GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HxlR - HxlR-like helix-turn-helix
Pfam: PF01638 (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: 90
Sequences: 31276
Seq/Len: 347.51
HH_delta: 0.023 (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
44_E51_R2.301032.040
50_E64_S2.184511.937
18_P64_S2.138321.896
52_R64_S2.10791.869
15_F73_L2.094981.858
25_Q33_P1.988811.764
54_Y62_E1.921761.704
20_R23_E1.919521.702
10_I39_R1.79481.592
13_A27_R1.777741.576
23_E26_R1.646481.460
34_K38_Q1.625011.441
51_R61_V1.622551.439
32_S35_V1.609211.427
66_T69_G1.558411.382
37_S41_K1.521171.349
50_E66_T1.519171.347
73_L77_E1.500091.330
40_L63_Y1.381611.225
31_I35_V1.335881.185
38_Q42_E1.324041.174
18_P52_R1.276691.132
21_F63_Y1.272991.129
74_P78_A1.266551.123
75_V78_A1.255651.113
53_V61_V1.25341.111
22_S26_R1.239081.099
34_K37_S1.230191.091
15_F77_E1.227951.089
71_E74_P1.215841.078
68_K71_E1.214791.077
9_L13_A1.208481.072
18_P62_E1.207011.070
18_P27_R1.19931.063
39_R42_E1.19541.060
12_R16_Q1.191711.057
52_R62_E1.168791.036
32_S38_Q1.165841.034
72_L75_V1.16091.029
21_F36_L1.144281.015
15_F65_L1.140241.011
33_P37_S1.136531.008
47_G68_K1.110080.984
19_M23_E1.106530.981
21_F40_L1.104910.980
11_L14_L1.100890.976
35_V38_Q1.100550.976
71_E75_V1.07920.957
41_K45_E1.078960.957
22_S33_P1.066070.945
23_E27_R1.028550.912
65_L69_G1.02820.912
41_K44_E1.017520.902
70_K74_P1.016920.902
48_L72_L1.0040.890
25_Q36_L1.00260.889
31_I36_L0.997560.885
67_E70_K0.99720.884
10_I14_L0.996210.883
38_Q41_K0.989760.878
48_L51_R0.977340.867
47_G50_E0.977290.867
67_E71_E0.970120.860
21_F37_S0.966090.857
28_L36_L0.960890.852
19_M27_R0.942130.835
13_A19_M0.915820.812
13_A28_L0.914490.811
13_A16_Q0.873270.774
14_L24_L0.865870.768
68_K72_L0.860810.763
14_L49_V0.843160.748
21_F61_V0.83940.744
35_V39_R0.831770.738
10_I36_L0.828110.734
20_R62_E0.80780.716
76_L79_L0.789530.700
75_V79_L0.772780.685
42_E46_A0.76610.679
18_P24_L0.7570.671
74_P77_E0.753030.668
15_F70_K0.7190.638
12_R15_F0.713190.632
11_L48_L0.709070.629
14_L65_L0.70880.629
28_L31_I0.705970.626
21_F33_P0.704040.624
41_K51_R0.703520.624
48_L68_K0.703260.624
24_L49_V0.694660.616
17_G27_R0.690460.612
70_K73_L0.683810.606
11_L15_F0.679250.602
36_L40_L0.669760.594
65_L70_K0.662470.587
13_A24_L0.661620.587
42_E45_E0.659890.585
15_F74_P0.651570.578
49_V63_Y0.641210.569
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
4a5nA199.30.023
2hztA199.30.055
2fswA0.955699.30.059
1yyvA199.30.061
2f2eA0.977899.30.062
1z7uA199.20.068
3df8A0.955699.20.105
4hqeA199.10.131
1hsjA0.9444990.161
1xmaA1990.171

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