GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pentapeptide_4 - Pentapeptide repeats (9 copies)
Pfam: PF13599 (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: CL0505
Length: 78
Sequences: 4754
Seq/Len: 60.95
HH_delta: 0.108 (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
32_N35_K1.301942.339
35_K53_D1.276412.293
40_S58_S1.046251.880
14_S32_N1.028621.848
9_S27_N0.950371.708
29_S48_D0.930781.672
36_E56_R0.927771.667
50_S68_D0.924391.661
8_F28_F0.917981.649
46_N66_N0.908981.633
45_D63_D0.90571.627
20_G41_N0.895411.609
33_F54_L0.872511.568
41_N61_N0.864261.553
30_N51_N0.84021.510
39_F59_F0.834431.499
24_K43_Q0.798391.434
51_N71_G0.787151.414
10_G30_N0.784271.409
15_G36_E0.775581.393
49_F69_F0.769491.383
18_F39_F0.760581.367
54_L59_F0.758081.362
25_N46_N0.746191.341
44_L64_L0.731051.313
35_K55_K0.72131.296
19_S38_N0.698151.254
45_D65_D0.678851.220
23_F44_L0.661271.188
28_F49_F0.659451.185
6_C11_C0.656811.180
42_C62_C0.643321.156
11_C31_C0.634791.141
19_S40_S0.625531.124
5_N25_N0.624671.122
14_S35_K0.622521.118
43_Q63_D0.612291.100
9_S29_S0.60421.086
48_D68_D0.583161.048
13_L33_F0.580921.044
59_F64_L0.569761.024
31_C52_C0.556921.001
37_A57_A0.54750.984
24_K45_D0.533850.959
38_N58_S0.529550.951
7_S27_N0.527310.947
16_A37_A0.526190.945
17_N38_N0.525020.943
44_L49_F0.520920.936
21_S42_C0.518150.931
64_L69_F0.517980.931
40_S60_S0.516230.928
50_S70_S0.513670.923
22_N43_Q0.512850.921
23_F28_F0.508120.913
23_F26_C0.501720.901
27_N48_D0.482970.868
33_F39_F0.475020.853
12_N32_N0.465320.836
32_N53_D0.447560.804
6_C26_C0.438060.787
26_C47_S0.427530.768
8_F11_C0.427280.768
11_C16_A0.425660.765
29_S50_S0.409890.736
47_S67_C0.400770.720
44_L62_C0.389630.700
64_L67_C0.38910.699
54_L57_A0.37230.669
15_G56_R0.370890.666
16_A21_S0.369440.664
33_F52_C0.363290.653
18_F37_A0.360150.647
39_F44_L0.360140.647
28_F33_F0.356410.640
19_S60_S0.347560.624
38_N62_C0.344460.619
8_F31_C0.339640.610
19_S41_N0.337190.606
18_F23_F0.333860.600
49_F54_L0.332810.598
6_C16_A0.329660.592
21_S26_C0.327760.589
68_D71_G0.307230.552
18_F21_S0.295590.531
51_N55_K0.291490.524
33_F37_A0.288990.519
13_L16_A0.288010.517
13_L31_C0.283330.509
12_N15_G0.264620.475
27_N52_C0.263070.473
29_S51_N0.26230.471
17_N20_G0.260030.467
18_F42_C0.259420.466
33_F57_A0.256780.461
23_F47_S0.25370.456
23_F42_C0.24610.442
44_L47_S0.245320.441
53_D57_A0.241180.433
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
3nb2A0.987299.10.108
3n90A0.987299.10.118
3nb2A0.987299.10.123
2w7zA0.9872990.145
3n90A0.9872990.146
2w7zA0.9872990.152
2bm5A0.9872990.153
2qyuA0.9872990.16
2f3lA0.9872990.16
2bm5A0.9872990.161

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