GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ala_racemase_N - Alanine racemase N-terminal domain
Pfam: PF01168 (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: 218
Sequences: 9084
Seq/Len: 41.67
HH_delta: 0.131 (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
112_K145_R1.720763.945
98_E137_A1.437123.295
59_E81_E1.160542.661
101_S143_N1.151442.640
101_S141_L1.102392.528
126_V134_L1.078432.473
49_G67_P1.033082.369
136_E180_A1.000492.294
112_K147_E0.990232.270
110_P145_R0.951022.180
147_E185_P0.93332.140
105_K143_N0.893752.049
132_E176_A0.889512.039
171_R175_E0.828391.899
151_T189_M0.816221.871
79_L100_L0.807391.851
94_L137_A0.797341.828
80_E106_K0.79281.818
61_L65_G0.785531.801
59_E85_Y0.778141.784
94_L98_E0.754431.730
8_H12_K0.720171.651
11_R15_Q0.713131.635
84_E107_Q0.699751.604
80_E103_A0.69871.602
118_D122_G0.69421.592
82_L89_P0.692151.587
5_A9_N0.657331.507
91_V100_L0.650471.491
133_E136_E0.648191.486
137_A140_A0.647141.484
81_E85_Y0.646261.482
12_K15_Q0.646231.482
3_L7_R0.645311.480
168_E172_E0.642881.474
103_A106_K0.624511.432
101_S142_P0.618821.419
132_E180_A0.616911.414
38_R43_L0.614981.410
145_R185_P0.613791.407
101_S105_K0.611241.401
80_E84_E0.608551.395
5_A8_H0.602371.381
62_R85_Y0.600271.376
26_V51_A0.599221.374
76_P102_K0.59541.365
32_Y36_I0.591581.356
27_V50_F0.588321.349
97_L138_I0.586371.344
151_T170_F0.580661.331
114_H186_I0.574821.318
94_L133_E0.573021.314
94_L134_L0.572931.314
169_R172_E0.56881.304
98_E102_K0.563381.292
52_V58_A0.562331.289
132_E136_E0.561011.286
80_E107_Q0.560961.286
138_I146_L0.551281.264
73_P124_L0.549491.260
7_R11_R0.546911.254
76_P99_A0.545091.250
55_L59_E0.544581.249
178_E183_P0.541811.242
174_A178_E0.536481.230
174_A187_V0.536391.230
130_E133_E0.533891.224
175_E179_K0.529161.213
97_L141_L0.521351.195
81_E84_E0.517511.187
4_D8_H0.517231.186
24_R49_G0.512981.176
22_K49_G0.508081.165
102_K106_K0.506331.161
22_K48_D0.505141.158
50_F61_L0.504721.157
29_A32_Y0.50251.152
11_R14_R0.501281.149
38_R41_K0.498041.142
103_A107_Q0.493891.132
131_L173_L0.492321.129
94_L130_E0.481781.105
86_N112_K0.481231.103
98_E141_L0.478061.096
11_R44_A0.477651.095
58_A87_I0.476441.092
10_I48_D0.472361.083
91_V113_V0.468821.075
25_A47_I0.464231.064
59_E63_E0.463771.063
119_T151_T0.462491.060
114_H188_S0.455961.045
135_A146_L0.453331.039
24_R69_L0.449891.031
39_V43_L0.44911.030
127_R130_E0.448681.029
86_N109_K0.445011.020
99_A102_K0.443291.016
24_R51_A0.443241.016
22_K186_I0.443191.016
90_T150_M0.441081.011
60_E64_A0.440261.009
10_I14_R0.439791.008
12_K16_R0.438521.005
172_E175_E0.434560.996
137_A141_L0.43280.992
136_E140_A0.432790.992
149_L187_V0.432210.991
13_I17_A0.431820.990
104_A111_L0.427120.979
7_R44_A0.425430.975
176_A180_A0.420140.963
74_I96_Q0.418580.960
105_K142_P0.418110.959
128_P169_R0.417330.957
51_A71_L0.415290.952
91_V97_L0.41480.951
7_R39_V0.413470.948
16_R196_L0.409290.938
176_A179_K0.408590.937
117_V173_L0.408430.936
155_H158_D0.407990.935
164_Q168_E0.405870.931
116_K124_L0.405660.930
167_F189_M0.403790.926
62_R68_I0.403730.926
133_E137_A0.401750.921
69_L188_S0.401720.921
35_G38_R0.401070.920
26_V71_L0.400310.918
83_V111_L0.399470.916
22_K67_P0.398760.914
61_L64_A0.396360.909
83_V103_A0.396170.908
99_A103_A0.394440.904
14_R21_T0.386030.885
55_L58_A0.385060.883
149_L177_L0.383990.880
88_I147_E0.382240.876
9_N12_K0.380960.873
33_G36_I0.38090.873
41_K48_D0.378260.867
73_P92_D0.377360.865
79_L103_A0.372590.854
