GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DapB_N - Dihydrodipicolinate reductase N-terminus
Pfam: PF01113 (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: CL0063
Length: 124
Sequences: 43830
Seq/Len: 353.47
HH_delta: 0.039 (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
4_G68_A3.04863.144
62_E86_Y2.384232.459
2_R27_E2.338232.412
81_Y85_E1.933051.994
2_R29_V1.923281.984
4_G64_L1.813721.871
2_R69_D1.805911.863
81_Y108_E1.790121.846
60_D63_E1.788611.845
81_Y105_Q1.655111.707
102_S105_Q1.649791.702
16_I72_I1.641861.693
20_I72_I1.576211.626
3_V26_F1.569081.618
85_E89_K1.5521.601
3_V70_V1.536041.584
75_T83_N1.43641.482
29_V68_A1.412961.457
5_I17_A1.340521.383
82_D86_Y1.313251.355
61_L86_Y1.306531.348
3_V20_I1.290541.331
68_A92_V1.283611.324
57_V60_D1.27941.320
19_A22_E1.232941.272
79_A83_N1.216211.254
59_D63_E1.216121.254
63_E66_E1.208531.247
36_P42_K1.185831.223
86_Y90_H1.178461.216
69_D93_P1.165831.202
66_E90_H1.156791.193
42_K45_G1.138941.175
62_E66_E1.133041.169
30_G58_T1.127691.163
18_E22_E1.126211.162
8_A31_A1.099441.134
5_I72_I1.095391.130
32_V61_L1.069641.103
6_V73_D1.055211.088
105_Q108_E1.049851.083
70_V93_P1.047391.080
12_M74_F1.036461.069
86_Y89_K1.036191.069
62_E90_H1.028521.061
107_D110_E1.025251.057
85_E108_E1.023091.055
4_G71_V1.022841.055
16_I74_F1.018911.051
29_V67_E1.013721.046
64_L68_A1.009791.042
82_D85_E0.99331.025
84_L96_I0.99171.023
62_E89_K0.980831.012
15_A18_E0.974741.005
8_A17_A0.973111.004
75_T79_A0.969341.000
15_A19_A0.958760.989
8_A30_G0.949740.980
36_P59_D0.942420.972
106_I110_E0.928770.958
7_G10_G0.9170.946
74_F97_G0.908040.937
73_D95_V0.906260.935
104_E108_E0.901910.930
6_V83_N0.901490.930
3_V72_I0.89450.923
101_F105_Q0.885440.913
79_A82_D0.878130.906
103_D107_D0.869910.897
33_D36_P0.862890.890
65_L87_A0.857850.885
89_K92_V0.851040.878
81_Y109_L0.843110.870
85_E88_L0.83120.857
63_E67_E0.825050.851
58_T67_E0.824980.851
53_L57_V0.813570.839
71_V92_V0.806830.832
8_A33_D0.805350.831
75_T80_V0.803870.829
74_F98_T0.802720.828
54_G57_V0.782270.807
58_T63_E0.776680.801
10_G13_G0.768810.793
104_E107_D0.765280.789
80_V98_T0.761940.786
73_D76_N0.761520.785
2_R68_A0.754650.778
84_L109_L0.753970.778
60_D64_L0.751790.775
11_R15_A0.751590.775
14_R18_E0.751040.775
85_E109_L0.750170.774
76_N79_A0.748840.772
71_V87_A0.741790.765
25_G28_L0.738850.762
73_D80_V0.731490.754
73_D84_L0.73090.754
29_V33_D0.719810.742
2_R67_E0.706180.728
58_T64_L0.705330.728
93_P96_I0.70390.726
18_E21_L0.69960.722
52_P55_V0.696070.718
64_L67_E0.687370.709
5_I28_L0.679270.701
19_A24_P0.67830.700
73_D83_N0.67620.697
2_R28_L0.674120.695
12_M15_A0.672140.693
11_R14_R0.67070.692
30_G68_A0.667820.689
4_G30_G0.667250.688
13_G18_E0.66260.683
53_L60_D0.656950.678
36_P57_V0.654820.675
100_G106_I0.65420.675
94_L98_T0.647750.668
61_L65_L0.644780.665
96_I99_T0.641910.662
80_V96_I0.64040.661
30_G67_E0.629660.649
90_H93_P0.627770.648
84_L94_L0.626870.647
6_V75_T0.626560.646
14_R43_D0.624370.644
61_L83_N0.62240.642
12_M97_G0.616690.636
102_S106_I0.612650.632
14_R52_P0.612270.632
6_V71_V0.611580.631
16_I97_G0.604080.623
5_I16_I0.598680.618
77_P98_T0.597290.616
57_V61_L0.597110.616
83_N86_Y0.588070.607
13_G17_A0.587590.606
5_I13_G0.581640.600
58_T82_D0.577680.596
17_A21_L0.577330.595
87_A92_V0.577140.595
14_R17_A0.575460.594
65_L90_H0.567970.586
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
3ijpA199.60.039
4f3yA0.991999.60.041
1dihA199.60.056
4gmfA0.919499.50.111
3db2A0.935599.50.118
3rc1A0.935599.40.121
3euwA0.935599.40.122
3e9mA0.935599.40.124
3moiA0.935599.40.126
4hktA0.927499.40.128

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