GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
K-box - K-box region
Pfam: PF01486 (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. )
Length: 100
Sequences: 1816
Seq/Len: 18.16
HH_delta: 0.85 (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
10_W14_H0.404242.200
68_R72_L0.380222.069
84_E87_L0.344671.876
37_H46_L0.336591.832
51_L55_E0.32021.743
59_E63_K0.315551.717
84_E91_N0.311581.696
71_Q75_E0.308961.681
91_N94_L0.306971.671
12_S15_E0.293651.598
80_L84_E0.293031.595
87_L91_N0.288851.572
78_E81_K0.279681.522
88_E92_N0.27451.494
33_K42_D0.26871.462
25_R37_H0.264691.440
35_L38_L0.260471.417
10_W13_Q0.260411.417
55_E58_L0.256481.396
62_L89_E0.250871.365
92_N96_Q0.247831.349
11_D15_E0.242441.319
35_L39_M0.240751.310
70_D73_L0.233731.272
48_L52_Q0.229041.246
91_N95_R0.225721.228
56_Q60_S0.222421.210
15_E19_Q0.22071.201
60_S63_K0.219061.192
25_R29_E0.213361.161
85_R89_E0.211041.148
31_L66_R0.201311.096
15_E18_Q0.19731.074
89_E94_L0.19711.073
10_W17_L0.196281.068
36_R41_E0.195521.064
57_Q61_A0.195041.061
53_Q56_Q0.190571.037
19_Q22_A0.190251.035
10_W28_N0.189791.033
20_E27_E0.188911.028
29_E42_D0.18771.021
10_W15_E0.186241.014
90_E96_Q0.183280.997
14_H17_L0.180760.984
29_E57_Q0.180530.982
89_E92_N0.176150.959
24_L40_G0.174970.952
28_N46_L0.174610.950
20_E66_R0.172360.938
34_E57_Q0.172150.937
21_I78_E0.171230.932
48_L54_L0.170650.929
23_K81_K0.170120.926
48_L63_K0.169440.922
65_V69_K0.167090.909
29_E38_L0.166970.909
44_E48_L0.16650.906
22_A98_I0.166190.904
58_L90_E0.166030.904
86_E90_E0.164950.898
38_L61_A0.163450.889
76_Q95_R0.16240.884
31_L34_E0.162180.883
52_Q55_E0.162140.882
14_H18_Q0.161720.880
56_Q72_L0.160570.874
39_M43_L0.160560.874
94_L97_K0.160090.871
17_L38_L0.15990.870
52_Q63_K0.159840.870
80_L87_L0.159580.868
69_K79_E0.1590.865
43_L48_L0.157560.857
29_E61_A0.155970.849
17_L68_R0.155650.847
42_D57_Q0.155390.846
81_K84_E0.154620.841
76_Q85_R0.153930.838
86_E95_R0.153180.834
74_M79_E0.152680.831
55_E66_R0.15250.830
63_K67_S0.152410.829
73_L84_E0.151520.825
16_E19_Q0.151340.824
59_E64_R0.150950.821
26_K29_E0.14930.812
15_E82_K0.149050.811
20_E23_K0.148990.811
60_S72_L0.148670.809
57_Q75_E0.148320.807
31_L57_Q0.147740.804
29_E92_N0.147150.801
25_R49_K0.147010.800
60_S64_R0.14630.796
39_M49_K0.14620.796
84_E88_E0.145540.792
80_L91_N0.145130.790
47_S54_L0.144560.787
30_S34_E0.144550.787
32_Q35_L0.143590.781
11_D98_I0.143540.781
64_R67_S0.14280.777
21_I28_N0.142510.776
32_Q46_L0.142470.775
58_L71_Q0.142430.775
48_L56_Q0.142020.773
85_R90_E0.141860.772
43_L65_V0.140730.766
50_E55_E0.140640.765
82_K92_N0.140260.763
11_D60_S0.139330.758
27_E37_H0.139190.757
75_E79_E0.139080.757
78_E86_E0.138610.754
18_Q22_A0.138450.753
36_R66_R0.138260.752
16_E21_I0.137970.751
34_E67_S0.13780.750
63_K70_D0.137640.749
32_Q39_M0.137590.749
10_W34_E0.137510.748
77_I80_L0.136260.742
18_Q24_L0.136230.741
71_Q77_I0.136110.741
16_E44_E0.135360.737
82_K86_E0.13510.735
63_K92_N0.134910.734
54_L74_M0.134270.731
33_K76_Q0.134090.730
28_N96_Q0.13390.729
33_K56_Q0.133560.727
78_E82_K0.133360.726
66_R72_L0.132230.720
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
2jeeA0.5256.60.85
2dfsA0.9635.50.867
2v71A0.9223.20.878
3s9gA0.8319.40.882
1go4E0.9119.10.882
3na7A0.9717.80.884
3ojaB115.80.887
1i84S0.9714.10.889
3ghgA0.9912.80.891
1m1jC0.9312.50.891
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.033 seconds.