GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pribosyltran - Phosphoribosyl transferase domain
Pfam: PF00156 (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: CL0533
Length: 125
Sequences: 12832
Seq/Len: 102.66
HH_delta: 0.185 (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
90_R117_K2.238223.732
90_R118_V2.086443.479
15_E48_A1.82493.043
104_L121_V1.566172.612
111_L116_A1.452872.423
98_I123_V1.356912.263
108_I112_K1.318322.198
34_I107_A1.284242.141
86_I89_K1.240662.069
87_K115_G1.139531.900
105_K109_E1.069721.784
90_R120_G1.022231.705
44_A47_R1.015461.693
30_V89_K0.989021.649
16_R19_E0.897211.496
11_E48_A0.895071.493
108_I121_V0.877651.463
46_A53_L0.862411.438
19_E22_K0.85941.433
31_I46_A0.847931.414
31_I92_L0.823971.374
104_L123_V0.812721.355
88_G117_K0.811121.353
18_A48_A0.802431.338
18_A49_L0.797541.330
110_L113_E0.792991.322
20_Q24_S0.79251.321
109_E113_E0.791821.320
18_A45_L0.783921.307
33_G42_A0.766871.279
93_I107_A0.764841.275
106_E109_E0.759621.267
14_A45_L0.753461.256
12_A16_R0.74491.242
109_E112_K0.720931.202
11_E47_R0.710321.184
24_S120_G0.708811.182
12_A15_E0.708141.181
18_A22_K0.703081.172
69_T73_K0.701181.169
17_L122_A0.69581.160
31_I49_L0.6841.141
94_V122_A0.682971.139
45_L94_V0.680841.135
56_V107_A0.679831.134
21_I122_A0.654561.091
29_D51_I0.654271.091
13_L16_R0.653651.090
15_E19_E0.648821.082
21_I45_L0.640671.068
30_V91_V0.636321.061
42_A53_L0.632181.054
27_D89_K0.626991.046
92_L122_A0.622091.037
28_F89_K0.618891.032
29_D89_K0.610131.017
32_V111_L0.603551.006
68_K77_E0.600281.001
31_I42_A0.595570.993
20_Q23_E0.590530.985
101_G105_K0.586940.979
11_E44_A0.586440.978
28_F90_R0.581240.969
43_A47_R0.579950.967
39_I55_F0.572160.954
21_I92_L0.570750.952
80_I83_K0.567590.946
16_R20_Q0.567440.946
28_F92_L0.565090.942
36_R39_I0.563180.939
29_D90_R0.557170.929
19_E23_E0.553190.922
70_S75_N0.552780.922
14_A48_A0.551190.919
90_R119_V0.547450.913
72_E76_Q0.544470.908
25_G120_G0.534490.891
32_V107_A0.52510.876
78_L81_I0.511870.854
14_A44_A0.50780.847
92_L120_G0.505480.843
32_V56_V0.500990.835
21_I24_S0.499350.833
22_K50_G0.494620.825
17_L20_Q0.490430.818
21_I120_G0.489370.816
93_I111_L0.483330.806
116_A119_V0.482830.805
68_K71_R0.482130.804
42_A46_A0.48080.802
91_V111_L0.477160.796
40_P43_A0.476810.795
44_A48_A0.475440.793
107_A110_L0.474280.791
98_I101_G0.467190.779
23_E26_F0.46690.779
30_V54_V0.462080.771
32_V54_V0.45620.761
17_L45_L0.45380.757
102_G106_E0.451080.752
68_K72_E0.443770.740
36_R40_P0.44340.739
93_I108_I0.441610.736
93_I104_L0.436530.728
38_G41_L0.434910.725
48_A51_I0.433870.723
11_E15_E0.432080.720
14_A18_A0.431880.720
112_K119_V0.429170.716
42_A94_V0.426280.711
70_S73_K0.420540.701
72_E75_N0.41920.699
31_I94_V0.416590.695
58_K61_S0.41540.693
43_A53_L0.41110.686
13_L124_L0.410190.684
95_D98_I0.409740.683
35_P39_I0.408890.682
17_L124_L0.40760.680
81_I114_A0.405340.676
11_E50_G0.398920.665
85_D89_K0.391620.653
86_I116_A0.390470.651
36_R99_D0.387060.645
35_P58_K0.385940.644
81_I84_E0.384750.642
27_D90_R0.383560.640
19_E48_A0.38290.638
32_V91_V0.382560.638
106_E110_L0.380330.634
112_K118_V0.373620.623
26_F29_D0.373170.622
86_I111_L0.368130.614
31_I51_I0.367390.613
46_A51_I0.365790.610
75_N78_L0.361850.603
57_R61_S0.361090.602
20_Q122_A0.361020.602
26_F51_I0.360880.602
105_K108_I0.356560.595
72_E102_G0.355990.594
108_I119_V0.354570.591
45_L49_L0.354210.591
15_E47_R0.352520.588
95_D123_V0.351880.587
41_L44_A0.351180.586
25_G90_R0.34880.582
91_V116_A0.348770.582
88_G116_A0.348580.581
37_G40_P0.345660.576
91_V119_V0.345190.576
70_S74_N0.340570.568
100_T123_V0.340260.567
83_K87_K0.339810.567
54_V89_K0.338150.564
73_K76_Q0.33680.562
33_G107_A0.334950.559
98_I104_L0.334370.558
71_R75_N0.333980.557
77_E80_I0.332220.554
33_G38_G0.331750.553
54_V58_K0.331570.553
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
3m3hA0.90499.70.185
1qb7A199.70.191
3dezA0.90499.70.194
1tc1A0.97699.70.204
2ywuA0.97699.70.206
1pzmA0.97699.70.209
1hgxA0.96899.70.209
3hvuA0.97699.70.211
1yfzA0.97699.70.211
2gebA0.97699.70.211

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