GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ANTAR - ANTAR domain
Pfam: PF03861 (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: 1425
Seq/Len: 25.45
HH_delta: -0.072 (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
39_R43_R1.002183.027
29_S32_E0.944452.853
35_R38_R0.657131.985
46_R54_E0.613691.854
21_I56_I0.608591.838
14_V53_E0.581131.755
23_M30_E0.572871.731
16_E19_K0.563671.703
12_R16_E0.55281.670
46_R51_V0.551641.666
40_Q44_R0.536661.621
13_R16_E0.49251.488
46_R50_D0.478781.446
31_D35_R0.447541.352
50_D53_E0.425241.285
7_R49_A0.419571.267
28_L36_L0.404441.222
13_R19_K0.395281.194
37_L55_I0.386921.169
17_Q30_E0.384291.161
47_S50_D0.373111.127
19_K30_E0.372491.125
26_Y41_A0.364981.103
37_L48_L0.351991.063
34_Y38_R0.350151.058
7_R11_S0.344641.041
11_S49_A0.340641.029
21_I25_R0.338131.021
44_R54_E0.336461.016
5_L9_L0.33171.002
26_Y36_L0.328120.991
16_E20_G0.328110.991
13_R30_E0.315990.955
22_L28_L0.314850.951
49_A53_E0.307460.929
12_R34_Y0.303010.915
36_L40_Q0.294990.891
34_Y42_M0.292660.884
41_A45_R0.291070.879
32_E36_L0.289410.874
23_M47_S0.285410.862
38_R48_L0.2810.849
3_E7_R0.278820.842
13_R17_Q0.271220.819
5_L8_A0.271120.819
12_R48_L0.26780.809
20_G23_M0.261070.789
35_R39_R0.258790.782
15_I52_A0.2540.767
18_A56_I0.244570.739
19_K34_Y0.243470.735
34_Y48_L0.238080.719
13_R42_M0.236410.714
22_L52_A0.235810.712
36_L51_V0.23380.706
4_Q8_A0.228450.690
26_Y54_E0.228380.690
20_G37_L0.226780.685
30_E42_M0.222630.673
25_R40_Q0.222450.672
12_R20_G0.215130.650
28_L32_E0.215070.650
30_E34_Y0.214610.648
37_L51_V0.214370.648
34_Y45_R0.21020.635
50_D54_E0.210090.635
12_R15_I0.207030.625
26_Y32_E0.204630.618
24_A31_D0.200230.605
20_G24_A0.199940.604
4_Q7_R0.198780.600
24_A53_E0.198460.600
14_V17_Q0.198220.599
9_L18_A0.197090.595
20_G34_Y0.196120.592
35_R42_M0.195870.592
11_S15_I0.194910.589
13_R28_L0.193650.585
42_M47_S0.192630.582
24_A36_L0.189260.572
10_E13_R0.188430.569
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
4akkA199.5-0.072
1qo0D198.60.303
1s8nA198.10.411
3kb9A0.982181.60.725
3v1vA1810.727
1di1A177.70.735
1ps1A0.982175.80.738
3bnyA173.20.744
4bb9A172.80.745
3b9tA0.9107540.773

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