GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SDH_alpha - Serine dehydratase alpha chain
Pfam: PF03313 (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: 282
Sequences: 1414
Seq/Len: 5.01
HH_delta: 0.926 (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
192_T195_Q0.537074.165
7_S187_Y0.433023.358
30_A140_E0.432553.355
186_V191_G0.427453.315
139_S142_K0.401473.114
30_A144_I0.399123.095
4_I12_K0.377222.925
168_C172_A0.368692.859
40_V131_Y0.353562.742
157_I176_A0.345822.682
15_M22_T0.342122.653
186_V238_A0.337972.621
153_I183_A0.329842.558
7_S145_R0.324672.518
145_R187_Y0.319552.478
204_L256_V0.308072.389
156_Y257_E0.297762.309
258_E262_N0.276892.147
261_K265_R0.275612.137
21_G24_E0.26232.034
141_E145_R0.262122.033
11_I26_G0.261682.029
98_I236_S0.255881.984
97_A235_I0.255261.980
22_T26_G0.245351.903
10_I152_L0.237991.846
253_F257_E0.232871.806
15_M25_V0.230951.791
157_I204_L0.230581.788
149_L187_Y0.224611.742
26_G144_I0.21921.700
4_I9_N0.215021.668
125_I174_A0.213831.658
191_G195_Q0.211161.638
34_G38_G0.206661.603
8_E12_K0.206511.602
162_G168_C0.206021.598
37_K140_E0.204311.584
138_L142_K0.200661.556
34_G140_E0.198441.539
23_E27_L0.197411.531
146_A188_L0.197221.530
26_G141_E0.196911.527
20_P28_E0.196681.525
26_G30_A0.195461.516
33_L143_L0.195431.516
6_L149_L0.193021.497
12_K15_M0.192541.493
42_K107_A0.191491.485
38_G42_K0.183881.426
266_I271_M0.182311.414
211_I271_M0.182051.412
96_R135_E0.179911.395
182_A203_A0.177181.374
142_K188_L0.176641.370
41_E45_E0.170831.325
31_A35_A0.169711.316
39_D49_G0.169361.313
140_E144_I0.16541.283
37_K131_Y0.165331.282
20_P24_E0.164221.274
138_L146_A0.16321.266
221_I250_G0.162841.263
205_G225_L0.162791.262
31_A34_G0.162681.262
29_M147_L0.161641.254
43_G103_A0.161291.251
44_L65_N0.160071.241
100_Y134_E0.159511.237
98_I229_S0.157621.222
15_M21_G0.155461.206
187_Y196_I0.154661.199
54_D57_K0.154421.198
166_A273_E0.154181.196
26_G140_E0.154041.195
232_S236_S0.153281.189
62_L66_K0.151571.175
39_D114_I0.150741.169
165_S228_A0.150331.166
176_A203_A0.148331.150
129_V231_A0.147251.142
191_G242_L0.145461.128
11_I22_T0.144721.122
155_I159_Q0.142731.107
202_N237_A0.141821.100
33_L37_K0.141491.097
68_L116_A0.140311.088
26_G145_R0.139621.083
198_Y249_D0.138731.076
185_I235_I0.138151.071
258_E261_K0.137511.066
8_E22_T0.137321.065
124_G150_S0.137181.064
238_A242_L0.13681.061
30_A141_E0.136271.057
205_G249_D0.136181.056
48_E66_K0.136071.055
149_L183_A0.135261.049
44_L99_A0.134261.041
131_Y134_E0.134061.040
119_T154_G0.132911.031
187_Y193_P0.132491.028
198_Y244_G0.132281.026
230_G240_M0.13211.024
162_G172_A0.131171.017
125_I210_L0.13111.017
190_G195_Q0.130751.014
107_A112_G0.130351.011
186_V195_Q0.129891.007
160_N258_E0.128410.996
20_P25_V0.128310.995
193_P196_I0.128310.995
141_E144_I0.126250.979
10_I155_I0.125220.971
201_A205_G0.124980.969
12_K16_A0.124960.969
203_A207_L0.124770.968
200_A253_F0.124540.966
