GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Agenet - Agenet domain
Pfam: PF05641 (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: CL0049
Length: 68
Sequences: 791
Seq/Len: 11.63
HH_delta: 0.233 (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
6_E39_D0.53132.748
22_P40_D0.444832.301
37_E52_K0.318421.647
26_L37_E0.306021.583
38_Y53_E0.293911.520
7_V23_A0.284421.471
22_P39_D0.283751.468
8_E61_R0.27951.446
9_V23_A0.271231.403
6_E24_T0.268911.391
7_V60_I0.262231.356
8_E63_C0.254191.315
17_R21_F0.23211.201
20_W59_R0.231391.197
35_L54_W0.230721.193
12_D53_E0.224081.159
56_D59_R0.222561.151
2_K30_G0.221871.148
26_L52_K0.212131.097
3_K27_K0.210171.087
22_P42_P0.208931.081
33_K54_W0.205931.065
8_E37_E0.204811.059
3_K26_L0.204011.055
34_Y57_A0.203981.055
9_V41_L0.194281.005
12_D59_R0.193341.000
13_E38_Y0.192130.994
28_E31_D0.191240.989
12_D18_G0.19070.986
2_K35_L0.189920.982
13_E18_G0.189840.982
31_D54_W0.186820.966
20_W61_R0.184350.954
17_R41_L0.181870.941
7_V34_Y0.176980.915
10_S59_R0.172410.892
17_R43_D0.171130.885
62_P65_P0.17040.881
18_G59_R0.169780.878
25_V40_D0.168990.874
36_V55_V0.168370.871
19_A61_R0.168240.870
7_V19_A0.167580.867
11_S38_Y0.167320.865
27_K35_L0.165830.858
5_D20_W0.165780.858
18_G42_P0.165760.857
11_S25_V0.164720.852
30_G57_A0.162080.838
19_A31_D0.161880.837
11_S41_L0.161550.836
40_D43_D0.159510.825
22_P63_C0.15660.810
26_L34_Y0.154920.801
24_T39_D0.152970.791
20_W38_Y0.148670.769
30_G33_K0.148480.768
35_L52_K0.14630.757
22_P35_L0.145560.753
17_R22_P0.145010.750
18_G62_P0.144370.747
29_N54_W0.143940.745
19_A38_Y0.143640.743
23_A28_E0.143620.743
11_S40_D0.142890.739
21_F38_Y0.142380.736
42_P63_C0.141450.732
5_D25_V0.140250.725
7_V61_R0.139160.720
9_V55_V0.138230.715
22_P25_V0.138090.714
12_D17_R0.136520.706
17_R36_V0.135870.703
13_E62_P0.135020.698
34_Y60_I0.134470.696
55_V58_R0.133340.690
10_S24_T0.13330.690
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
1g5vA0.838299.20.233
1mhnA0.808899.20.242
2d9tA0.838299.10.26
3pnwC0.838299.10.27
2equA0.808899.10.286
3s6wA0.764799.10.287
4a4fA0.808899.10.288
2eqkA0.838299.10.292
2ldmA0.8088990.3
3fdrA0.8382990.3

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