GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LytTR - LytTr DNA-binding domain
Pfam: PF04397 (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: 98
Sequences: 4029
Seq/Len: 41.11
HH_delta: -0.011 (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
40_E50_R1.502913.097
51_I83_I1.260822.598
74_E82_E1.119182.306
2_R64_S1.042212.147
40_E56_I1.006022.073
52_H55_Y0.967291.993
22_R29_S0.966661.992
44_P47_N0.903241.861
13_Y55_Y0.885661.825
20_Y31_E0.837091.725
90_K94_K0.836731.724
25_T30_Y0.833771.718
64_S76_I0.812181.673
86_S89_Y0.804411.657
91_K95_E0.796481.641
12_L61_H0.782561.612
14_I21_V0.774471.596
34_G38_E0.767871.582
7_P10_D0.756841.559
12_L79_N0.743821.533
17_E22_R0.737671.520
61_H78_K0.727041.498
34_G42_Q0.701061.444
35_T38_E0.700531.443
13_Y83_I0.685091.412
15_E24_H0.684841.411
49_I93_L0.67711.395
66_D82_E0.672711.386
57_V75_L0.671371.383
26_K61_H0.670121.381
63_K78_K0.651431.342
15_E22_R0.647141.333
52_H84_P0.619851.277
43_L48_F0.619361.276
92_E96_K0.607111.251
10_D26_K0.602061.240
47_N60_D0.601111.239
13_Y81_E0.599981.236
73_Y90_K0.598141.232
14_I39_L0.596781.230
76_I82_E0.586591.209
55_Y83_I0.577261.189
12_L26_K0.575541.186
22_R31_E0.56771.170
13_Y24_H0.565961.166
62_I75_L0.543081.119
58_N61_H0.541351.115
49_I59_L0.532871.098
21_V34_G0.532551.097
89_Y92_E0.520441.072
16_S19_H0.519911.071
23_I39_L0.509911.051
92_E95_E0.507091.045
2_R66_D0.505451.041
55_Y84_P0.499321.029
59_L96_K0.483190.996
49_I89_Y0.475360.979
16_S53_R0.474490.978
14_I23_I0.471660.972
63_K76_I0.447050.921
24_H29_S0.44340.914
17_E31_E0.426770.879
57_V77_L0.426630.879
23_I32_I0.420590.867
51_I75_L0.419590.865
66_D74_E0.416540.858
57_V62_I0.415090.855
14_I56_I0.415080.855
47_N58_N0.413240.851
75_L85_V0.410230.845
48_F56_I0.40870.842
38_E41_E0.406470.837
66_D76_I0.400250.825
12_L77_L0.395930.816
11_I14_I0.394910.814
19_H33_R0.390890.805
50_R89_Y0.388790.801
11_I23_I0.380770.785
36_L50_R0.378710.780
65_I73_Y0.374770.772
36_L56_I0.370510.763
15_E55_Y0.366130.754
72_R90_K0.359450.741
16_S20_Y0.357640.737
20_Y33_R0.355520.733
4_I64_S0.352180.726
72_R85_V0.351960.725
85_V93_L0.348590.718
65_I93_L0.34280.706
11_I48_F0.336790.694
51_I57_V0.33530.691
9_D60_D0.334880.690
21_V39_L0.329770.679
10_D27_N0.327860.676
16_S54_S0.323010.666
3_I65_I0.322070.664
21_V33_R0.318810.657
15_E54_S0.314320.648
37_K50_R0.313180.645
44_P56_I0.31180.642
24_H81_E0.309680.638
37_K53_R0.307030.633
61_H77_L0.30470.628
77_L83_I0.304350.627
34_G39_L0.296220.610
6_I30_Y0.295140.608
14_I32_I0.290580.599
17_E29_S0.289370.596
72_R93_L0.289170.596
63_K77_L0.28080.579
21_V36_L0.28040.578
37_K41_E0.279790.576
8_L44_P0.27280.562
12_L25_T0.270380.557
4_I63_K0.270230.557
25_T28_G0.269480.555
6_I23_I0.263840.544
53_R88_R0.263390.543
52_H83_I0.261480.539
77_L80_G0.252950.521
19_H31_E0.25010.515
38_E42_Q0.244250.503
52_H86_S0.243440.502
49_I92_E0.243370.501
75_L93_L0.240740.496
36_L39_L0.240240.495
41_E44_P0.240060.495
76_I80_G0.238390.491
65_I94_K0.235660.486
8_L32_I0.234380.483
4_I28_G0.232960.480
58_N77_L0.232930.480
18_G53_R0.232430.479
5_R64_S0.232020.478
52_H89_Y0.231080.476
43_L56_I0.230570.475
19_H35_T0.230080.474
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
3d6wA199.8-0.011
4g4kA0.89899.70.091
3bs1A0.89899.70.107
3tdgA0.8988.20.892
1eu3A0.71437.50.893
2wshA0.65317.20.894
1mg7A0.98984.80.902
1sg5A0.77554.80.902
4bkwA0.91843.50.908
2y9tA0.62243.40.908

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