GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
His_biosynth - Histidine biosynthesis protein
Pfam: PF00977 (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: 229
Sequences: 10436
Seq/Len: 45.57
HH_delta: 0.081 (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
89_E93_D1.172012.600
36_K71_E1.164992.584
33_E36_K1.141792.533
206_L217_V1.090812.420
39_N73_G1.019792.262
69_A97_D0.994382.206
113_E117_E0.983472.182
202_S205_D0.938662.082
39_N74_I0.919832.041
113_E159_L0.899811.996
207_R211_K0.890471.975
195_I216_G0.887731.969
37_A41_Q0.884391.962
88_A115_L0.87461.940
154_K189_A0.865541.920
200_V209_L0.856331.900
36_K40_E0.8361.855
193_P215_D0.83021.842
157_E192_I0.82881.839
110_E114_E0.795081.764
90_R93_D0.785021.741
155_R159_L0.774591.718
89_E119_Y0.769951.708
151_E154_K0.757441.680
67_E70_K0.756731.679
84_S87_D0.747611.658
63_E66_K0.741291.644
63_E67_E0.740711.643
180_L208_E0.739151.640
155_R158_E0.738191.638
187_A215_D0.729371.618
219_V222_A0.715751.588
182_L185_Q0.70611.566
89_E118_R0.70221.558
204_E207_R0.688091.526
203_L207_R0.681571.512
205_D208_E0.68051.510
210_K217_V0.670871.488
150_E185_Q0.667881.482
204_E208_E0.663491.472
108_D114_E0.659121.462
157_E191_N0.654921.453
110_E159_L0.652061.447
181_E184_K0.648881.439
78_V96_A0.643911.428
187_A194_V0.640311.420
181_E185_Q0.63881.417
185_Q189_A0.620771.377
148_D151_E0.615851.366
185_Q188_E0.614481.363
208_E211_K0.613271.360
45_E98_R0.610041.353
219_V223_L0.603481.339
85_I114_E0.59411.318
46_L74_I0.590531.310
39_N72_T0.586921.302
62_L90_R0.584391.296
184_K188_E0.582941.293
115_L118_R0.581341.290
99_V121_S0.551251.223
196_A214_I0.548881.218
111_L114_E0.542121.203
107_E139_N0.533531.184
114_E118_R0.533361.183
82_I91_L0.531831.180
87_D90_R0.530231.176
110_E113_E0.527011.169
196_A209_L0.52551.166
114_E117_E0.52551.166
69_A76_I0.524781.164
54_A83_R0.524011.162
92_L119_Y0.517961.149
184_K212_A0.511851.135
183_L214_I0.502651.115
90_R94_A0.502531.115
66_K94_A0.501981.114
85_I118_R0.50161.113
33_E37_A0.5011.111
209_L214_I0.500561.110
39_N42_G0.498911.107
66_K93_D0.493721.095
34_V37_A0.492161.092
154_K157_E0.487821.082
88_A119_Y0.480181.065
150_E189_A0.478131.061
83_R107_E0.474841.053
50_D54_A0.472811.049
44_D75_P0.472631.048
86_E89_E0.470951.045
35_A46_L0.470911.045
59_G90_R0.462161.025
141_W185_Q0.460491.022
166_L182_L0.458421.017
66_K70_K0.457131.014
208_E212_A0.453861.007
186_L189_A0.452161.003
59_G94_A0.446290.990
45_E216_G0.444140.985
85_I115_L0.442740.982
157_E190_V0.441890.980
98_R131_R0.439280.974
103_T152_F0.438620.973
64_L67_E0.436020.967
115_L119_Y0.435470.966
206_L222_A0.432630.960
87_D182_L0.430960.956
209_L217_V0.429780.953
150_E154_K0.426160.945
48_I76_I0.424560.942
91_L96_A0.423120.939
221_S225_E0.419780.931
183_L194_V0.419730.931
37_A40_E0.419320.930
183_L187_A0.418890.929
201_R205_D0.415560.922
154_K158_E0.412450.915
36_K39_N0.411090.912
89_E115_L0.409110.908
205_D209_L0.406890.903
35_A68_I0.404040.896
171_R176_Q0.403790.896
193_P216_G0.403640.895
188_E213_G0.403380.895
48_I65_I0.398490.884
101_I109_P0.398270.884
153_A190_V0.397890.883
92_L121_S0.396150.879
107_E111_L0.39580.878
61_N64_L0.395340.877
75_P98_R0.395190.877
