GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CheR - CheR methyltransferase SAM binding domain
Pfam: PF01739 (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: CL0063
Length: 196
Sequences: 2243
Seq/Len: 11.44
HH_delta: 0.232 (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
42_T76_A0.614142.911
94_P97_Y0.607522.879
36_W70_T0.581162.754
138_D166_K0.555692.634
140_I161_L0.530682.515
165_L169_G0.516412.448
46_P69_A0.488252.314
44_E89_S0.481892.284
70_T125_H0.468782.222
15_L139_L0.460322.182
35_I49_L0.455182.157
11_Q172_F0.440572.088
84_I111_R0.438272.077
54_L116_L0.436862.070
162_H186_F0.40871.937
69_A120_V0.407261.930
127_L145_V0.397791.885
140_I165_L0.394521.870
1_N76_A0.393761.866
13_E17_D0.382161.811
84_I109_G0.37961.799
128_L153_T0.370461.756
49_L141_F0.369951.753
54_L115_E0.362241.717
90_L98_L0.359841.705
48_S52_L0.358471.699
97_Y101_Y0.357451.694
54_L119_M0.356151.688
66_R121_R0.351661.667
74_P124_R0.343181.626
114_P118_K0.34271.624
116_L119_M0.341311.618
86_P89_S0.332921.578
46_P120_V0.332091.574
95_P99_R0.325871.544
77_L124_R0.322151.527
55_E100_R0.321071.522
114_P117_R0.320571.519
55_E97_Y0.315381.495
38_A127_L0.308791.464
37_S141_F0.306661.453
146_L173_L0.306631.453
8_D11_Q0.303221.437
95_P98_L0.293221.390
112_V116_L0.292691.387
3_T42_T0.292531.386
146_L157_V0.291691.382
142_C161_L0.29091.379
150_D153_T0.289851.374
151_P154_Q0.287181.361
146_L158_L0.286871.360
53_L65_F0.284871.350
13_E16_R0.283921.346
78_E81_R0.283251.342
68_L123_R0.280071.327
83_G112_V0.278971.322
159_R185_L0.278811.321
6_F48_S0.276141.309
156_R160_R0.275361.305
50_A119_M0.273951.298
65_F119_M0.272551.292
41_S76_A0.272031.289
15_L49_L0.267631.268
34_R66_R0.267361.267
35_I53_L0.266121.261
170_Y189_V0.264931.256
74_P78_E0.264821.255
1_N41_S0.25921.228
155_Q159_R0.257211.219
39_G145_V0.255951.213
51_M102_F0.254851.208
46_P67_I0.253681.202
147_I174_G0.252821.198
51_M101_Y0.251131.190
162_H185_L0.250931.189
78_E82_A0.249371.182
105_R108_G0.249141.181
11_Q175_H0.246251.167
37_S49_L0.245161.162
50_A67_I0.242761.151
79_K82_A0.242611.150
16_R55_E0.242341.149
51_M55_E0.241351.144
4_Y92_G0.237781.127
87_E110_Y0.237221.124
68_L137_F0.234611.112
9_P13_E0.234031.109
47_Y117_R0.228421.083
145_V149_F0.228141.081
6_F97_Y0.228031.081
32_P64_D0.227111.076
40_C46_P0.226151.072
38_A145_V0.225011.066
39_G161_L0.224441.064
12_F48_S0.216061.024
67_I119_M0.214121.015
90_L110_Y0.210740.999
102_F112_V0.209610.993
141_F172_F0.209550.993
54_L101_Y0.206230.977
90_L93_L0.205560.974
14_A172_F0.203310.964
1_N73_S0.201950.957
76_A80_A0.200120.948
6_F93_L0.199840.947
8_D175_H0.199220.944
24_L53_L0.198180.939
144_N148_Y0.198060.939
88_R91_R0.196740.932
2_E154_Q0.196330.931
116_L120_V0.194210.920
88_R154_Q0.193230.916
37_S40_C0.192060.910
106_D111_R0.191960.910
69_A142_C0.191490.908
161_L186_F0.190070.901
87_E98_L0.188970.896
153_T157_V0.186930.886
39_G157_V0.186260.883
51_M97_Y0.185650.880
70_T123_R0.183940.872
15_L141_F0.182790.866
47_Y122_F0.182610.865
96_A100_R0.182090.863
79_K89_S0.180960.858
126_N129_D0.179440.850
174_G177_E0.179350.850
183_P186_F0.179270.850
98_L102_F0.179030.849
22_P170_Y0.178870.848
41_S126_N0.178570.846
4_Y154_Q0.177040.839
73_S76_A0.176490.836
54_L65_F0.176070.834
21_P24_L0.172090.816
2_E73_S0.171530.813
125_H131_D0.170780.809
