GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bac_globin - Bacterial-like globin
Pfam: PF01152 (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: CL0090
Length: 120
Sequences: 3191
Seq/Len: 26.59
HH_delta: 0.046 (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
78_T81_H0.99123.573
22_R91_Q0.768972.772
17_D42_K0.624992.253
18_A22_R0.594332.142
18_A95_E0.584272.106
18_A21_D0.548231.976
90_K107_L0.526531.898
22_R95_E0.526261.897
13_R46_A0.509291.836
99_P102_L0.50621.825
26_D84_R0.505941.824
94_D103_I0.504661.819
58_L61_G0.481151.734
98_V103_I0.434151.565
71_A74_H0.424351.530
94_D100_E0.402771.452
17_D21_D0.395191.424
15_L96_L0.376551.357
22_R92_A0.376181.356
26_D29_L0.371041.337
43_E47_E0.367111.323
41_H45_Q0.364081.312
84_R88_L0.357421.288
108_A112_S0.348521.256
86_L111_E0.347691.253
28_R84_R0.344951.243
22_R88_L0.344281.241
24_L38_L0.343111.237
53_L106_L0.340941.229
23_V84_R0.340561.228
13_R43_E0.336131.212
71_A75_L0.334471.206
94_D107_L0.334461.206
18_A96_L0.328881.185
100_E104_D0.328881.185
21_D25_A0.328821.185
67_M70_E0.327311.180
92_A96_L0.327181.179
32_F81_H0.325651.174
40_K44_K0.32451.170
104_D108_A0.321771.160
13_R17_D0.321671.159
104_D107_L0.318531.148
86_L110_L0.318271.147
23_V88_L0.31121.122
106_L110_L0.308511.112
15_L18_A0.30651.105
19_F89_L0.302241.089
24_L33_F0.300431.083
47_E50_S0.295731.066
103_I107_L0.294351.061
107_L111_E0.290641.048
61_G64_G0.289451.043
21_D42_K0.282421.018
87_E91_Q0.2821.016
19_F85_W0.278411.003
86_L90_K0.278351.003
102_L105_E0.274990.991
48_F51_Q0.272730.983
69_R117_I0.271630.979
114_R118_V0.267110.963
90_K103_I0.267050.963
33_F72_H0.265180.956
93_L103_I0.264190.952
52_L109_R0.26390.951
26_D88_L0.262410.946
18_A92_A0.261050.941
55_G59_Y0.258960.933
41_H44_K0.25860.932
26_D87_E0.258490.932
88_L91_Q0.256060.923
29_L88_L0.255590.921
69_R116_D0.253570.914
91_Q95_E0.247430.892
16_V46_A0.24660.889
52_L113_L0.246290.888
46_A50_S0.244210.880
28_R31_P0.239920.865
89_L110_L0.237770.857
93_L106_L0.23510.847
29_L32_F0.234530.845
90_K111_E0.234310.845
54_G59_Y0.232220.837
14_A18_A0.231650.835
90_K94_D0.229550.827
42_K45_Q0.229130.826
40_K47_E0.227850.821
24_L34_E0.226510.816
15_L92_A0.225510.813
56_P59_Y0.22540.812
40_K45_Q0.224680.810
85_W89_L0.222650.803
111_E114_R0.221810.799
40_K43_E0.221550.799
82_F89_L0.221120.797
50_S54_G0.221040.797
24_L27_P0.216980.782
33_F41_H0.216530.780
85_W110_L0.215840.778
91_Q94_D0.215440.777
16_V49_L0.214890.775
20_Y41_H0.214550.773
80_E83_D0.213890.771
72_H77_I0.213790.771
47_E61_G0.212020.764
109_R113_L0.210890.760
53_L56_P0.209870.756
71_A117_I0.209520.755
19_F92_A0.204760.738
15_L50_S0.204140.736
41_H82_F0.203030.732
77_I81_H0.203020.732
115_D118_V0.199860.720
112_S116_D0.199780.720
97_G103_I0.199080.718
41_H49_L0.198760.716
25_A73_A0.198620.716
86_L107_L0.197730.713
24_L30_K0.197360.711
45_Q48_F0.196580.709
86_L114_R0.194840.702
55_G58_L0.193980.699
55_G64_G0.191840.691
61_G66_P0.190260.686
61_G67_M0.189930.685
28_R87_E0.187360.675
113_L117_I0.187180.675
100_E107_L0.186630.673
49_L110_L0.18540.668
69_R73_A0.182910.659
37_D40_K0.182660.658
110_L113_L0.182280.657
51_Q54_G0.180660.651
33_F82_F0.179340.646
97_G105_E0.179220.646
73_A108_A0.179020.645
22_R25_A0.177980.642
14_A96_L0.177850.641
16_V42_K0.17730.639
28_R80_E0.176630.637
48_F113_L0.176150.635
27_P80_E0.174750.630
105_E109_R0.173890.627
44_K68_M0.17380.626
111_E115_D0.173470.625
90_K93_L0.173170.624
66_P70_E0.172010.620
29_L84_R0.171740.619
20_Y48_F0.170890.616
14_A102_L0.170390.614
13_R22_R0.170160.613
50_S53_L0.169920.612
79_E114_R0.168910.609
55_G60_T0.168680.608
51_Q59_Y0.168590.608
20_Y45_Q0.168150.606
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
2bmmA199.90.046
2qrwA199.90.06
2bkmA0.991799.90.068
1s69A0.966799.90.075
1ux8A0.983399.90.078
3aq9A0.966799.90.082
1dlwA0.966799.90.082
2gkmA0.966799.90.085
1dlyA0.966799.90.089
2kscA0.966799.90.092

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