75_P97_D0.395140.877
195_I218_I0.394860.876
106_L138_T0.391140.868
111_L115_L0.390170.866
108_D155_R0.388610.862
149_L186_L0.386020.856
163_E216_G0.378720.840
65_I76_I0.376740.836
220_G224_H0.372560.826
168_D182_L0.369680.820
78_V91_L0.366120.812
168_D196_A0.36370.807
161_A164_I0.361560.802
184_K208_E0.360790.800
166_L186_L0.354440.786
151_E155_R0.353370.784
45_E75_P0.352910.783
112_L115_L0.351640.780
79_G98_R0.348570.773
108_D111_L0.346630.769
68_I74_I0.34420.764
153_A194_V0.343160.761
120_G162_G0.342030.759
60_S63_E0.340960.756
49_V165_I0.33750.749
201_R222_A0.337110.748
165_I218_I0.335130.743
77_Q100_V0.332410.737
116_A160_G0.330770.734
203_L222_A0.330320.733
166_L194_V0.328150.728
200_V206_L0.326450.724
101_I104_E0.324320.719
186_L190_V0.322630.716
183_L196_A0.322570.716
150_E153_A0.32190.714
48_I68_I0.320740.712
100_V163_E0.320110.710
45_E163_E0.31920.708
88_A99_V0.319170.708
172_D177_G0.318920.707
116_A121_S0.318660.707
109_P155_R0.316640.702
164_I192_I0.314660.698
149_L153_A0.312790.694
153_A164_I0.312430.693
172_D175_M0.310710.689
112_L116_A0.310120.688
184_K211_K0.309990.688
98_R163_E0.308920.685
85_I89_E0.308390.684
163_E193_P0.308220.684
104_E148_D0.305240.677
162_G193_P0.305170.677
88_A92_L0.304870.676
45_E193_P0.303340.673
35_A72_T0.300720.667
66_K90_R0.299780.665
206_L219_V0.29970.665
69_A77_Q0.297120.659
65_I96_A0.296590.658
46_L72_T0.296350.657
107_E138_T0.293710.652
109_P112_L0.292760.649
62_L91_L0.29190.648
85_I111_L0.291340.646
168_D179_D0.290480.644
209_L212_A0.289350.642
54_A84_S0.285250.633
49_V167_T0.284710.632
86_E112_L0.284230.631
62_L94_A0.28320.628
133_G148_D0.283040.628
72_T75_P0.282610.627
117_E132_D0.282020.626
160_G192_I0.281190.624
173_G176_Q0.280310.622
200_V217_V0.279930.621
84_S111_L0.278050.617
187_A214_I0.276270.613
49_V218_I0.275950.612
65_I69_A0.275780.612
103_T156_L0.275690.612
116_A161_A0.275360.611
52_D56_E0.275110.610
76_I97_D0.274450.609
117_E162_G0.274430.609
113_E155_R0.274120.608
187_A212_A0.273050.606
163_E195_I0.272580.605
150_E155_R0.271980.603
103_T109_P0.27180.603
201_R225_E0.271620.603
190_V194_V0.270850.601
35_A71_E0.270530.600
103_T107_E0.269020.597
47_H218_I0.268810.596
53_A58_R0.268810.596
180_L183_L0.268170.595
53_A56_E0.268030.595
149_L152_F0.266910.592
45_E77_Q0.264470.587
82_I87_D0.263690.585
45_E195_I0.263680.585
171_R174_T0.263660.585
190_V193_P0.262980.583
35_A42_G0.260580.578
79_G100_V0.260460.578
38_F43_A0.260420.578
60_S65_I0.260110.577
153_A189_A0.258810.574
133_G163_E0.258610.574
42_G74_I0.257980.572
35_A76_I0.257560.571
54_A103_T0.257150.570
179_D182_L0.256960.570
173_G179_D0.256430.569
72_T76_I0.255040.566
171_R175_M0.25460.565
117_E159_L0.253910.563
38_F224_H0.253530.562
178_P200_V0.252720.561
86_E106_L0.251860.559
69_A72_T0.251750.558
40_E71_E0.25080.556
158_E161_A0.250310.555
86_E90_R0.249170.553
180_L184_K0.248950.552
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
4gj1A0.99561000.081
4axkA0.98251000.128
2agkA0.96071000.136
1jvnA0.99561000.156
1vzwA0.97821000.178
2y88A0.97821000.19
1qo2A0.98251000.205
1thfD0.98691000.219
1ka9F0.98691000.247
2w6rA0.98251000.291

Page generated in 0.0328 seconds.