150_M188_S0.372120.853
6_L39_V0.37070.850
115_L134_L0.367430.842
117_V131_L0.367370.842
161_Y164_Q0.365480.838
8_H11_R0.364750.836
25_A29_A0.363920.834
88_I186_I0.363140.833
43_L46_G0.362870.832
93_S96_Q0.361070.828
14_R48_D0.360530.827
114_H148_G0.360160.826
14_R17_A0.359150.823
76_P95_E0.356720.818
63_E85_Y0.355760.816
9_N196_L0.355150.814
96_Q99_A0.355050.814
10_I43_L0.355010.814
29_A53_A0.353390.810
172_E176_A0.353190.810
139_K180_A0.352160.807
41_K50_F0.351570.806
170_F174_A0.34920.801
135_A177_L0.349090.800
92_D96_Q0.347140.796
190_G194_A0.345760.793
37_V60_E0.345250.792
95_E99_A0.34450.790
158_D161_Y0.341020.782
41_K66_A0.340960.782
38_R64_A0.340920.782
113_V144_L0.34070.781
37_V64_A0.33920.778
101_S137_A0.338340.776
104_A110_P0.334990.768
173_L176_A0.332730.763
7_R46_G0.332420.762
116_K152_H0.33220.762
132_E135_A0.331190.759
74_I82_L0.330140.757
163_N168_E0.327010.750
79_L89_P0.325510.746
97_L144_L0.32450.744
175_E178_E0.324270.743
110_P143_N0.324120.743
95_E98_E0.32080.736
48_D67_P0.318930.731
36_I40_A0.31750.728
55_L81_E0.316490.726
131_L135_A0.316220.725
114_H147_E0.315850.724
75_P78_E0.314940.722
10_I47_I0.31470.722
171_R174_A0.31120.714
126_V131_L0.311080.713
90_T114_H0.310740.712
7_R43_L0.310060.711
55_L70_V0.309880.710
83_V104_A0.308360.707
128_P132_E0.308120.706
11_R46_G0.306750.703
88_I112_K0.305910.701
58_A68_I0.304650.698
67_P86_N0.303640.696
69_L90_T0.302440.693
167_F171_R0.300030.688
34_H38_R0.297980.683
154_A166_Q0.297320.682
97_L134_L0.296970.681
108_G143_N0.295780.678
149_L174_A0.295690.678
157_D193_A0.295560.678
89_P100_L0.295490.677
105_K108_G0.295370.677
4_D7_R0.294620.675
55_L78_E0.293710.673
44_A66_A0.293640.673
40_A44_A0.29170.669
91_V96_Q0.290770.667
36_I39_V0.290430.666
10_I40_A0.290280.666
37_V41_K0.288910.662
104_A108_G0.288520.662
27_V61_L0.28590.656
168_E171_R0.285310.654
14_R18_G0.284420.652
10_I23_L0.284110.651
29_A57_E0.284030.651
10_I13_I0.281940.646
79_L99_A0.278110.638
156_A193_A0.278090.638
71_L90_T0.276710.634
89_P111_L0.276550.634
61_L68_I0.27610.633
79_L96_Q0.274570.630
100_L144_L0.274240.629
123_R152_H0.272910.626
177_L180_A0.272480.625
9_N13_I0.270590.620
128_P173_L0.26910.617
117_V126_V0.269030.617
13_I23_L0.267910.614
17_A23_L0.266770.612
55_L82_L0.26610.610
14_R23_L0.265530.609
147_E186_I0.265490.609
138_I144_L0.264470.606
119_T169_R0.263670.605
153_F166_Q0.263460.604
141_L144_L0.260550.597
119_T170_F0.258480.593
27_V32_Y0.257890.591
136_E139_K0.256930.589
16_R19_P0.256910.589
6_L9_N0.255560.586
155_H162_T0.254720.584
10_I44_A0.254160.583
166_Q170_F0.253890.582
160_D164_Q0.253830.582
69_L114_H0.252720.579
169_R173_L0.252530.579
167_F190_G0.251970.578
128_P176_A0.251130.576
115_L146_L0.250610.575
34_H37_V0.25030.574
24_R67_P0.250060.573
182_I185_P0.249330.572
131_L134_L0.249170.571
118_D121_M0.247640.568
119_T166_Q0.246990.566
3_L39_V0.246470.565
70_V73_P0.245680.563
62_R65_G0.243050.557
50_F66_A0.2430.557
27_V52_V0.242420.556
6_L40_A0.242150.555
36_I60_E0.241810.554
100_L113_V0.239970.550
180_A183_P0.239790.550
40_A61_L0.23960.549
113_V138_I0.239420.549
37_V40_A0.238620.547
171_R187_V0.238110.546
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
1xfcA0.99081000.131
2vd8A0.99081000.137
1vfsA0.99081000.146
2dy3A0.97711000.15
3e5pA0.98171000.151
4eclA0.97251000.157
1bd0A0.96791000.159
4a3qA0.97251000.163
3mubA0.97251000.169
3kw3A0.96791000.171

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