GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MutS_II - MutS domain II
Pfam: PF05188 (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: 137
Sequences: 2297
Seq/Len: 16.77
HH_delta: 0.173 (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
19_Y45_L0.522992.976
20_I124_L0.493772.810
27_F117_L0.483172.750
16_G116_A0.463382.637
83_F119_A0.395492.251
89_S93_E0.393692.240
4_A42_L0.390632.223
4_A19_Y0.381192.169
91_D125_E0.380692.166
17_L41_E0.365282.079
41_E44_R0.344221.959
31_E113_A0.333321.897
3_L120_L0.314271.788
31_E110_K0.302971.724
98_V104_F0.291811.661
4_A45_L0.288991.645
2_Y24_T0.287581.637
90_E94_E0.284931.621
4_A50_I0.278521.585
110_K113_A0.277841.581
5_A120_L0.266031.514
89_S108_E0.254841.450
78_T82_Y0.251261.430
85_S89_S0.250631.426
30_T41_E0.249461.420
114_L118_G0.24771.410
3_L20_I0.247661.409
4_A47_P0.246471.403
101_L104_F0.241461.374
49_E123_Y0.241341.373
18_A116_A0.23471.336
2_Y21_D0.227881.297
8_E15_Y0.22661.290
29_V117_L0.225641.284
20_I120_L0.220151.253
31_E112_L0.219081.247
93_E99_A0.217951.240
82_Y122_K0.211661.205
27_F96_F0.206951.178
85_S111_E0.206631.176
106_L110_K0.205351.169
93_E98_V0.193681.102
39_K46_S0.188431.072
103_G106_L0.187651.068
7_Y53_P0.187391.066
98_V101_L0.1871.064
102_D108_E0.186831.063
2_Y26_E0.185081.053
88_A115_S0.184761.051
87_F90_E0.181321.032
7_Y115_S0.181051.030
4_A17_L0.180351.026
1_N21_D0.17991.024
98_V103_G0.176631.005
88_A91_D0.175841.001
51_I58_S0.174880.995
16_G31_E0.171150.974
6_I38_L0.170880.972
71_S77_E0.170370.970
87_F91_D0.169640.965
122_K126_E0.16890.961
32_F37_E0.165290.941
19_Y28_Y0.164950.939
51_I119_A0.162880.927
112_L115_S0.162650.926
83_F92_I0.161470.919
20_I117_L0.161440.919
28_Y45_L0.161060.917
15_Y32_F0.161030.916
22_L127_T0.160920.916
67_S71_S0.160510.913
16_G29_V0.159940.910
115_S119_A0.159510.908
7_Y112_L0.158110.900
126_E129_K0.157440.896
122_K125_E0.157340.895
18_A27_F0.157170.894
81_W98_V0.157170.894
14_S31_E0.156550.891
81_W94_E0.156310.890
97_G100_D0.155120.883
98_V105_G0.153720.875
70_N114_L0.153190.872
78_T120_L0.152450.868
40_S44_R0.151910.864
91_D122_K0.151250.861
39_K43_A0.151210.860
8_E53_P0.151180.860
84_D122_K0.15010.854
88_A96_F0.14980.852
16_G113_A0.149130.849
22_L129_K0.148920.847
68_L71_S0.147790.841
8_E11_D0.147730.841
86_E89_S0.147160.837
21_D24_T0.146040.831
2_Y19_Y0.1440.819
53_P77_E0.142190.809
92_I95_Q0.140620.800
8_E58_S0.140220.798
27_F47_P0.139390.793
17_L108_E0.1390.791
84_D87_F0.138450.788
85_S115_S0.138050.786
19_Y22_L0.137510.783
79_P84_D0.137410.782
18_A120_L0.137010.780
124_L129_K0.136710.778
29_V113_A0.136610.777
33_E37_E0.136390.776
40_S129_K0.135810.773
92_I97_G0.135380.770
92_I116_A0.135160.769
51_I128_Q0.134740.767
67_S70_N0.134720.767
86_E94_E0.134310.764
17_L45_L0.13410.763
36_S70_N0.134080.763
35_Y38_L0.133560.760
5_A116_A0.131730.750
29_V41_E0.131430.748
42_L130_S0.131420.748
76_T79_P0.131310.747
42_L50_I0.130580.743
69_K72_F0.130170.741
88_A92_I0.130170.741
23_S49_E0.130090.740
5_A51_I0.129870.739
5_A119_A0.129770.738
83_F115_S0.129120.735
92_I101_L0.129010.734
79_P82_Y0.128970.734
32_F41_E0.128950.734
83_F118_G0.128780.733
23_S124_L0.128160.729
37_E122_K0.127560.726
54_E77_E0.126620.721
49_E127_T0.126290.719
100_D104_F0.12610.718
92_I124_L0.125610.715
98_V108_E0.125570.715
52_I75_V0.124930.711
100_D117_L0.121930.694
79_P83_F0.121890.694
40_S91_D0.121710.693
44_R117_L0.12170.693
15_Y38_L0.120960.688
124_L133_L0.120960.688
86_E91_D0.120840.688
72_F75_V0.120610.686
65_L77_E0.120470.686
75_V86_E0.120340.685
5_A83_F0.120240.684
47_P89_S0.119980.683
2_Y129_K0.119960.683
109_D113_A0.119520.680
96_F113_A0.119210.678
38_L114_L0.119120.678
2_Y28_Y0.118710.676
51_I82_Y0.118710.676
55_G80_S0.117940.671
18_A30_T0.117870.671
34_D37_E0.117740.670
11_D39_K0.117380.668
25_G28_Y0.116970.666
51_I101_L0.11670.664
113_A116_A0.11660.664
87_F122_K0.115860.659
22_L44_R0.115430.657
106_L109_D0.115230.656
119_A122_K0.115220.656
22_L124_L0.115160.655
34_D94_E0.114540.652
27_F41_E0.114490.652
1_N26_E0.114390.651
51_I126_E0.113970.649
105_G108_E0.113650.647
111_E115_S0.113630.647
25_G123_Y0.113460.646
66_S86_E0.11340.645
8_E34_D0.113170.644
59_S65_L0.113010.643
59_S69_K0.112780.642
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
1wb9A0.919799.80.173
3thxB0.992799.70.219
3thxA0.992799.60.262
2o8bB199.60.3
1ewqA0.788399.60.3
1nu0A0.875958.70.854
1vhxA0.941646.60.864
3psfA0.956218.90.887
3psiA0.956218.20.888
3hrgA0.890515.30.892

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