166_A274_T0.123870.961
34_G37_K0.123820.960
30_A34_G0.123530.958
207_L210_L0.123330.956
277_G280_A0.123190.955
100_Y160_N0.120820.937
5_S8_E0.120360.933
50_I56_K0.119250.925
21_G25_V0.119040.923
197_E249_D0.118440.919
142_K145_R0.117660.912
7_S149_L0.117360.910
204_L263_V0.116650.905
91_G239_D0.116110.900
11_I15_M0.1160.900
29_M148_A0.115580.896
41_E134_E0.115080.892
211_I263_V0.112350.871
28_E31_A0.112130.870
207_L229_S0.11210.869
266_I270_G0.112030.869
7_S11_I0.111930.868
63_E67_R0.111740.867
66_K134_E0.111350.864
149_L184_G0.111060.861
102_A228_A0.11070.859
27_L31_A0.110140.854
37_K134_E0.109350.848
119_T151_H0.109340.848
9_N275_D0.109260.847
158_K169_G0.109060.846
263_V266_I0.108720.843
98_I232_S0.108590.842
6_L11_I0.108560.842
208_L263_V0.108120.839
28_E32_A0.108110.838
4_I240_M0.107990.838
51_T224_A0.107720.835
28_E35_A0.107280.832
98_I228_A0.107260.832
57_K60_K0.107180.831
100_Y130_L0.107050.830
27_L30_A0.106880.829
118_P124_G0.106880.829
125_I165_S0.105640.819
42_K49_G0.105380.817
176_A236_S0.105050.815
138_L188_L0.105020.814
41_E65_N0.104880.813
8_E188_L0.104660.812
49_G273_E0.104580.811
265_R269_E0.10430.809
100_Y135_E0.104160.808
59_R281_I0.103990.806
270_G276_K0.103780.805
153_I184_G0.103660.804
101_A128_G0.103630.804
50_I54_D0.103610.804
38_G45_E0.103450.802
16_A23_E0.103280.801
95_N239_D0.102520.795
244_G249_D0.102520.795
5_S187_Y0.102460.795
202_N228_A0.102440.794
182_A237_A0.102430.794
165_S168_C0.102310.793
56_K194_E0.101720.789
37_K41_E0.101650.788
17_V20_P0.101570.788
22_T141_E0.101270.785
271_M274_T0.101240.785
160_N264_G0.101170.785
169_G220_K0.101010.783
129_V235_I0.100910.783
124_G154_G0.100890.782
258_E265_R0.10080.782
105_S146_A0.100550.780
134_E144_I0.099960.775
275_D281_I0.09990.775
106_E252_P0.099760.774
4_I13_N0.099690.773
34_G144_I0.099690.773
176_A204_L0.099680.773
125_I129_V0.099340.770
12_K17_V0.098910.767
63_E140_E0.098620.765
58_A63_E0.098620.765
21_G31_A0.098510.764
11_I207_L0.098430.763
221_I249_D0.098160.761
111_G168_C0.098090.761
142_K187_Y0.098040.760
42_K112_G0.0980.760
183_A196_I0.09780.758
191_G238_A0.09760.757
206_N233_A0.097290.755
116_A220_K0.096960.752
125_I231_A0.096940.752
194_E198_Y0.096480.748
62_L92_D0.096050.745
244_G261_K0.095780.743
5_S48_E0.095640.742
48_E62_L0.095630.742
193_P197_E0.095620.742
90_P239_D0.095610.741
141_E268_P0.095570.741
158_K220_K0.095470.740
110_S221_I0.095440.740
44_L103_A0.094740.735
198_Y256_V0.094330.732
21_G27_L0.094220.731
264_G274_T0.09410.730
3_N194_E0.09390.728
28_E151_H0.093840.728
41_E131_Y0.093690.727
221_I224_A0.093620.726
256_V279_L0.093560.726
189_L238_A0.09340.724
171_Q227_N0.093360.724
176_A261_K0.092860.720
96_R134_E0.092340.716
118_P173_E0.092280.716
62_L65_N0.092270.716
262_N265_R0.092110.714
96_R132_A0.092080.714
267_M277_G0.092050.714
11_I29_M0.09190.713
17_V30_A0.091890.713
39_D42_K0.091820.712
186_V196_I0.091720.711
68_L135_E0.091680.711
54_D205_G0.091650.711
