GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PRAI - N-(5phosphoribosyl)anthranilate (PRA) isomerase
Pfam: PF00697 (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: CL0036
Length: 197
Sequences: 13129
Seq/Len: 66.64
HH_delta: 0.114 (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
161_V173_V1.487783.104
44_V73_D1.400912.923
162_R166_R1.209682.524
13_R17_E1.203892.512
13_R46_A1.196042.495
14_L18_L1.160492.421
151_I172_G1.14982.399
157_N160_N1.040162.170
38_D41_R0.955181.993
42_E45_S0.906031.890
110_Y113_R0.879961.836
156_L164_A0.866681.808
13_R16_A0.865411.806
112_E147_P0.863421.801
135_W163_E0.852341.778
163_E166_R0.847531.768
90_R118_D0.846151.765
109_D144_S0.834731.742
85_Y88_L0.80821.686
37_P69_E0.799871.669
16_A48_P0.785421.639
109_D112_E0.784181.636
12_A23_L0.777081.621
142_V171_Y0.771091.609
142_V150_V0.769941.606
87_K91_A0.767641.602
149_P171_Y0.752581.570
41_R70_L0.749681.564
165_I173_V0.737281.538
12_A43_L0.73461.533
109_D113_R0.728121.519
10_E13_R0.727951.519
41_R45_S0.714121.490
37_P41_R0.709261.480
82_S85_Y0.70741.476
96_I119_Y0.706551.474
75_V93_L0.706151.473
16_A47_V0.703271.467
88_L91_A0.701051.463
136_S139_K0.660051.377
14_L17_E0.657621.372
37_P66_I0.656091.369
39_Q42_E0.653621.364
15_A20_A0.65361.364
31_S34_Y0.639721.335
41_R69_E0.633081.321
160_N163_E0.631.314
175_V178_G0.627281.309
37_P70_L0.617171.288
44_V48_P0.616931.287
139_K143_E0.613181.279
10_E14_L0.611471.276
42_E46_A0.606591.266
11_D14_L0.596721.245
40_A70_L0.587421.226
66_I69_E0.583761.218
38_D42_E0.582441.215
66_I70_L0.575431.201
76_Q98_A0.572981.195
16_A49_P0.568181.185
105_I109_D0.559311.167
22_Y74_V0.554111.156
158_P162_R0.553361.155
58_Q61_E0.54311.133
16_A19_G0.536931.120
139_K142_V0.534491.115
67_V93_L0.533671.113
164_A170_P0.53261.111
83_P87_K0.53161.109
26_I176_S0.526961.099
110_Y114_Y0.526441.098
76_Q119_Y0.525941.097
122_L137_L0.525331.096
157_N178_G0.52491.095
22_Y172_G0.520121.085
137_L140_K0.517121.079
74_V96_I0.516341.077
71_G95_V0.514141.073
112_E148_K0.511771.068
135_W164_A0.510251.065
108_L141_I0.506791.057
111_L120_F0.506351.056
136_S140_K0.500311.044
152_L164_A0.496881.037
104_D140_K0.495181.033
122_L141_I0.495041.033
53_G72_L0.494261.031
152_L170_P0.493581.030
13_R47_V0.490031.022
159_E163_E0.488341.019
158_P178_G0.487981.018
58_Q66_I0.484341.011
112_E146_S0.484051.010
16_A52_V0.480531.003
139_K168_V0.476960.995
149_P172_G0.474960.991
25_F40_A0.474880.991
140_K144_S0.474520.990
84_E88_L0.469530.980
177_S181_T0.458910.957
160_N164_A0.453160.945
90_R95_V0.452350.944
119_Y149_P0.450570.940
16_A46_A0.446150.931
123_D153_A0.443520.925
111_L114_Y0.442580.923
44_V70_L0.442110.922
16_A50_K0.441630.921
60_P85_Y0.441030.920
127_G130_G0.440730.920
140_K143_E0.436640.911
151_I174_D0.434370.906
105_I140_K0.430710.899
95_V118_D0.422010.880
126_S176_S0.421940.880
104_D109_D0.420030.876
81_E85_Y0.41930.875
119_Y172_G0.414660.865
108_L146_S0.413640.863
25_F43_L0.411550.859
133_F138_L0.410680.857
87_K90_R0.409710.855
27_F30_K0.408120.851