86_P90_L0.16950.803
39_G70_T0.169490.803
2_E131_D0.168170.797
16_R56_L0.168020.796
159_R182_L0.167060.792
68_L134_F0.16670.790
53_L67_I0.166350.788
111_R117_R0.166190.788
159_R163_R0.164990.782
42_T79_K0.164490.780
147_I176_S0.163920.777
155_Q184_D0.162980.772
136_R166_K0.162260.769
40_C72_I0.160070.759
3_T41_S0.159540.756
102_F110_Y0.157950.749
20_L56_L0.157780.748
16_R52_L0.157130.745
185_L188_P0.156550.742
158_L182_L0.154720.733
144_N149_F0.154630.733
10_E13_E0.154290.731
38_A70_T0.154290.731
19_V170_Y0.15290.725
41_S147_I0.152410.722
125_H164_S0.151510.718
149_F153_T0.151440.718
182_L185_L0.151330.717
1_N154_Q0.151130.716
33_L53_L0.150050.711
41_S175_H0.149920.711
137_F140_I0.14980.710
143_R174_G0.149290.708
105_R109_G0.149240.707
38_A141_F0.14910.707
22_P25_A0.148410.703
158_L173_L0.148120.702
140_I164_S0.148010.701
37_S46_P0.145560.690
123_R145_V0.145150.688
51_M112_V0.144880.687
21_P25_A0.144430.685
14_A18_E0.144380.684
175_H178_S0.144140.683
97_Y100_R0.143070.678
50_A116_L0.143060.678
36_W39_G0.143010.678
111_R114_P0.14290.677
55_E101_Y0.142780.677
148_Y174_G0.141850.672
73_S185_L0.140980.668
11_Q154_Q0.140440.666
183_P188_P0.140420.666
2_E88_R0.139890.663
20_L53_L0.139380.661
24_L56_L0.13890.658
126_N175_H0.138790.658
35_I67_I0.138780.658
42_T175_H0.138260.655
96_A99_R0.138160.655
81_R118_K0.137670.652
24_L30_G0.136730.648
45_E148_Y0.136710.648
12_F143_R0.136680.648
104_E113_K0.13650.647
10_E175_H0.136420.647
85_Y112_V0.136420.647
31_R63_W0.136390.646
12_F52_L0.136380.646
144_N147_I0.136230.646
21_P170_Y0.135840.644
23_L33_L0.135810.644
45_E144_N0.13530.641
179_L182_L0.135210.641
40_C120_V0.134560.638
140_I157_V0.133950.635
133_P157_V0.133860.634
31_R166_K0.133710.634
125_H133_P0.133620.633
131_D134_F0.133550.633
17_D59_G0.133420.632
94_P99_R0.133170.631
18_E22_P0.133130.631
87_E105_R0.132890.630
6_F98_L0.132890.630
7_R144_N0.132570.628
12_F175_H0.131950.625
41_S148_Y0.131760.624
19_V53_L0.131590.624
93_L97_Y0.131360.623
184_D187_E0.131010.621
89_S92_G0.130390.618
76_A79_K0.130050.616
20_L25_A0.129780.615
93_L102_F0.129740.615
18_E21_P0.129590.614
3_T11_Q0.129560.614
143_R148_Y0.129340.613
105_R110_Y0.128650.610
41_S144_N0.128580.609
57_L60_A0.128520.609
157_V161_L0.128470.609
82_A111_R0.128290.608
12_F15_L0.127970.607
15_L20_L0.127920.606
148_Y177_E0.127710.605
19_V172_F0.126730.601
3_T7_R0.126660.600
124_R129_D0.126280.599
56_L60_A0.126220.598
160_R163_R0.126170.598
8_D125_H0.125890.597
157_V160_R0.125890.597
2_E126_N0.125150.593
161_L164_S0.124870.592
165_L186_F0.124850.592
106_D109_G0.124840.592
146_L161_L0.124620.591
173_L179_L0.124030.588
152_E155_Q0.123920.587
17_D64_D0.123810.587
21_P56_L0.123640.586
30_G60_A0.123470.585
55_E116_L0.123470.585
16_R97_Y0.122740.582
53_L57_L0.122590.581
30_G83_G0.122330.580
36_W164_S0.12230.580
4_Y91_R0.122180.579
159_R183_P0.121990.578
7_R148_Y0.121780.577
154_Q158_L0.121730.577
73_S154_Q0.121640.577
127_L149_F0.121270.575
75_S78_E0.121260.575
112_V120_V0.121060.574
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
1af7A0.9491000.232
1o9gA0.954199.70.703
3g07A0.918499.60.74
2r3sA0.806199.50.747
3i53A0.80199.50.748
3gwzA0.795999.50.753
1qzzA0.80199.40.771
2ip2A0.795999.40.771
4a6dA0.795999.30.782
4gekA0.811299.30.782

Page generated in 0.0144 seconds.