GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MAPEG - MAPEG family
Pfam: PF01124 (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: 129
Sequences: 1367
Seq/Len: 10.6
HH_delta: 0.105 (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
69_V86_A0.410562.894
92_A115_V0.379552.675
99_G112_G0.345792.437
62_L66_L0.302592.133
89_F116_G0.292942.065
85_L119_C0.259481.829
12_L58_F0.255211.799
61_N89_F0.252761.782
92_A116_G0.252121.777
92_A119_C0.244151.721
85_L122_A0.235491.660
84_L88_V0.216651.527
65_F89_F0.214771.514
92_A112_G0.21381.507
57_N93_R0.211351.490
7_L90_V0.207171.460
58_F96_Y0.204931.444
58_F62_L0.202561.428
49_E53_R0.19821.397
11_L58_F0.197081.389
63_P67_V0.192751.359
118_L122_A0.192041.354
100_Y106_P0.1891.332
80_S84_L0.186151.312
65_F69_V0.180221.270
52_Q56_Q0.179921.268
94_V98_V0.179651.266
58_F97_A0.175511.237
5_S66_L0.173931.226
79_P83_A0.1721.212
51_A101_I0.169631.196
19_V55_H0.166211.172
121_L125_L0.166191.171
46_P49_E0.158521.117
54_A97_A0.156421.103
88_V119_C0.155341.095
105_I108_L0.154381.088
46_P50_R0.153311.081
95_A112_G0.152471.075
87_W91_V0.152181.073
19_V23_R0.151631.069
57_N60_E0.151171.066
116_G120_L0.149971.057
20_G117_L0.148291.045
57_N100_Y0.147381.039
68_A120_L0.147331.038
110_S113_F0.147061.037
50_R100_Y0.146921.036
6_A124_A0.144951.022
96_Y100_Y0.14481.021
6_A64_L0.144541.019
26_A47_W0.143971.015
88_V92_A0.143861.014
50_R54_A0.14351.011
61_N116_G0.143391.011
114_L118_L0.143111.009
26_A45_P0.141851.000
14_Y17_Y0.141670.999
113_F117_L0.141610.998
95_A125_L0.14150.997
12_L62_L0.139540.984
9_V12_L0.139040.980
53_R58_F0.138970.980
18_I101_I0.13770.971
49_E52_Q0.137420.969
16_S55_H0.136440.962
5_S67_V0.135980.958
16_S97_A0.135860.958
56_Q59_L0.135110.952
117_L121_L0.13480.950
47_W51_A0.134390.947
81_L85_L0.134340.947
17_Y21_A0.133860.944
18_I22_A0.132580.934
56_Q60_E0.132120.931
78_S102_A0.13170.928
15_L94_V0.131640.928
114_L117_L0.131440.926
10_L124_A0.131210.925
102_A105_I0.129910.916
76_G80_S0.129430.912
54_A100_Y0.128840.908
12_L59_L0.127980.902
103_G108_L0.12790.901
75_T78_S0.127810.901
23_R48_L0.12590.887
62_L120_L0.125250.883
113_F116_G0.125160.882
15_L54_A0.124830.880
11_L97_A0.123740.872
8_L58_F0.123490.870
24_F110_S0.122670.865
65_F123_L0.122650.864
13_F110_S0.122580.864
21_A79_P0.122340.862
53_R57_N0.122290.862
95_A99_G0.121890.859
83_A96_Y0.121320.855
91_V94_V0.121070.853
10_L17_Y0.120720.851
60_E65_F0.120190.847
81_L84_L0.120190.847
22_A51_A0.119990.846
107_P111_L0.119760.844
71_L80_S0.119420.842
65_F100_Y0.119150.840
47_W101_I0.11910.839
7_L16_S0.118250.833
79_P126_A0.117720.830
20_G55_H0.116390.820
88_V98_V0.116170.819
110_S114_L0.1160.818
83_A124_A0.115670.815
111_L117_L0.115040.811
6_A70_L0.114920.810
122_A125_L0.114470.807
62_L100_Y0.114020.804
119_C123_L0.113990.803
115_V119_C0.113950.803
111_L115_V0.113840.802
78_S84_L0.113390.799
65_F90_V0.112860.795
5_S65_F0.112780.795
5_S124_A0.111960.789
7_L80_S0.111530.786
110_S115_V0.111510.786
6_A90_V0.11150.786
13_F17_Y0.111140.783
84_L87_W0.110950.782
42_P52_Q0.110850.781
22_A25_K0.11080.781
61_N117_L0.110740.781
83_A87_W0.110440.778
15_L51_A0.109680.773
54_A62_L0.109490.772
67_V70_L0.109190.770
65_F86_A0.109180.770
19_V53_R0.108850.767
108_L114_L0.108840.767
68_A85_L0.108480.765
122_A126_A0.1080.761
14_Y18_I0.107890.760
10_L125_L0.10750.758
64_L69_V0.107460.757
20_G31_G0.106210.749
120_L124_A0.104420.736
86_A123_L0.10430.735
32_E46_P0.104180.734
72_A82_A0.103670.731
51_A72_A0.103570.730
12_L89_F0.10350.730
90_V94_V0.103420.729
23_R55_H0.103370.729
7_L10_L0.103350.728
42_P125_L0.103270.728
11_L111_L0.103080.727
64_L67_V0.103060.726
41_P122_A0.103020.726
12_L51_A0.102970.726
70_L84_L0.102930.725
99_G110_S0.102480.722
88_V121_L0.102020.719
67_V72_A0.1020.719
73_I76_G0.101870.718
50_R105_I0.10170.717
99_G102_A0.101010.712
55_H66_L0.100760.710
112_G115_V0.100540.709
8_L20_G0.099690.703
21_A108_L0.099560.702
61_N120_L0.099540.702
16_S61_N0.099220.699
42_P49_E0.0990.698
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
3dwwA199.90.105
2h8aA199.80.134
4al0A199.80.156
2q7rA0.90799.80.226
3pcvA0.90799.80.227
3hd6A0.65125.80.917
4ainA0.395340.922
2kncB0.47293.60.924
3giaA0.34882.80.928
2b2hA0.40312.70.928

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