GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Rubrerythrin - Rubrerythrin
Pfam: PF02915 (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: CL0044
Length: 137
Sequences: 6682
Seq/Len: 48.77
HH_delta: 0.204 (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
86_E90_E1.028462.491
48_F121_E0.871752.111
40_E43_Q0.809511.961
84_N87_E0.806531.953
7_I53_L0.799761.937
42_E45_H0.742811.799
93_I130_E0.737251.786
52_L115_I0.69181.676
104_A123_A0.691521.675
31_L85_L0.646191.565
93_I97_K0.626261.517
53_L58_P0.621681.506
108_R116_R0.615751.491
101_E105_E0.614241.488
14_A43_Q0.597621.447
21_A39_A0.595521.442
10_E45_H0.591881.434
117_K121_E0.589291.427
24_A88_A0.58151.408
100_Y104_A0.577581.399
42_E129_H0.571151.383
120_E124_K0.570521.382
116_R120_E0.569761.380
52_L118_L0.564081.366
18_R43_Q0.552531.338
91_M94_K0.551721.336
49_L122_L0.548551.329
105_E109_K0.545421.321
8_K12_E0.537271.301
108_R120_E0.526071.274
43_Q47_K0.524051.269
14_A39_A0.521261.262
80_E83_E0.513761.244
94_K97_K0.497461.205
102_F106_L0.495721.201
25_K36_R0.490791.189
21_A36_R0.48891.184
33_E37_R0.488251.183
11_L46_A0.487161.180
55_K114_E0.486711.179
126_E129_H0.483731.172
3_L53_L0.479741.162
4_E53_L0.477671.157
100_Y123_A0.476511.154
44_E48_F0.472941.145
7_I46_A0.469081.136
24_A85_L0.466181.129
33_E36_R0.46561.128
39_A43_Q0.462691.121
6_A103_Y0.462511.120
6_A102_F0.461021.117
18_R39_A0.456271.105
3_L49_L0.45071.092
32_K36_R0.443131.073
98_D102_F0.438731.063
90_E94_K0.435331.054
112_D115_I0.432641.048
107_A123_A0.432161.047
9_M13_A0.428291.037
47_K51_K0.425981.032
124_K127_K0.422091.022
5_M102_F0.421851.022
10_E42_E0.417231.011
45_H129_H0.416041.008
107_A120_E0.415721.007
48_F125_E0.412030.998
10_E126_E0.410750.995
25_K29_P0.409760.992
127_K131_D0.408120.988
14_A18_R0.407140.986
34_L38_L0.406230.984
24_A35_F0.40370.978
117_K120_E0.402860.976
14_A46_A0.402810.976
49_L118_L0.399530.968
36_R40_E0.399460.967
6_A119_F0.399430.967
83_E87_E0.392050.950
25_K32_K0.390950.947
18_R36_R0.390760.946
9_M102_F0.389410.943
48_F118_L0.385710.934
111_P116_R0.380430.921
12_E16_F0.374650.907
87_E90_E0.373960.906
34_L132_L0.372680.903
113_P117_K0.372620.902
20_L92_A0.370970.898
100_Y130_E0.368610.893
104_A108_R0.368560.893
51_K54_R0.365660.886
22_E50_E0.36230.877
52_L56_L0.361940.877
41_E44_E0.361610.876
42_E126_E0.360690.874
29_P32_K0.360630.873
11_L15_K0.3560.862
125_E128_E0.355360.861
19_E22_E0.353190.855
20_L87_E0.352370.853
4_E58_P0.35090.850
52_L55_K0.347960.843
6_A49_L0.34710.841
121_E124_K0.346530.839
47_K50_E0.346240.839
100_Y127_K0.345520.837
53_L57_G0.345460.837
105_E108_R0.343690.832
48_F52_L0.342820.830
3_L52_L0.342430.829
45_H126_E0.342010.828
41_E128_E0.341410.827
35_F88_A0.336280.814
38_L132_L0.335710.813
102_F105_E0.335590.813
13_A42_E0.334950.811
34_L37_R0.332440.805
108_R113_P0.327050.792
107_A119_F0.32620.790
118_L122_L0.324760.787
104_A107_A0.324250.785
37_R132_L0.323040.782
103_Y126_E0.322440.781
35_F92_A0.321350.778
113_P116_R0.320130.775
6_A106_L0.319690.774
57_G60_E0.318530.771
99_A103_Y0.316870.767
4_E8_K0.315840.765
49_L119_F0.313240.759
97_K130_E0.310890.753
29_P33_E0.310120.751
79_E82_D0.307980.746
117_K124_K0.307060.744
46_A50_E0.304960.739
120_E123_A0.300730.728
98_D101_E0.299530.725
15_K19_E0.298180.722
50_E54_R0.296090.717
108_R111_P0.295170.715
17_Y96_E0.292170.708
97_K101_E0.290990.705
10_E13_A0.290840.704
48_F122_L0.28990.702
18_R40_E0.287520.696
94_K98_D0.285550.692
124_K128_E0.282230.684
49_L99_A0.28220.683
128_E131_D0.280340.679
18_R21_A0.279460.677
90_E93_I0.277670.673
41_E125_E0.277590.672
18_R22_E0.276990.671
40_E44_E0.27570.668
87_E91_M0.27550.667
24_A32_K0.271530.658
110_A116_R0.271060.657
80_E84_N0.269970.654
45_H96_E0.2690.652
17_Y129_H0.268370.650
123_A127_K0.267820.649
42_E99_A0.266480.645
11_L14_A0.265720.644
79_E91_M0.262810.637
38_L92_A0.261770.634
41_E45_H0.261530.633
23_K82_D0.260790.632
9_M99_A0.257360.623
80_E91_M0.252590.612
54_R59_G0.252220.611
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
2fzfA0.978199.50.204
2oh3A0.978199.50.223
1vjxA0.963599.50.24
4am5A0.919799.40.284
1nfvA0.919799.30.315
3unoA0.92799.30.318
1krqA0.92799.30.321
3qb9A0.919799.30.322
2qqyA0.912499.30.322
1s3qA0.92799.30.323

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