GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAPS_reduct - Phosphoadenosine phosphosulfate reductase family
Pfam: PF01507 (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: CL0039
Length: 174
Sequences: 13434
Seq/Len: 77.21
HH_delta: 0.124 (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
27_P56_I1.762233.185
17_H21_E1.35362.446
17_H151_N1.265252.287
3_V100_K1.259672.277
14_V148_I1.23172.226
45_D49_K1.229792.223
46_E50_R1.213342.193
140_T143_D1.204422.177
30_F55_I1.192142.155
94_A97_E1.113962.013
146_D150_A1.091741.973
16_L28_V1.072481.938
21_E151_N1.041581.883
4_V16_L1.020871.845
94_A98_Y0.999061.806
27_P54_P0.980081.771
10_K148_I0.972061.757
143_D146_D0.968931.751
13_T47_L0.957691.731
10_K141_E0.95271.722
42_E46_E0.946171.710
147_Y150_A0.939531.698
38_P42_E0.934911.690
17_H20_R0.888091.605
28_V53_I0.885211.600
27_P98_Y0.882021.594
6_F13_T0.857491.550
19_A104_I0.843221.524
17_H147_Y0.831191.502
56_I98_Y0.830911.502
3_V29_V0.82131.484
2_I104_I0.809891.464
62_E66_Q0.796451.440
48_A55_I0.786121.421
46_E49_K0.786071.421
42_E45_D0.767391.387
146_D149_K0.764741.382
27_P100_K0.763051.379
41_Y45_D0.762351.378
32_D38_P0.756321.367
17_H51_Y0.754431.364
18_L147_Y0.750091.356
15_M104_I0.737981.334
15_M136_I0.733141.325
6_F28_V0.728771.317
3_V27_P0.72361.308
32_D59_R0.723421.308
149_K155_Y0.714321.291
90_P93_R0.700431.266
85_I89_K0.697241.260
14_V147_Y0.69421.255
28_V48_A0.693351.253
14_V144_V0.693241.253
147_Y151_N0.687841.243
41_Y57_V0.686881.241
18_L136_I0.68471.238
17_H153_L0.676561.223
142_E146_D0.653921.182
10_K145_W0.647731.171
56_I94_A0.643911.164
50_R154_P0.642841.162
89_K93_R0.640391.157
102_V133_V0.638291.154
6_F47_L0.632451.143
139_W147_Y0.627351.134
34_G59_R0.621531.123
47_L51_Y0.61341.109
108_R111_E0.610291.103
44_V55_I0.59661.078
4_V15_M0.594071.074
45_D55_I0.59281.071
148_I155_Y0.590821.068
10_K144_V0.584861.057
30_F41_Y0.584541.056
46_E154_P0.579321.047
58_Y90_P0.575181.040
75_S78_W0.57451.038
18_L22_A0.572651.035
39_E42_E0.571611.033
83_C87_K0.571551.033
56_I97_E0.57121.032
29_V94_A0.564181.020
44_V48_A0.562191.016
74_P78_W0.55841.009
20_R23_G0.555761.004
32_D57_V0.552830.999
60_P90_P0.551520.997
141_E145_W0.551510.997
122_E125_E0.548630.992
45_D57_V0.544230.984
74_P77_L0.526940.952
16_L53_I0.526110.951
96_K124_D0.525460.950
20_R51_Y0.525070.949
32_D41_Y0.520860.941
28_V55_I0.516120.933
5_S91_L0.514840.931
145_W149_K0.510030.922
95_L103_W0.505160.913
119_P122_E0.494610.894
69_I72_G0.492510.890
93_R97_E0.490950.887
61_P65_E0.48350.874
40_T44_V0.474720.858
9_G12_S0.474250.857
7_S12_S0.472140.853
95_L100_K0.470070.850
89_K92_R0.466750.844
6_F44_V0.464970.840
66_Q70_L0.463730.838
48_A51_Y0.462820.837
48_A53_I0.461090.833
63_T93_R0.460990.833
