GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FeoC - FeoC like transcriptional regulator
Pfam: PF09012 (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: 69
Sequences: 7091
Seq/Len: 102.77
HH_delta: 0.171 (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
39_I46_K1.265772.312
8_Y23_E1.141782.086
16_S19_E1.048251.915
21_A28_P0.998651.824
6_R43_Y0.956241.747
37_Q41_K0.886481.619
8_Y12_R0.85511.562
17_L28_P0.840171.535
9_L44_I0.820031.498
15_V23_E0.756861.382
36_E39_I0.742471.356
39_I44_I0.735881.344
29_E32_E0.726641.327
30_A33_A0.713611.303
4_E7_D0.700491.280
8_Y11_E0.67681.236
17_L32_E0.67541.234
36_E46_K0.671711.227
19_E23_E0.648911.185
26_I31_V0.609491.113
37_Q40_R0.604761.105
33_A36_E0.583361.066
18_A28_P0.579151.058
34_M37_Q0.575991.052
20_L35_L0.571311.044
6_R38_L0.559561.022
31_V35_L0.555561.015
18_A22_R0.548871.003
9_L12_R0.54761.000
14_R47_V0.538950.984
33_A37_Q0.532520.973
47_V50_S0.52650.962
49_M52_C0.522080.954
7_D11_E0.514230.939
38_L43_Y0.512130.935
4_E24_F0.51030.932
6_R10_R0.508780.929
20_L31_V0.507460.927
32_E36_E0.504290.921
30_A34_M0.503410.920
11_E23_E0.501030.915
4_E8_Y0.491410.898
17_L35_L0.469260.857
36_E40_R0.451080.824
9_L15_V0.437640.799
28_P32_E0.43630.797
19_E22_R0.431020.787
20_L24_F0.424760.776
27_S30_A0.421780.770
4_E23_E0.415580.759
12_R23_E0.413710.756
14_R18_A0.412450.753
18_A21_A0.409310.748
15_V19_E0.402440.735
16_S27_S0.400790.732
28_P36_E0.396980.725
21_A26_I0.390510.713
48_D52_C0.379830.694
6_R9_L0.378680.692
37_Q49_M0.37150.679
8_Y24_F0.364190.665
24_F34_M0.352710.644
17_L29_E0.352390.644
15_V49_M0.351360.642
25_G45_R0.349130.638
12_R15_V0.345350.631
20_L30_A0.343990.628
17_L31_V0.343590.628
42_G45_R0.341520.624
31_V34_M0.338660.619
5_I34_M0.329820.602
7_D10_R0.329220.601
17_L33_A0.328970.601
32_E50_S0.328310.600
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
1xn7A198.60.171
2k02A198.60.188
2fe3A0.985598.20.282
3eyyA0.985598.10.311
2htjA198.10.313
2xigA0.985598.10.317
4i7hA0.985598.10.317
3mwmA0.985598.10.319
1mzbA0.985598.10.319
2jt1A0.97198.10.321

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