GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAN_2 - PAN-like domain
Pfam: PF08276 (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: CL0168
Length: 66
Sequences: 1391
Seq/Len: 21.08
HH_delta: 0.696 (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
34_K38_S0.377941.847
30_E33_E0.335411.639
10_L13_M0.305381.493
32_C36_C0.291531.425
7_F45_Y0.279881.368
36_C42_C0.270271.321
25_S48_S0.266881.304
15_L45_Y0.261981.280
5_D9_K0.261871.280
13_M60_Y0.256821.255
48_S54_G0.25271.235
18_F57_L0.252651.235
57_L65_D0.247851.211
32_C42_C0.247571.210
42_C56_C0.247471.210
45_Y59_W0.24211.183
10_L29_L0.241411.180
35_A57_L0.23921.169
18_F21_A0.235311.150
33_E38_S0.235221.150
14_K65_D0.231121.130
35_A58_L0.226371.106
11_P44_A0.225681.103
12_N25_S0.225311.101
6_G21_A0.223951.095
9_K34_K0.223611.093
16_P59_W0.222041.085
31_E39_N0.221961.085
33_E37_L0.219341.072
5_D59_W0.212521.039
25_S54_G0.211241.032
15_L37_L0.207091.012
27_V54_G0.204761.001
47_Y54_G0.20430.999
18_F43_T0.203890.997
16_P45_Y0.20280.991
18_F65_D0.201780.986
48_S57_L0.200760.981
35_A40_C0.198510.970
4_G61_G0.197030.963
11_P57_L0.192010.938
58_L62_D0.191810.937
9_K27_V0.187430.916
31_E34_K0.185720.908
43_T57_L0.184870.904
14_K18_F0.184570.902
14_K17_D0.18440.901
25_S29_L0.183430.897
13_M64_V0.181790.889
30_E43_T0.181710.888
30_E34_K0.181410.887
40_C44_A0.180770.884
5_D16_P0.179620.878
22_I35_A0.178460.872
46_A59_W0.176690.864
18_F53_G0.176120.861
16_P46_A0.176030.860
56_C63_L0.175780.859
19_D47_Y0.174950.855
19_D22_I0.17440.852
9_K38_S0.174340.852
12_N33_E0.174140.851
8_L12_N0.173960.850
36_C56_C0.172440.843
25_S38_S0.170980.836
55_G59_W0.168660.824
21_A29_L0.167730.820
28_S34_K0.167240.817
16_P21_A0.167050.816
4_G41_S0.166170.812
11_P18_F0.165460.809
26_S35_A0.162820.796
20_N48_S0.162820.796
21_A60_Y0.161780.791
8_L13_M0.160480.784
18_F47_Y0.160360.784
13_M58_L0.159960.782
8_L33_E0.158850.776
8_L58_L0.158740.776
20_N39_N0.158260.774
37_L64_V0.157820.771
11_P19_D0.157490.770
28_S31_E0.157190.768
8_L17_D0.156020.763
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
4a5vA0.924290.30.696
2f83A0.984890.30.696
4a5vA0.939489.40.701
2f83A0.893988.80.705
4durA0.939484.50.722
2ll3A0.924280.90.733
2yilA0.863676.80.743
3hmsA0.969771.50.752
3sp8A0.969769.70.756
2qj2A0.969735.90.799
If you are interested in a protein containing this domain,
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