GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Skp1_POZ - Skp1 family tetramerisation domain
Pfam: PF03931 (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: CL0033
Length: 62
Sequences: 821
Seq/Len: 13.24
HH_delta: 0.001 (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_V12_E0.523852.451
4_K12_E0.515172.410
9_D47_S0.486862.278
13_F47_S0.412931.932
7_S50_L0.406471.902
41_P44_N0.390091.825
7_S13_F0.337271.578
22_Q57_C0.32081.501
11_Q51_K0.315191.475
52_K55_E0.307681.440
21_K27_K0.300661.407
15_V54_I0.291831.365
16_S58_E0.277941.300
8_S46_S0.271841.272
16_S19_A0.267841.253
51_K58_E0.266821.248
33_L56_W0.25871.210
23_S27_K0.251741.178
11_Q47_S0.243561.140
6_V39_P0.242151.133
50_L53_V0.241181.128
46_S49_I0.238271.115
29_M56_W0.23571.103
56_W61_K0.228071.067
49_I53_V0.22761.065
5_L50_L0.225041.053
4_K14_E0.220851.033
30_L51_K0.217941.020
29_M40_I0.215221.007
22_Q25_T0.215021.006
49_I52_K0.212960.996
15_V20_A0.211660.990
4_K52_K0.207190.969
8_S42_L0.206660.967
18_E61_K0.205020.959
25_T43_P0.203880.954
25_T28_N0.203150.951
28_N32_D0.202650.948
23_S26_I0.199060.931
13_F54_I0.195330.914
42_L45_V0.192630.901
16_S61_K0.19080.893
17_R30_L0.190740.892
28_N34_G0.190370.891
20_A25_T0.190080.889
12_E38_E0.184890.865
2_Y14_E0.18480.865
54_I58_E0.184690.864
14_E18_E0.183240.857
3_V26_I0.180040.842
5_L15_V0.179420.840
10_G17_R0.178030.833
20_A45_V0.177160.829
43_P48_R0.176640.827
16_S26_I0.175460.821
31_E43_P0.174250.815
57_C60_H0.172460.807
13_F51_K0.172060.805
36_E39_P0.171860.804
19_A22_Q0.169750.794
29_M38_E0.168350.788
7_S22_Q0.167260.783
32_D45_V0.165260.773
18_E51_K0.163020.763
43_P52_K0.16290.762
14_E17_R0.162160.759
3_V20_A0.159060.744
23_S52_K0.157730.738
54_I60_H0.157290.736
17_R28_N0.157170.735
11_Q22_Q0.156620.733
28_N35_D0.154550.723
3_V52_K0.15410.721
19_A58_E0.153840.720
32_D43_P0.153550.718
19_A54_I0.152970.716
2_Y18_E0.151860.711
5_L54_I0.151570.709
40_I48_R0.151060.707
21_K45_V0.150830.706
21_K24_K0.15060.705
14_E49_I0.148390.694
24_K28_N0.147760.691
7_S54_I0.147510.690
32_D41_P0.147110.688
17_R48_R0.146950.688
56_W60_H0.146890.687
3_V42_L0.142770.668
2_Y37_D0.142640.667
16_S36_E0.141780.663
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
1vcbB199.60.001
3v7dA199.60.008
2fnjC199.60.008
1hv2A0.983999.60.012
1fs1B0.967799.50.056
4ajyC199.50.058
2p1mA0.983999.50.06
2astA199.50.106
2vkpA196.10.659
3htmA0.9839960.662

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