GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pou - Pou domain - N-terminal to homeobox domain
Pfam: PF00157 (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: CL0123
Length: 75
Sequences: 7185
Seq/Len: 95.8
HH_delta: 0.243 (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
20_R51_E2.721123.280
28_A44_Q1.83072.207
19_R23_L1.818022.191
33_A66_L1.753972.114
19_R22_K1.504811.814
46_T50_F1.451651.750
49_R54_Q1.370181.652
44_Q48_C1.354451.633
48_C52_A1.353641.632
29_D33_A1.335771.610
46_T49_R1.247241.503
26_T29_D1.224751.476
18_Q22_K1.215231.465
34_L66_L1.193711.439
27_Q48_C1.150361.387
30_V47_I1.118521.348
59_N62_K1.115441.345
15_E18_Q1.110851.339
28_A32_A1.106861.334
13_A53_L1.106821.334
45_T48_C1.106721.334
25_Y33_A1.028471.240
15_E19_R0.9681.167
50_F55_L0.923431.113
11_Q53_L0.895491.079
27_Q44_Q0.882771.064
50_F59_N0.864941.043
42_F59_N0.850061.025
64_K69_K0.848371.023
29_D32_A0.813390.980
34_L42_F0.81290.980
17_K51_E0.809630.976
25_Y29_D0.799720.964
11_Q15_E0.795280.959
23_L68_E0.792750.956
57_F61_C0.791850.955
12_F16_F0.786930.949
43_S46_T0.762360.919
60_M64_K0.762150.919
61_C65_P0.75450.909
25_Y30_V0.75010.904
42_F46_T0.724140.873
10_E14_K0.719370.867
31_G47_I0.716250.863
19_R69_K0.691040.833
19_R67_L0.684760.825
31_G44_Q0.663280.800
17_K21_I0.654980.790
55_L59_N0.643220.775
30_V67_L0.616030.743
14_K18_Q0.606230.731
31_G34_L0.58490.705
63_L67_L0.568260.685
42_F47_I0.557540.672
25_Y66_L0.549870.663
16_F67_L0.549690.663
30_V66_L0.533460.643
50_F56_S0.528860.637
11_Q14_K0.521820.629
34_L59_N0.514760.621
41_E62_K0.512740.618
30_V63_L0.51260.618
58_K62_K0.510870.616
58_K61_C0.506110.610
56_S59_N0.49950.602
57_F60_M0.497950.600
15_E69_K0.48180.581
23_L67_L0.476210.574
13_A17_K0.470890.568
34_L63_L0.468320.565
16_F30_V0.468310.565
47_I50_F0.460660.555
45_T49_R0.440370.531
13_A51_E0.438440.529
14_K53_L0.431820.521
20_R27_Q0.428660.517
27_Q45_T0.421140.508
20_R30_V0.417170.503
16_F50_F0.414420.500
46_T56_S0.41340.498
12_F60_M0.412610.497
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
4ghjA0.92990.243
3mlfA0.9298.90.257
4ichA0.9298.90.27
3op9A0.893398.80.277
3vk0A0.9298.80.284
3ivpA0.9298.80.29
1y9qA0.9298.80.299
3g5gA0.9298.80.301
4f8dA0.9298.70.305
3fymA0.813398.70.306

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