GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SRR1 - SRR1
Pfam: PF07985 (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. )
Length: 56
Sequences: 283
Seq/Len: 5.05
HH_delta: 0.82 (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
9_S48_D0.40712.836
10_F48_D0.30112.098
2_I23_L0.290192.022
3_V6_G0.278311.939
20_L44_F0.260961.818
4_C17_R0.212411.480
2_I27_K0.210411.466
23_L27_K0.193751.350
7_L20_L0.190761.329
4_C16_A0.182381.271
7_L10_F0.181891.267
3_V38_S0.178391.243
30_L50_A0.165841.155
43_V50_A0.164181.144
12_S43_V0.162041.129
4_C7_L0.15851.104
7_L41_D0.158241.103
25_L37_V0.157961.101
26_L49_K0.154181.074
33_P55_L0.154121.074
16_A44_F0.152911.065
11_S47_V0.152311.061
46_E49_K0.151161.053
10_F51_F0.151061.053
22_L40_Y0.149551.042
24_L28_E0.148921.038
46_E53_E0.14881.037
15_S52_L0.14621.019
22_L26_L0.144361.006
21_A24_L0.142490.993
32_I35_D0.142170.991
3_V25_L0.138220.963
30_L45_T0.138090.962
31_S53_E0.133280.929
9_S21_A0.132770.925
23_L44_F0.132090.920
4_C27_K0.130650.910
13_S40_Y0.130530.909
39_I48_D0.126810.884
5_L48_D0.126230.880
4_C44_F0.125450.874
17_R24_L0.12430.866
5_L39_I0.123920.863
21_A49_K0.123810.863
47_V53_E0.123580.861
14_R49_K0.12340.860
6_G55_L0.123320.859
26_L54_S0.122180.851
5_L40_Y0.12190.849
22_L45_T0.121280.845
35_D40_Y0.120850.842
33_P50_A0.120580.840
1_K5_L0.119770.834
17_R41_D0.116520.812
5_L14_R0.116430.811
5_L54_S0.116030.808
44_F52_L0.114730.799
48_D52_L0.114720.799
16_A38_S0.114520.798
10_F44_F0.114090.795
18_Y21_A0.11380.793
15_S43_V0.113510.791
28_E53_E0.111450.777
36_Q53_E0.110530.770
31_S46_E0.109550.763
17_R44_F0.109090.760
20_L52_L0.108370.755
15_S25_L0.107970.752
22_L32_I0.107450.749
9_S13_S0.106690.743
4_C23_L0.106650.743
35_D53_E0.106470.742
15_S22_L0.106280.741
39_I52_L0.105870.738
17_R40_Y0.10410.725
29_E50_A0.103520.721
37_V53_E0.103410.721
2_I12_S0.102710.716
1_K47_V0.102150.712
30_L53_E0.101860.710
32_I53_E0.101260.706
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
3vtfA0.964346.30.82
2y0cA0.910741.10.825
2o3jA0.964336.80.83
1mv8A0.964336.30.83
1dljA0.946435.30.831
3gg2A0.839329.50.837
4a7pA0.964328.80.838
3pidA0.892928.70.839
2q3eA0.964323.40.845
3g79A0.964322.20.846
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