138_L143_L0.091150.707
164_L167_E0.091090.706
54_D94_L0.091010.706
136_L189_L0.090840.704
116_A211_I0.090680.703
160_N165_S0.090440.701
91_G134_E0.090310.700
33_L140_E0.090210.700
12_K65_N0.090080.699
255_E258_E0.090060.698
41_E92_D0.089960.698
274_T278_G0.089940.698
241_A279_L0.089810.697
62_L242_L0.089680.696
10_I23_E0.089650.695
11_I141_E0.089640.695
92_D250_G0.089630.695
229_S236_S0.08940.693
273_E280_A0.089230.692
276_K281_I0.088780.689
262_N270_G0.088750.688
97_A128_G0.088710.688
208_L279_L0.088510.686
186_V234_A0.088490.686
94_L229_S0.088070.683
116_A206_N0.088020.683
34_G65_N0.087880.682
56_K63_E0.087710.680
45_E139_S0.08770.680
94_L230_G0.087660.680
31_A194_E0.087550.679
8_E145_R0.087520.679
58_A192_T0.087420.678
6_L152_L0.087410.678
54_D240_M0.087360.678
112_G193_P0.087360.678
261_K272_R0.087230.677
175_G251_I0.087220.676
68_L96_R0.087170.676
118_P227_N0.086830.673
149_L153_I0.086820.673
33_L188_L0.08670.672
58_A65_N0.086630.672
64_M240_M0.086570.671
128_G181_A0.08630.669
149_L196_I0.086290.669
38_G250_G0.086110.668
198_Y281_I0.0860.667
15_M30_A0.085990.667
11_I145_R0.085980.667
7_S196_I0.085960.667
167_E177_A0.085860.666
93_L132_A0.085810.665
260_M273_E0.085790.665
182_A238_A0.085760.665
31_A46_V0.085560.664
162_G264_G0.085540.663
206_N230_G0.085430.663
15_M26_G0.085070.660
17_V26_G0.085030.659
94_L192_T0.084980.659
154_G163_R0.084970.659
162_G167_E0.084880.658
4_I194_E0.084870.658
31_A38_G0.084820.658
50_I145_R0.084690.657
21_G65_N0.084660.657
29_M94_L0.084630.656
62_L250_G0.084580.656
27_L34_G0.084450.655
171_Q174_A0.084430.655
23_E139_S0.084350.654
267_M272_R0.08430.654
103_A123_A0.084280.654
155_I230_G0.084180.653
95_N243_A0.084170.653
12_K30_A0.083860.650
212_C223_C0.083840.650
99_A198_Y0.083830.650
36_M61_A0.083770.650
119_T125_I0.083650.649
165_S264_G0.083560.648
62_L136_L0.083460.647
17_V25_V0.083150.645
17_V21_G0.08310.644
21_G30_A0.083090.644
264_G277_G0.083070.644
7_S10_I0.082990.644
94_L232_S0.082980.644
112_G164_L0.082910.643
197_E253_F0.082870.643
22_T25_V0.082840.642
63_E139_S0.082740.642
12_K141_E0.08240.639
50_I139_S0.0820.636
91_G100_Y0.081950.636
269_E272_R0.081920.635
16_A194_E0.081880.635
5_S145_R0.081850.635
90_P261_K0.081790.634
253_F262_N0.081730.634
45_E65_N0.08170.634
126_L147_L0.081620.633
203_A263_V0.081520.632
207_L230_G0.081430.632
7_S250_G0.081320.631
46_V62_L0.081250.630
124_G151_H0.081240.630
12_K188_L0.081110.629
12_K38_G0.081030.628
95_N207_L0.081020.628
38_G41_E0.080940.628
157_I256_V0.08090.627
171_Q277_G0.080870.627
38_G92_D0.080730.626
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
2hp0A0.872396.80.926
1szqA0.854696.40.931
2hh6A0.294313.90.971
2d9sA0.163111.40.972
4b3hA0.8448.60.974
3iwlA0.23055.70.976
4eb5C0.52135.70.976
4a4jA0.22345.20.976
3fryA0.237650.976
2xmmA0.21284.90.976
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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