GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MutS_V - MutS domain V
Pfam: PF00488 (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: CL0023
Length: 235
Sequences: 3640
Seq/Len: 15.49
HH_delta: 0.145 (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
16_E79_E1.274555.503
14_I17_G1.204585.201
87_D121_T0.851183.675
13_K82_E0.837973.618
5_K82_E0.832073.593
15_K80_S0.777293.356
7_S82_E0.72843.145
16_E35_D0.683482.951
13_K37_E0.680342.938
17_G66_I0.588572.541
3_R75_F0.575282.484
64_G127_L0.56482.439
219_E223_E0.554512.394
213_K219_E0.525392.269
6_I83_I0.509362.199
67_V86_F0.498882.154
213_K226_K0.494522.135
67_V125_L0.494222.134
17_G62_Q0.490742.119
15_K79_E0.485462.096
11_S82_E0.474472.049
224_R227_E0.471592.036
114_S118_R0.45621.970
45_I148_L0.45571.968
5_K80_S0.450411.945
63_I160_I0.441031.904
149_E224_R0.439541.898
115_S119_N0.432871.869
36_I63_I0.431391.863
71_Q85_I0.413461.785
15_K35_D0.412771.782
184_E199_K0.403381.742
66_I76_V0.397221.715
44_R177_N0.392451.695
152_L175_N0.391721.691
46_I181_Y0.384691.661
181_Y200_E0.384451.660
70_A83_I0.381951.649
122_E156_G0.379761.640
10_K84_P0.37761.630
15_K37_E0.362611.566
12_L63_I0.361531.561
59_F198_L0.357931.545
113_L147_I0.35321.525
18_R23_E0.351171.516
68_I89_I0.347691.501
103_L111_K0.347271.499
224_R228_I0.346681.497
87_D123_K0.340691.471
113_L128_I0.339421.466
175_N178_V0.333731.441
42_K179_Q0.331171.430
66_I77_P0.32641.409
170_E173_E0.324391.401
71_Q86_F0.305521.319
16_E197_K0.305081.317
14_I66_I0.30491.317
128_I131_L0.302111.304
36_I59_F0.298711.290
184_E197_K0.296641.281
48_I160_I0.295721.277
98_S101_S0.290331.254
13_K80_S0.289911.252
105_T134_G0.285771.234
151_L155_S0.285761.234
182_H199_K0.282811.221
35_D197_K0.282261.219
210_E226_K0.281911.217
39_S42_K0.280331.210
69_L74_C0.275781.191
76_V81_A0.268851.161
179_Q200_E0.268381.159
70_A76_V0.268311.159
220_E224_R0.266221.149
182_H202_I0.264571.142
121_T124_S0.264011.140
94_G105_T0.262671.134
113_L131_L0.256131.106
38_L46_I0.253561.095
144_A165_F0.253361.094
12_L84_P0.252771.091
126_V151_L0.25241.090
7_S84_P0.252381.090
6_I70_A0.249661.078
213_K222_I0.24931.076
98_S103_L0.248441.073
226_K230_K0.248271.072
190_D226_K0.244841.057
90_F119_N0.244331.055
67_V71_Q0.243251.050
86_F158_F0.241181.041
145_I149_E0.240791.040
47_I178_V0.239751.035
120_A155_S0.239411.034
11_S39_S0.237191.024
67_V84_P0.236511.021
223_E227_E0.235531.017
132_G140_G0.233041.006
34_N59_F0.2321.002
116_I126_V0.231721.001
60_L162_A0.231310.999
150_Y220_E0.230580.996
10_K123_K0.229110.989
45_I152_L0.228790.988
8_E123_K0.227430.982
45_I159_V0.22690.980
111_K115_S0.226830.979
151_L159_V0.226150.976
172_L200_E0.226050.976
46_I179_Q0.225310.973
152_L178_V0.224980.971
92_R109_E0.224830.971
7_S10_K0.223160.964
92_R112_R0.221740.957
143_I147_I0.221310.956
48_I198_L0.220760.953
60_L127_L0.220660.953
12_L67_V0.219440.948
182_H185_V0.219280.947
149_E171_L0.218230.942
53_M61_K0.21810.942
14_I81_A0.21710.937
149_E153_E0.216630.935
7_S11_S0.215450.930
223_E226_K0.215350.930
23_E31_F0.2140.924
183_M198_L0.213480.922
38_L160_I0.21170.914
10_K122_E0.21130.912
31_F58_T0.210640.910
44_R158_F0.206920.893
49_T52_N0.205750.888
22_L31_F0.203080.877
169_A202_I0.20030.865
18_R33_P0.20020.864
88_R119_N0.199680.862
10_K158_F0.199670.862
22_L58_T0.199640.862
17_G36_I0.19860.858
93_I166_H0.197850.854
52_N56_K0.197470.853
222_I226_K0.197220.852
11_S40_N0.196520.849
152_L177_N0.195370.844
145_I171_L0.194630.840
42_K200_E0.193010.833
67_V83_I0.192960.833
103_L107_M0.192820.833
16_E219_E0.191330.826
117_L151_L0.190840.824
141_I167_E0.190680.823
66_I81_A0.190350.822
63_I125_L0.189630.819
140_G165_F0.189340.818
210_E213_K0.189180.817
18_R31_F0.187820.811
87_D124_S0.187020.808
144_A168_L0.186910.807
36_I62_Q0.186040.803
50_G55_G0.185850.802
172_L180_N0.185580.801
212_A217_L0.185510.801
109_E133_R0.183550.793
227_E230_K0.183270.791
4_P70_A0.182750.789
9_E82_E0.181750.785
126_V157_C0.18150.784
