GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Homeobox - Homeobox domain
Pfam: PF00046 (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: 57
Sequences: 4523
Seq/Len: 79.35
HH_delta: -0.206 (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
18_Y29_E1.205522.262
19_F55_E1.185032.224
8_T11_Q1.181612.217
16_E51_R1.090362.046
30_R41_E0.975761.831
14_V36_E0.96531.811
46_N50_N0.831431.560
32_E36_E0.828431.555
14_V17_E0.816811.533
22_N29_E0.792181.487
40_T43_Q0.762721.431
30_R45_K0.748561.405
3_K9_K0.706751.326
26_S29_E0.686561.288
7_F39_L0.6811.278
39_L43_Q0.656081.231
49_Q53_R0.620111.164
33_L44_V0.614591.153
31_E41_E0.609841.144
23_P55_E0.59551.117
47_W50_N0.592741.112
34_A44_V0.590951.109
25_P48_F0.578911.086
27_K31_E0.57621.081
17_E21_E0.564581.059
46_N49_Q0.563241.057
17_E20_Q0.561781.054
7_F43_Q0.557721.047
32_E35_K0.556721.045
18_Y33_L0.551221.034
52_R56_K0.547231.027
31_E35_K0.546371.025
9_K13_K0.540541.014
48_F52_R0.539291.012
18_Y22_N0.538891.011
27_K53_R0.532560.999
6_R9_K0.53050.996
7_F24_Y0.503880.946
50_N54_K0.498140.935
14_V33_L0.495470.930
13_K17_E0.491580.922
29_E32_E0.470540.883
18_Y21_E0.468240.879
34_A37_L0.464860.872
47_W52_R0.460.863
9_K12_L0.451490.847
18_Y25_P0.447080.839
28_E32_E0.424990.798
19_F51_R0.422240.792
10_E14_V0.420960.790
21_E28_E0.404140.758
11_Q37_L0.40380.758
51_R55_E0.4030.756
49_Q56_K0.401280.753
27_K41_E0.400660.752
12_L16_E0.39970.750
14_V37_L0.396190.743
46_N53_R0.393150.738
10_E35_K0.384710.722
16_E20_Q0.384490.722
51_R54_K0.383560.720
14_V18_Y0.37780.709
42_R45_K0.374520.703
16_E19_F0.3720.698
45_K53_R0.360880.677
34_A38_G0.358130.672
10_E13_K0.354320.665
53_R56_K0.354180.665
6_R12_L0.351660.660
3_K6_R0.34240.643
10_E36_E0.334450.628
25_P30_R0.328120.616
50_N53_R0.327540.615
42_R49_Q0.322490.605
14_V21_E0.321930.604
45_K51_R0.320110.601
3_K29_E0.319470.599
23_P28_E0.313720.589
44_V47_W0.312640.587
50_N56_K0.310330.582
28_E35_K0.310270.582
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
2m34A199.2-0.206
1e3oC199.2-0.198
2xsdC199.2-0.198
3d1nI199.1-0.19
1au7A199.1-0.189
2dmtA199.1-0.187
2da3A199.1-0.184
2cueA199.1-0.181
3a01A199.1-0.181
2craA199.1-0.18

Page generated in 0.0404 seconds.