GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NMT1_2 - NMT1-like family
Pfam: PF13379 (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: CL0177
Length: 252
Sequences: 46535
Seq/Len: 184.66
HH_delta: 0.206 (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
7_T38_E2.3972.970
108_S111_D2.307932.859
11_G57_I2.216522.746
7_T36_D2.205362.732
84_L230_Q2.089322.588
9_R38_E2.039782.527
166_L174_A1.864462.310
91_G178_E1.725532.138
107_K111_D1.681252.083
86_G89_Q1.660892.058
163_V184_A1.654182.049
50_E54_A1.649022.043
82_V212_R1.638342.030
51_A56_E1.617882.004
134_D138_R1.463781.813
123_K153_T1.436081.779
27_K228_A1.434871.778
167_R189_I1.42181.761
162_M174_A1.402471.738
28_G32_K1.401321.736
167_R184_A1.382531.713
93_A192_I1.377711.707
223_K227_E1.371071.699
96_V193_V1.368791.696
9_R40_V1.366381.693
51_A57_I1.353191.676
83_V207_V1.34821.670
125_A162_M1.32651.643
93_A178_E1.323861.640
224_A227_E1.318911.634
89_Q205_C1.311421.625
157_V165_A1.30111.612
48_I60_A1.298861.609
86_G205_C1.271011.575
226_L230_Q1.269611.573
80_D212_R1.246981.545
52_L60_A1.240771.537
182_S186_A1.230561.525
125_A172_D1.228951.523
96_V173_A1.225521.518
141_L146_L1.222041.514
18_Y160_P1.202451.490
164_A167_R1.186521.470
219_P222_V1.183661.466
97_R169_G1.182141.465
123_K154_L1.172641.453
98_N191_K1.167241.446
32_K231_E1.165761.444
164_A168_A1.151341.426
218_N222_V1.148871.423
27_K31_E1.147521.422
33_E227_E1.132911.404
28_G35_L1.128891.399
220_E224_A1.120591.388
28_G31_E1.102161.365
183_Q187_K1.087891.348
5_P34_G1.086131.346
184_A189_I1.076831.334
82_V210_A1.06051.314
178_E182_S1.058021.311
192_I195_D1.057861.311
105_D191_K1.047941.298
104_S111_D1.030971.277
157_V162_M1.027391.273
227_E230_Q1.021681.266
228_A231_E1.018451.262
62_V209_V1.002561.242
122_K173_A0.990531.227
84_L210_A0.978741.213
163_V167_R0.976741.210
218_N221_A0.970391.202
123_K172_D0.962591.193
42_F51_A0.959941.189
214_F218_N0.959411.189
53_A80_D0.950111.177
40_V51_A0.945071.171
28_G225_F0.944271.170
59_I210_A0.933681.157
211_R214_F0.923261.144
99_D169_G0.919361.139
11_G48_I0.918891.138
169_G172_D0.9161.135
124_I173_A0.91251.131
122_K172_D0.907551.124
208_I226_L0.901791.117
83_V86_G0.899731.115
47_D50_E0.894631.108
33_E231_E0.887771.100
51_A54_A0.882541.093
63_L207_V0.877941.088
227_E231_E0.876651.086
59_I208_I0.875971.085
213_D217_E0.875041.084
73_G80_D0.868811.076
176_L181_A0.861941.068
84_L226_L0.850741.054
90_N179_P0.847641.050
28_G228_A0.84631.048
98_N189_I0.842891.044
27_K30_F0.841681.043
10_I59_I0.837921.038
110_A144_A0.833981.033
11_G62_V0.833111.032
40_V57_I0.817211.012
94_L175_V0.813511.008
6_T35_L0.803680.996
65_P73_G0.803210.995
29_L32_K0.79830.989
42_F47_D0.797280.988
220_E223_K0.795630.986
29_L123_K0.788190.976
9_R58_D0.784970.973
95_V181_A0.784950.972
49_L53_A0.781660.968
137_L140_L0.781560.968
178_E192_I0.780460.967
210_A226_L0.779530.966
222_V226_L0.778660.965
8_L225_F0.777980.964
140_L144_A0.77680.962
32_K224_A0.769420.953
59_I222_V0.768580.952
224_A228_A0.76790.951
185_E188_G0.764430.947
139_Y143_K0.762610.945
110_A120_K0.76070.942
135_M138_R0.743690.921
123_K155_V0.742560.920
24_A228_A0.739650.916
184_A187_K0.737320.913
26_E30_F0.731190.906
94_L173_A0.730520.905
86_G207_V0.730250.905
104_S107_K0.728980.903
185_E192_I0.728760.903
74_A80_D0.715720.887
47_D51_A0.709570.879
6_T221_A0.705370.874
98_N188_G0.704590.873
139_Y142_K0.70420.872
82_V86_G0.699580.867
5_P36_D0.694420.860
57_I60_A0.692260.858
59_I225_F0.690720.856
107_K191_K0.680720.843
83_V209_V0.6770.839
183_Q186_A0.676130.838