11_D15_A0.407260.850
164_A173_V0.405270.846
35_V39_Q0.404990.845
13_R49_P0.404140.843
116_S148_K0.398390.831
159_E162_R0.398150.831
74_V119_Y0.395210.825
67_V75_V0.394040.822
47_V50_K0.392750.819
34_Y38_D0.391790.817
122_L150_V0.391730.817
67_V72_L0.390730.815
97_K117_V0.390520.815
77_L97_K0.385710.805
86_I117_V0.384140.801
86_I90_R0.38390.801
87_K116_S0.382860.799
125_G129_T0.38190.797
142_V168_V0.380430.794
32_P59_S0.379210.791
12_A16_A0.377880.788
57_N83_P0.377260.787
106_D110_Y0.373190.779
105_I144_S0.37280.778
44_V47_V0.369270.770
13_R50_K0.365430.762
30_K35_V0.364550.761
60_P88_L0.36350.758
44_V71_G0.362070.755
153_A174_D0.361520.754
146_S149_P0.359420.750
98_A121_L0.358740.748
77_L86_I0.356360.743
76_Q96_I0.355870.742
30_K34_Y0.354370.739
67_V71_G0.351980.734
28_Y31_S0.351110.733
163_E168_V0.35030.731
119_Y151_I0.349490.729
100_H125_G0.349030.728
175_V179_V0.348290.727
85_Y89_L0.347940.726
77_L95_V0.347320.725
11_D180_E0.34710.724
156_L173_V0.346860.724
87_K114_Y0.346740.723
138_L142_V0.344680.719
57_N80_D0.343630.717
83_P110_Y0.338450.706
134_D137_L0.336520.702
52_V72_L0.335680.700
26_I54_V0.3330.695
156_L175_V0.331890.692
95_V98_A0.330190.689
24_G121_L0.329860.688
48_P73_D0.329260.687
22_Y96_I0.327930.684
77_L81_E0.327580.683
12_A47_V0.326890.682
43_L46_A0.325970.680
121_L174_D0.325760.680
165_I170_P0.324690.677
102_D125_G0.324510.677
84_E87_K0.323860.676
150_V170_P0.321650.671
20_A179_V0.320220.668
103_K106_D0.318660.665
152_L156_L0.318240.664
74_V94_P0.318060.664
15_A19_G0.317140.662
161_V175_V0.313290.654
15_A23_L0.312550.652
83_P86_I0.312190.651
119_Y171_Y0.311420.650
60_P82_S0.310440.648
97_K114_Y0.309720.646
101_V137_L0.30830.643
15_A18_L0.307930.642
120_F148_K0.307730.642
117_V148_K0.30730.641
59_S66_I0.306410.639
150_V171_Y0.305190.637
86_I116_S0.301140.628
157_N177_S0.300030.626
99_I120_F0.299530.625
34_Y39_Q0.299510.625
12_A19_G0.297720.621
28_Y34_Y0.292220.610
161_V165_I0.292190.610
61_E88_L0.292160.610
27_F40_A0.291480.608
86_I89_L0.290360.606
133_F137_L0.289070.603
151_I171_Y0.287630.600
78_H153_A0.286750.598
23_L49_P0.286290.597
100_H126_S0.285480.596
117_V120_F0.284940.594
135_W139_K0.28460.594
40_A44_V0.284420.593
129_T132_T0.283370.591
178_G182_S0.283070.591
113_R116_S0.282890.590
25_F51_I0.280230.585
105_I108_L0.277980.580
82_S86_I0.277840.580
126_S131_K0.277350.579
94_P118_D0.277220.578
73_D93_L0.277050.578
27_F35_V0.276210.576
22_Y151_I0.275240.574
45_S48_P0.274620.573
138_L170_P0.274260.572
125_G128_G0.27260.569
86_I97_K0.271880.567
155_G177_S0.271760.567
34_Y37_P0.271550.567
104_D144_S0.271090.566
164_A168_V0.270440.564
39_Q43_L0.269930.563
118_D149_P0.26990.563
35_V40_A0.269670.563
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
1nsjA0.97971000.114
1v5xA0.96951000.125
1piiA0.95431000.147
4aajA0.95431000.197
2tpsA0.944299.80.375
1xi3A0.93499.80.38
3o63A0.944299.80.383
3nl6A0.949299.80.385
1yadA0.928999.80.391
3ceuA0.913799.80.41

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