GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Clr5 - Clr5 domain
Pfam: PF14420 (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: 54
Sequences: 259
Seq/Len: 4.8
HH_delta: 0.815 (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
14_R19_E0.558833.363
46_R49_K0.400692.411
38_A43_Y0.37652.266
13_E52_F0.368482.217
30_M43_Y0.365252.198
21_K25_E0.28041.687
40_K44_K0.274891.654
30_M38_A0.26441.591
15_L26_V0.245181.475
28_E32_E0.232131.397
12_I47_F0.2311.390
8_H11_E0.227611.370
45_R48_K0.216811.305
47_F53_R0.21271.280
4_D7_P0.208011.252
14_R18_D0.203821.227
9_K13_E0.200771.208
9_K52_F0.200711.208
31_K37_K0.173721.045
30_M47_F0.170541.026
39_T42_Q0.169521.020
12_I53_R0.165280.995
4_D41_R0.162340.977
17_I24_E0.16030.965
4_D8_H0.157190.946
47_F52_F0.156550.942
18_D32_E0.153250.922
27_M40_K0.153190.922
20_N52_F0.151850.914
5_W42_Q0.1510.909
9_K51_G0.150380.905
27_M39_T0.148620.894
6_E9_K0.148560.894
23_L27_M0.147010.885
23_L38_A0.146170.880
44_K48_K0.145990.879
44_K52_F0.143540.864
16_Y23_L0.1420.854
30_M34_H0.141640.852
35_G49_K0.138190.832
4_D39_T0.137770.829
15_L29_I0.1350.812
3_E40_K0.133970.806
4_D37_K0.132650.798
13_E40_K0.132410.797
42_Q46_R0.129510.779
13_E17_I0.126760.763
3_E39_T0.125110.753
29_I51_G0.124960.752
19_E22_T0.124390.749
11_E34_H0.12390.746
10_E35_G0.122080.735
45_R53_R0.121840.733
29_I33_E0.120820.727
14_R28_E0.120670.726
2_D42_Q0.120160.723
25_E51_G0.120120.723
11_E15_L0.120110.723
2_D46_R0.120020.722
3_E38_A0.118730.714
10_E18_D0.117730.708
14_R53_R0.116530.701
45_R49_K0.116330.700
22_T26_V0.114940.692
34_H44_K0.114810.691
14_R33_E0.114410.688
5_W36_F0.112670.678
10_E14_R0.11240.676
10_E28_E0.112080.674
12_I43_Y0.111320.670
10_E32_E0.109490.659
40_K47_F0.109380.658
20_N28_E0.109010.656
24_E40_K0.10860.654
17_I52_F0.108130.651
4_D31_K0.106130.639
3_E42_Q0.106060.638
20_N51_G0.106040.638
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
2lvsA0.851960.60.815
1b4aA0.944456.80.819
1pdnC0.925950.90.825
1k78A147.50.828
3eb7A0.981538.60.836
3v4gA0.925936.20.839
1w99A0.981529.30.846
3lapA0.925928.40.847
1u78A0.907427.40.848
2k27A127.30.848
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