GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MCPsignal - Methyl-accepting chemotaxis protein (MCP) signalling domain
Pfam: PF00015 (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: 213
Sequences: 13330
Seq/Len: 62.58
HH_delta: 0.044 (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
34_E108_Q1.241912.357
38_S108_Q1.154252.191
18_M21_I1.148692.180
38_S104_E1.147772.179
174_E177_E1.111072.109
128_E132_E1.049261.992
37_E40_E1.04291.979
86_K89_E0.936321.777
23_E27_E0.929471.764
41_D44_E0.923381.753
132_E135_E0.898551.705
124_E128_E0.897161.703
167_Q170_E0.887261.684
131_E135_E0.879541.669
27_E30_E0.864061.640
156_E160_E0.847291.608
146_E149_D0.846541.607
187_E191_E0.840551.595
44_E47_S0.838461.591
34_E37_E0.833041.581
43_S106_Q0.829831.575
135_E138_E0.827661.571
33_E37_E0.823881.564
47_S51_E0.822711.562
159_E163_E0.819881.556
30_E34_E0.815471.548
50_N99_S0.813911.545
195_E198_E0.811431.540
138_E142_E0.811291.540
184_A188_E0.803051.524
188_E191_E0.799151.517
93_E97_E0.796781.512
178_I182_I0.788091.496
145_E149_D0.787611.495
202_E205_E0.777641.476
125_E128_E0.766371.455
177_E181_Q0.756021.435
26_E30_E0.747681.419
166_E170_E0.74751.419
99_S103_E0.737981.401
206_L209_R0.736461.398
54_E65_I0.736161.397
30_E33_E0.733491.392
156_E159_E0.727861.382
198_E202_E0.72751.381
38_S41_D0.726781.379
121_E125_E0.726741.379
177_E180_E0.726231.378
91_T95_A0.72621.378
89_E93_E0.723591.373
93_E96_K0.722961.372
135_E139_E0.72141.369
163_E167_Q0.719811.366
37_E41_D0.717121.361
142_E146_E0.715291.358
201_E205_E0.714181.356
160_E164_S0.713411.354
139_E142_E0.713031.353
21_I126_G0.709911.347
64_S82_D0.706831.342
48_L94_S0.701621.332
163_E166_E0.699321.327
204_Q208_D0.696081.321
36_S40_E0.688091.306
198_E201_E0.687661.305
103_E107_E0.686021.302
128_E131_E0.681511.294
184_A187_E0.676731.284
176_S180_E0.675651.282
41_D97_E0.671571.275
149_D153_E0.669331.270
19_E23_E0.668521.269
96_K100_E0.658271.249
167_Q171_S0.657161.247
20_E23_E0.652661.239
23_E26_E0.651591.237
25_I123_I0.643351.221
41_D101_I0.639111.213
160_E163_E0.636481.208
20_E122_Q0.635191.206
104_E108_Q0.631641.199
173_E177_E0.630021.196
92_S96_K0.629861.196
121_E124_E0.623911.184
194_E198_E0.619411.176
100_E104_E0.616571.170
205_E208_D0.615381.168
170_E174_E0.612721.163
61_L69_R0.611531.161
137_L140_I0.600851.140
149_D152_E0.597991.135
33_E36_S0.597641.134
97_E100_E0.588451.117
153_E156_E0.579391.100
96_K99_S0.579011.099
170_E173_E0.575781.093
103_E106_Q0.571161.084
25_I119_S0.571081.084
146_E150_S0.567031.076
50_N95_A0.554751.053
34_E38_S0.549241.042
41_D104_E0.548981.042
191_E195_E0.544531.034
100_E103_E0.541681.028
129_S132_E0.534471.014
51_E90_Q0.533871.013
24_S27_E0.533721.013
164_S167_Q0.531911.010
205_E209_R0.527491.001
50_N96_K0.524880.996
201_E204_Q0.524710.996
40_E44_E0.52450.996
180_E184_A0.523210.993
22_Q26_E0.520530.988
21_I123_I0.517540.982
50_N54_E0.514340.976
82_D86_K0.513430.975
184_A191_E0.508390.965
196_L200_A0.505150.959
139_E143_S0.504870.958
45_I94_S0.496780.943
166_E169_N0.496220.942
24_S122_Q0.495160.940
193_A200_A0.491360.933
39_S45_I0.490790.932
191_E194_E0.489860.930
26_E120_R0.488540.927
35_L105_I0.485420.921
25_I28_I0.485050.921
71_G74_G0.48390.918
142_E145_E0.483430.918
64_S85_R0.479490.910
152_E156_E0.479320.910
199_S202_E0.477130.906
21_I24_S0.475360.902
161_Q164_S0.472870.898
39_S105_I0.471120.894
90_Q97_E0.470720.893