18_L139_W0.460460.832
13_T43_F0.460070.832
108_R144_V0.459310.830
91_L103_W0.458350.828
58_Y94_A0.458320.828
107_V134_Y0.454760.822
47_L50_R0.453820.820
34_G61_P0.45310.819
104_I133_V0.449810.813
65_E69_I0.445860.806
31_I60_P0.44540.805
6_F16_L0.445370.805
50_R152_G0.439420.794
65_E70_L0.4380.792
66_Q69_I0.428330.774
2_I102_V0.423340.765
111_E114_R0.423090.765
58_Y93_R0.422190.763
110_D141_E0.420310.760
43_F46_E0.418530.756
63_T86_L0.416110.752
30_F44_V0.413920.748
84_S87_K0.41280.746
3_V103_W0.410510.742
86_L89_K0.410180.741
14_V17_H0.409210.740
8_G11_D0.409040.739
43_F47_L0.40850.738
4_V19_A0.4080.737
72_G82_C0.40570.733
10_K155_Y0.404890.732
29_V91_L0.402170.727
120_M123_F0.400890.725
5_S103_W0.400320.724
92_R96_K0.398960.721
13_T153_L0.398240.720
14_V136_I0.397960.719
39_E43_F0.396260.716
16_L51_Y0.391730.708
73_W76_K0.391480.708
67_R85_I0.388940.703
61_P64_F0.387140.700
124_D129_K0.386330.698
45_D48_A0.386240.698
44_V57_V0.379880.687
121_F125_E0.379680.686
142_E145_W0.379510.686
136_I144_V0.37950.686
105_I134_Y0.373880.676
67_R86_L0.372520.673
148_I153_L0.37060.670
108_R112_S0.370380.669
102_V134_Y0.370380.669
123_F126_D0.369530.668
84_S88_V0.36880.667
20_R53_I0.367920.665
82_C86_L0.366560.663
139_W144_V0.36590.661
84_S89_K0.365440.660
30_F45_D0.361940.654
4_V26_V0.361730.654
38_P41_Y0.359950.651
68_F72_G0.359380.650
13_T155_Y0.35770.647
110_D113_P0.357520.646
20_R24_R0.356920.645
7_S11_D0.356570.644
121_F124_D0.355920.643
118_L124_D0.352330.637
114_R117_K0.351850.636
10_K14_V0.351630.636
30_F36_E0.350310.633
27_P94_A0.34960.632
117_K121_F0.348510.630
31_I58_Y0.34620.626
96_K130_I0.346180.626
123_F129_K0.345810.625
151_N154_P0.345580.625
18_L21_E0.344780.623
59_R64_F0.344740.623
67_R71_Y0.3410.616
9_G106_G0.338810.612
119_P123_F0.338330.611
72_G76_K0.33820.611
118_L121_F0.337420.610
126_D129_K0.334310.604
93_R96_K0.328770.594
2_I24_R0.328690.594
29_V58_Y0.327810.592
36_E40_T0.325980.589
3_V94_A0.325690.589
2_I26_V0.325620.589
148_I151_N0.325050.587
92_R130_I0.324710.587
37_F40_T0.324080.586
136_I139_W0.323140.584
102_V131_I0.322240.582
115_R119_P0.321170.580
144_V148_I0.319630.578
109_A140_T0.319440.577
118_L122_E0.317510.574
139_W143_D0.316660.572
113_P116_A0.315240.570
14_V18_L0.315210.570
30_F40_T0.314770.569
32_D37_F0.314550.569
96_K129_K0.3110.562
20_R52_G0.310960.562
110_D140_T0.310940.562
41_Y44_V0.309550.559
10_K13_T0.308940.558
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
2o8vA0.98281000.124
2oq2A0.99431000.126
1zunA0.9771000.165
1surA0.94831000.175
2goyA0.98281000.179
3fwkA0.87931000.217
2wsiA0.89661000.219
3vrhA0.982899.90.38
2ywbA0.959899.80.389
2hmaA0.965599.80.389

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