35_L221_A0.675140.836
30_F33_E0.672060.833
111_D121_G0.669990.830
29_L33_E0.667150.827
109_L197_G0.661220.819
24_A229_L0.656440.813
141_L148_P0.654710.811
148_P152_V0.653610.810
161_E164_A0.651850.808
223_K226_L0.651380.807
218_N223_K0.650870.806
95_V185_E0.649010.804
158_P161_E0.648070.803
22_Y26_E0.647380.802
55_G211_R0.64720.802
35_L224_A0.645280.799
95_V192_I0.63740.790
33_E224_A0.635770.788
42_F48_I0.632330.783
38_E156_N0.631850.783
20_P24_A0.62640.776
141_L144_A0.625640.775
177_W180_F0.625180.775
53_A81_I0.618990.767
8_L59_I0.612890.759
181_A185_E0.61090.757
58_D214_F0.60990.756
30_F229_L0.607260.752
138_R142_K0.604610.749
219_P223_K0.604440.749
106_I111_D0.604040.748
134_D156_N0.601690.745
53_A56_E0.601030.745
11_G60_A0.599830.743
138_R141_L0.591880.733
29_L154_L0.590480.732
26_E168_A0.579670.718
12_Y21_L0.577290.715
55_G213_D0.577090.715
95_V174_A0.576330.714
28_G224_A0.571690.708
23_V27_K0.57160.708
125_A166_L0.566310.702
17_D41_Q0.56570.701
20_P23_V0.564290.699
46_A50_E0.562060.696
120_K147_D0.561090.695
97_R172_D0.558920.692
81_I209_V0.558020.691
9_R57_I0.554470.687
92_N177_W0.554350.687
90_N177_W0.55430.687
225_F229_L0.552730.685
221_A224_A0.551140.683
161_E165_A0.55020.682
89_Q201_G0.548420.679
210_A222_V0.544520.675
141_L145_G0.543140.673
127_P162_M0.541370.671
18_Y164_A0.538870.668
53_A73_G0.538470.667
157_V161_E0.537530.666
155_V159_P0.534990.663
148_P153_T0.534210.662
65_P72_K0.531990.659
23_V168_A0.531860.659
12_Y17_D0.531510.658
201_G204_P0.530310.657
18_Y159_P0.529740.656
112_L120_K0.52960.656
29_L225_F0.529420.656
160_P164_A0.529080.655
12_Y41_Q0.528770.655
166_L190_G0.528130.654
14_P41_Q0.526870.653
125_A165_A0.526820.653
123_K152_V0.523150.648
197_G200_W0.522320.647
10_I37_V0.521940.647
110_A146_L0.521630.646
95_V176_L0.5210.645
29_L228_A0.520850.645
82_V217_E0.51910.643
21_L24_A0.518370.642
23_V26_E0.517720.641
135_M139_Y0.517530.641
16_P20_P0.517320.641
96_V191_K0.516160.639
163_V176_L0.514230.637
11_G40_V0.512740.635
129_P156_N0.512720.635
196_S199_V0.511710.634
137_L141_L0.511560.634
104_S122_K0.511480.634
17_D22_Y0.510470.632
210_A214_F0.509610.631
31_E231_E0.508960.631
136_L139_Y0.508710.630
88_S206_C0.507840.629
126_V153_T0.506390.627
195_D198_D0.504280.625
50_E53_A0.504030.624
120_K146_L0.502960.623
106_I122_K0.501610.621
210_A217_E0.499080.618
138_R148_P0.498690.618
207_V210_A0.49690.616
58_D222_V0.496120.615
43_A47_D0.492460.610
181_A184_A0.492310.610
97_R104_S0.490980.608
225_F228_A0.488330.605
61_F229_L0.486650.603
10_I225_F0.486450.603
126_V154_L0.485840.602
52_L81_I0.484520.600
214_F219_P0.484220.600
163_V166_L0.482540.598
32_K228_A0.48250.598
61_F87_L0.481280.596
93_A96_V0.479120.594
166_L172_D0.478880.593
140_L143_K0.47470.588
14_P159_P0.474320.588
91_G201_G0.472370.585
154_L157_V0.469760.582
133_H136_L0.469190.581
15_G90_N0.467350.579
189_I192_I0.466010.577
82_V213_D0.463810.575
96_V106_I0.458540.568
12_Y39_W0.453780.562
90_N204_P0.45330.562
26_E29_L0.453040.561
176_L180_F0.453020.561
167_R187_K0.449710.557
194_A197_G0.449610.557
162_M166_L0.449250.557
112_L173_A0.448610.556
52_L211_R0.44840.556
94_L193_V0.447880.555
19_A22_Y0.44590.552
98_N190_G0.444920.551
10_I39_W0.444320.550
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
3un6A0.932599.80.206
2g29A0.948499.80.212
2y7pA0.857199.80.213
3oxnA0.86999.80.225
4ab5A0.86999.80.226
2i49A0.976299.80.228
1i6aA0.865199.80.23
3fxqA0.865199.80.233
3ksxA0.912799.80.237
2esnA0.841399.80.237

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