16_E220_E0.180070.778
182_H201_G0.180050.777
54_S196_Y0.178770.772
2_C80_S0.178740.772
220_E223_E0.177570.767
66_I83_I0.176370.762
63_I66_I0.176060.760
181_Y198_L0.175370.757
172_L178_V0.172240.744
184_E195_T0.172190.743
2_C5_K0.170870.738
11_S37_E0.170480.736
162_A185_V0.168330.727
48_I181_Y0.167950.725
50_G56_K0.167770.724
53_M136_N0.167660.724
16_E33_P0.166960.721
145_I228_I0.166840.720
71_Q83_I0.166470.719
148_L161_I0.166390.718
95_D133_R0.166380.718
51_P62_Q0.166310.718
5_K13_K0.165620.715
115_S118_R0.165490.715
60_L63_I0.165480.715
3_R18_R0.165410.714
120_A124_S0.165270.714
105_T133_R0.16510.713
10_K40_N0.16440.710
68_I72_I0.163780.707
92_R95_D0.163470.706
73_G76_V0.163330.705
186_E189_N0.162670.702
11_S84_P0.16210.700
36_I46_I0.161870.699
219_E230_K0.161420.697
149_E175_N0.161350.697
118_R218_P0.160570.693
142_A145_I0.160490.693
37_E223_E0.160410.693
53_M215_A0.159090.687
142_A146_A0.158330.684
97_D109_E0.158070.683
7_S12_L0.157350.679
60_L204_S0.157210.679
127_L162_A0.156740.677
111_K114_S0.156270.675
58_T97_D0.155890.673
11_S158_F0.155540.672
39_S158_F0.155430.671
8_E13_K0.155410.671
62_Q66_I0.15520.670
61_K97_D0.154530.667
191_S213_K0.154220.666
52_N55_G0.153810.664
105_T144_A0.153630.663
206_S211_I0.153290.662
10_K85_I0.153040.661
13_K79_E0.152450.658
6_I85_I0.15170.655
95_D194_F0.151620.655
171_L175_N0.15130.653
92_R97_D0.150770.651
10_K44_R0.150730.651
22_L196_Y0.14920.644
2_C75_F0.149080.644
44_R156_G0.149030.643
153_E177_N0.14850.641
95_D206_S0.148460.641
20_P65_L0.148430.641
58_T169_A0.148380.641
128_I161_I0.148310.640
2_C223_E0.148180.640
105_T206_S0.147770.638
6_I9_E0.147690.638
54_S185_V0.14760.637
45_I178_V0.147210.636
46_I74_C0.146920.634
109_E112_R0.14680.634
217_L221_I0.146770.634
10_K13_K0.14590.630
58_T183_M0.145780.629
54_S228_I0.144440.624
57_S162_A0.143930.621
145_I168_L0.143810.621
122_E174_R0.143520.620
206_S212_A0.143260.619
13_K40_N0.142630.616
128_I151_L0.142430.615
96_D108_A0.142370.615
16_E41_N0.141920.613
170_E174_R0.141890.613
79_E82_E0.14180.612
117_L221_I0.141750.612
84_P158_F0.14170.612
150_Y153_E0.141280.610
153_E174_R0.141120.609
101_S208_A0.14050.607
68_I71_Q0.140370.606
14_I67_V0.140160.605
136_N139_E0.13960.603
131_L147_I0.13920.601
128_I147_I0.138870.600
10_K156_G0.138670.599
94_G144_A0.138510.598
9_E123_K0.137710.595
128_I165_F0.137580.594
37_E200_E0.137520.594
137_P194_F0.137270.593
54_S206_S0.136830.591
153_E224_R0.136150.588
133_R144_A0.136040.587
103_L108_A0.135660.586
58_T61_K0.135650.586
120_A126_V0.135510.585
54_S210_E0.135350.584
135_T208_A0.134760.582
5_K87_D0.134520.581
151_L157_C0.134510.581
113_L161_I0.134320.580
39_S44_R0.134320.580
98_S196_Y0.134310.580
92_R133_R0.134270.580
144_A161_I0.134020.579
5_K122_E0.133920.578
151_L209_I0.133650.577
60_L64_G0.133480.576
18_R75_F0.133420.576
121_T157_C0.132920.574
18_R77_P0.132810.573
54_S182_H0.13270.573
132_G144_A0.132650.573
143_I181_Y0.131720.569
53_M139_E0.131680.569
220_E230_K0.131670.569
32_V196_Y0.131430.567
30_K40_N0.131310.567
171_L180_N0.130710.564
103_L217_L0.130380.563
132_G212_A0.130360.563
53_M211_I0.130280.563
94_G132_G0.13020.562
94_G140_G0.130180.562
113_L132_G0.130130.562
140_G144_A0.130050.562
69_L77_P0.129910.561
5_K219_E0.129660.560
186_E193_T0.129270.558
90_F124_S0.129250.558
190_D227_E0.128930.557
195_T207_Y0.128920.557
40_N122_E0.128650.555
37_E40_N0.128420.554
51_P54_S0.128370.554
46_I59_F0.127990.553
183_M194_F0.127760.552
54_S194_F0.127690.551
94_G97_D0.127690.551
41_N176_P0.12760.551
92_R161_I0.127480.550
69_L72_I0.127440.550
34_N166_H0.127140.549
14_I83_I0.126760.547
147_I151_L0.12670.547
167_E180_N0.126580.547
53_M58_T0.126560.546
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
3thxB11000.145
3thxA0.99571000.151
1wb9A0.99151000.159
2o8bB11000.172
1ewqA0.95321000.211
3tifA0.76699.70.707
4hluD0.940499.70.71
4huqB0.944799.70.714
3tuiC0.953299.60.717
3gfoA0.931999.60.718

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