196_L210_F0.466290.885
45_I102_I0.465670.884
134_S138_E0.465360.883
131_E134_S0.462720.878
46_L50_N0.461120.875
57_N85_R0.460630.874
174_E178_I0.459610.872
194_E197_S0.459460.872
147_I151_I0.457160.868
104_E107_E0.457080.868
66_E69_R0.456620.867
82_D85_R0.449660.853
181_Q184_A0.446130.847
188_E192_A0.441360.838
91_T101_I0.439530.834
169_N173_E0.438180.832
19_E131_E0.43790.831
202_E206_L0.435650.827
29_A33_E0.435610.827
165_I169_N0.433040.822
130_V133_T0.431430.819
197_S201_E0.428470.813
28_I119_S0.426140.809
45_I48_L0.425720.808
29_A120_R0.424890.806
54_E92_S0.423580.804
90_Q93_E0.422620.802
88_A91_T0.421010.799
45_I101_I0.419880.797
53_A56_T0.418920.795
18_M126_G0.41890.795
51_E54_E0.417940.793
35_L45_I0.413960.786
150_S153_E0.411940.782
141_A145_E0.410990.780
133_T137_L0.409340.777
46_L99_S0.407310.773
64_S73_A0.405070.769
40_E43_S0.403010.765
64_S90_Q0.401170.761
185_S188_E0.399520.758
72_E75_R0.397620.755
207_V210_F0.396910.753
157_S161_Q0.395210.750
70_A74_G0.395020.750
21_I35_L0.393610.747
105_I161_Q0.393450.747
120_R124_E0.392430.745
27_E132_E0.392210.744
20_E24_S0.391620.743
155_S162_S0.390580.741
176_S179_S0.390320.741
179_S183_S0.389420.739
22_Q127_S0.389340.739
148_S152_E0.386490.734
123_I126_G0.386020.733
125_E129_S0.386010.733
31_S108_Q0.385990.733
189_I192_A0.385970.733
197_S204_Q0.385450.732
183_S186_S0.384510.730
102_I106_Q0.384440.730
190_A194_E0.384120.729
154_I161_Q0.376980.716
42_I102_I0.376310.714
18_M127_S0.374760.711
133_T136_S0.374760.711
181_Q185_S0.37380.709
27_E31_S0.369510.701
164_S171_S0.366160.695
123_I127_S0.365610.694
157_S160_E0.364630.692
43_S46_L0.364350.692
195_E199_S0.363950.691
127_S131_E0.361750.687
153_E157_S0.360060.683
172_I176_S0.356860.677
183_S190_A0.35350.671
155_S159_E0.350320.665
49_I91_T0.349970.664
52_I91_T0.348420.661
137_L150_S0.347290.659
140_I144_V0.346080.657
143_S147_I0.344250.653
192_A195_E0.343810.653
158_A162_S0.342860.651
47_S50_N0.34250.650
172_I182_I0.342150.649
149_D156_E0.341510.648
101_I105_I0.341360.648
186_S190_A0.338020.642
32_I35_L0.337820.641
25_I29_A0.33660.639
119_S126_G0.335430.637
31_S34_E0.335250.636
73_A78_A0.335120.636
203_L210_F0.334920.636
198_E205_E0.329340.625
126_G133_T0.329150.625
44_E48_L0.327670.622
45_I95_A0.326880.620
126_G130_V0.326230.619
46_L98_I0.325910.619
173_E176_S0.325370.618
69_R76_G0.324620.616
18_M130_V0.322170.611
43_S47_S0.320650.609
26_E124_E0.320050.607
154_I157_S0.319850.607
66_E77_F0.319690.607
46_L95_A0.31960.607
200_A203_L0.318250.604
57_N64_S0.315720.599
193_A196_L0.315150.598
136_S140_I0.314560.597
74_G79_V0.3130.594
18_M35_L0.311970.592
143_S146_E0.311150.591
77_F87_L0.311090.590
76_G79_V0.310740.590
122_Q125_E0.310170.589
132_E136_S0.310070.589
127_S130_V0.309220.587
60_A85_R0.30880.586
190_A193_A0.308590.586
59_L76_G0.308450.585
156_E163_E0.306780.582
48_L88_A0.30670.582
76_G80_V0.303520.576
50_N92_S0.302480.574
54_E58_L0.302060.573
29_A32_I0.301860.573
186_S193_A0.300870.571
136_S139_E0.300690.571
85_R89_E0.298820.567
56_T61_L0.298620.567
48_L51_E0.298140.566
162_S166_E0.297080.564
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
1qu7A0.93431000.044
3zx6A0.93431000.051
2ch7A0.990699.90.146
3g67A0.826399.90.187
3c98B0.948499.30.528
2ch7A0.93999.30.533
3zx6A198.90.618
1qu7A0.93998.70.644
3g67A0.859298.40.675
3c98B0.981297.10.775

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