GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Protoglobin - Protoglobin
Pfam: PF11563 (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: 158
Sequences: 2570
Seq/Len: 16.27
HH_delta: 0.142 (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
18_D139_K0.741853.675
15_T18_D0.594372.944
21_L136_A0.492062.438
30_E72_R0.484732.401
25_L133_L0.4782.368
32_H35_E0.447632.218
16_E20_E0.409212.027
100_P103_W0.402091.992
93_V96_R0.384231.903
15_T139_K0.38421.903
25_L137_L0.351411.741
20_E24_S0.35121.740
17_E132_D0.346531.717
70_H144_D0.337171.670
17_E20_E0.315091.561
38_D42_D0.310921.540
18_D136_A0.30881.530
39_D43_H0.306511.518
82_E85_E0.301151.492
39_D42_D0.291851.446
93_V97_I0.287651.425
104_Y148_V0.27661.370
68_R72_R0.272881.352
71_W74_L0.271311.344
59_T63_L0.268611.331
22_L140_L0.260381.290
41_Y104_Y0.259121.284
21_L133_L0.257951.278
116_L138_S0.252611.251
70_H74_L0.251991.248
146_Q150_E0.249041.234
50_T53_I0.246871.223
135_R139_K0.246781.223
91_G148_V0.246761.222
65_A68_R0.244081.209
63_L66_T0.242841.203
16_E19_L0.241651.197
73_E86_R0.240591.192
111_L116_L0.23771.178
66_T70_H0.237281.175
120_A131_A0.236951.174
130_R133_L0.235081.165
87_R144_D0.228731.133
64_K70_H0.226561.122
57_E60_I0.223121.105
18_D135_R0.222351.102
31_P35_E0.219661.088
112_R115_L0.219541.088
79_F82_E0.218421.082
45_L51_A0.215351.067
17_E21_L0.213121.056
32_H118_A0.212111.051
62_R66_T0.209651.039
142_D146_Q0.209071.036
138_S142_D0.206261.022
112_R116_L0.205861.020
59_T64_K0.204831.015
34_P68_R0.203981.011
112_R145_L0.203111.006
47_F50_T0.202581.004
26_A29_I0.198870.985
54_F94_H0.19810.981
90_I94_H0.198060.981
66_T69_R0.195720.970
38_D64_K0.195120.967
110_F114_F0.194910.966
112_R142_D0.192120.952
113_E117_E0.190570.944
23_R78_D0.187750.930
120_A134_L0.186630.925
119_L122_E0.186440.924
91_G94_H0.185740.920
112_R141_L0.185530.919
20_E65_A0.18530.918
58_S64_K0.185080.917
57_E62_R0.184990.916
65_A69_R0.184520.914
34_P38_D0.183920.911
14_L22_L0.183860.911
26_A37_V0.183650.910
51_A56_S0.183570.909
36_I39_D0.182160.902
61_E68_R0.18160.900
41_Y94_H0.181080.897
43_H117_E0.179860.891
63_L74_L0.17810.882
102_R105_I0.177190.878
111_L114_F0.176320.873
123_Y137_L0.174960.867
68_R71_W0.1740.862
112_R119_L0.173250.858
42_D46_R0.173230.858
131_A135_R0.172240.853
19_L79_F0.171520.850
39_D117_E0.171040.847
70_H73_E0.170690.846
59_T70_H0.170430.844
69_R73_E0.170.842
21_L25_L0.169980.842
67_Q71_W0.168910.837
88_R147_L0.168420.834
35_E38_D0.16840.834
118_A123_Y0.168230.833
21_L24_S0.167580.830
113_E118_A0.166820.826
88_R92_Q0.166760.826
114_F117_E0.166280.824
80_D83_Y0.165660.821
117_E120_A0.165380.819
140_L144_D0.164770.816
20_E146_Q0.164470.815
145_L149_I0.164290.814
54_F104_Y0.164010.812
60_I64_K0.162410.805
68_R74_L0.162310.804
83_Y144_D0.162040.803
60_I63_L0.1610.798
104_Y149_I0.160480.795
116_L120_A0.159060.788
74_L140_L0.15860.786
111_L115_L0.158010.783
99_L103_W0.157930.782
83_Y87_R0.157030.778
26_A30_E0.15670.776
119_L130_R0.156560.776
118_A122_E0.156070.773
53_I97_I0.155960.773
67_Q111_L0.155750.772
63_L70_H0.155520.770
41_Y90_I0.155490.770
53_I99_L0.155410.770
39_D121_E0.154130.764
50_T103_W0.153710.761
67_Q148_V0.15340.760
59_T62_R0.152470.755
141_L145_L0.152460.755
134_L138_S0.151990.753
58_S79_F0.151230.749
110_F115_L0.151050.748
62_R68_R0.150680.746
89_R93_V0.150570.746
67_Q87_R0.150090.744
44_L49_E0.149830.742
20_E23_R0.149370.740
111_L118_A0.14880.737
21_L132_D0.148350.735
44_L47_F0.148070.734
18_D21_L0.147630.731
112_R122_E0.14750.731
61_E65_A0.147390.730
42_D121_E0.147380.730
35_E46_R0.147090.729
100_P105_I0.146560.726
132_D136_A0.146060.724
14_L143_L0.145820.722
58_S61_E0.145710.722
92_Q123_Y0.145440.721
116_L134_L0.145390.720
40_F98_G0.144760.717
89_R92_Q0.144540.716
27_P31_P0.143740.712
114_F118_A0.142890.708
37_V45_L0.142080.704
64_K68_R0.141360.700
37_V71_W0.141330.700
28_I31_P0.140970.698
69_R86_R0.140960.698
112_R138_S0.140240.695
57_E64_K0.139960.693
133_L136_A0.139770.692
28_I131_A0.139420.691
116_L119_L0.13920.690
117_E121_E0.138640.687
38_D41_Y0.138520.686
22_L43_H0.138460.686
39_D118_A0.138460.686
62_R74_L0.138230.685
113_E116_L0.137920.683
137_L145_L0.137410.681
139_K143_L0.137390.681
25_L29_I0.137370.681
62_R96_R0.137370.681
40_F67_Q0.137330.680
88_R96_R0.136950.678
25_L123_Y0.136160.675
37_V64_K0.135930.673
57_E63_L0.135780.673
61_E64_K0.135730.672
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
2w31A0.987399.90.142
1or4A0.94399.90.17
2vebA0.993799.80.261
2vhbA0.886199.70.336
1gdjA0.879799.70.345
2oifA0.924199.70.347
1q1fA0.860899.70.351
1binA0.841899.60.361
2dc3A0.96299.60.362
2w72C0.848199.60.366

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