_E5_E0.71421.630
60_S94_S0.713921.629
60_S93_G0.71181.624
54_V98_A0.657811.501
62_P67_A0.642191.465
55_R92_F0.640861.462
64_V67_A0.605871.382
14_S97_V0.602231.374
12_V58_F0.600031.369
15_V54_V0.589211.344
9_I12_V0.586281.338
15_V98_A0.585591.336
89_N97_V0.576451.315
20_R101_T0.544531.242
40_G44_L0.539731.232
47_G102_A0.533171.217
90_F98_A0.532221.214
19_F46_L0.529191.207
15_V58_F0.522241.192
17_G50_Q0.510311.164
90_F100_L0.507461.158
47_G50_Q0.496961.134
52_D56_W0.493241.125
45_D104_F0.491481.121
87_F99_T0.487731.113
43_L88_A0.475681.085
3_L9_I0.47231.078
7_G10_G0.463041.057
14_S83_A0.461641.053
81_E84_A0.461241.052
84_A102_A0.457571.044
42_A102_A0.447851.022
54_V92_F0.443171.011
61_P64_V0.441311.007
18_E101_T0.432450.987
88_A100_L0.432060.986
92_F96_A0.428340.977
5_E59_G0.424950.970
7_G11_K0.420170.959
1_K4_I0.419770.958
58_F92_F0.41070.937
65_V68_A0.405510.925
61_P93_G0.403130.920
68_A91_E0.400510.914
42_A46_L0.399390.911
44_L48_I0.395660.903
4_I9_I0.378870.864
62_P92_F0.376440.859
11_K94_S0.375770.857
42_A49_H0.372880.851
62_P91_E0.371420.847
41_G80_D0.371150.847
8_E11_K0.36790.839
16_Q99_T0.366260.836
4_I57_L0.363930.830
87_F97_V0.363050.828
95_G98_A0.362190.826
1_K57_L0.362180.826
55_R60_S0.361180.824
41_G81_E0.359130.819
84_A88_A0.359090.819
14_S101_T0.359080.819
43_L84_A0.358520.818
91_E97_V0.354640.809
54_V100_L0.352210.804
43_L47_G0.350810.800
24_A27_P0.350790.800
87_F101_T0.346040.790
61_P92_F0.336840.769
12_V15_V0.334430.763
14_S87_F0.334350.763
39_G81_E0.330970.755
51_I55_R0.329670.752
47_G88_A0.327730.748
14_S99_T0.326010.744
82_D105_N0.325310.742
42_A81_E0.325270.742
66_A89_N0.325150.742
45_D48_I0.323930.739
31_R34_R0.320520.731
30_W34_R0.320160.731
2_E8_E0.316630.722
61_P65_V0.312760.714
26_R29_R0.311910.712
42_A84_A0.310780.709
62_P66_A0.307110.701
101_T105_N0.304970.696
46_L102_A0.304850.696
25_P29_R0.304780.695
4_I12_V0.302820.691
12_V96_A0.302550.690
89_N99_T0.301490.688
58_F61_P0.299260.683
34_R37_E0.298380.681
33_R37_E0.292790.668
23_R28_P0.292320.667
83_A103_S0.291360.665
30_W33_R0.289550.661
47_G100_L0.286180.653
28_P31_R0.284770.650
1_K59_G0.284480.649
103_S106_N0.284470.649
39_G80_D0.283920.648
19_F50_Q0.28340.647
21_F46_L0.283020.646
42_A45_D0.282550.645
75_P82_D0.282450.644
49_H82_D0.281980.643
68_A97_V0.280610.640
25_P28_P0.275820.629
61_P66_A0.273930.625
99_T102_A0.269910.616
63_T66_A0.269650.615
43_L51_I0.267450.610
46_L50_Q0.265590.606
29_R32_W0.264620.604
83_A101_T0.264120.603
24_A28_P0.263180.601
23_R26_R0.260910.595
42_A47_G0.260070.593
4_I7_G0.250430.571
29_R34_R0.250290.571
61_P90_F0.250110.571
83_A105_N0.248240.566
5_E8_E0.247070.564
40_G45_D0.246570.563
73_Q78_Q0.245290.560
48_I51_I0.244720.558
64_V68_A0.243950.557
97_V101_T0.243490.556
58_F94_S0.242130.552
52_D57_L0.240640.549
65_V89_N0.239890.547
73_Q76_E0.23970.547
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
3rc1A0.930499.50.182
3e9mA0.921799.50.192
3evnA0.921799.50.196
1h6dA0.973999.50.199
3v5nA0.965299.50.201
3ip3A0.956599.50.205
3dtyA0.973999.50.206
3u3xA0.965299.50.213
3e18A0.930499.50.215
3q2iA0.956599.50.216

Page generated in 0.0374 seconds.