GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SpoIIE - Stage II sporulation protein E (SpoIIE)
Pfam: PF07228 (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: CL0238
Length: 193
Sequences: 8616
Seq/Len: 44.64
HH_delta: 0.106 (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
126_R191_R1.410113.775
75_T118_E1.303633.490
90_R125_D1.223893.276
75_T120_Q0.970742.599
7_I190_I0.963952.581
122_E125_D0.922052.468
76_L119_I0.903092.418
77_T118_E0.900572.411
162_P189_V0.771022.064
65_C86_P0.769132.059
128_L189_V0.768522.057
134_L185_I0.759882.034
6_F68_I0.73881.978
130_Y135_F0.727911.949
6_F66_Y0.722651.935
77_T116_E0.707131.893
166_I189_V0.673651.803
41_E116_E0.660061.767
26_L62_A0.651161.743
132_D183_D0.640381.714
67_A76_L0.636371.704
70_D73_T0.628091.681
90_R122_E0.627111.679
63_T83_H0.612471.640
13_S61_Y0.595321.594
78_Y117_Q0.591911.585
78_Y86_P0.577251.545
161_S164_E0.577161.545
128_L187_V0.567351.519
39_D116_E0.552321.479
172_A175_R0.551791.477
19_A23_S0.542241.452
88_L127_L0.535921.435
181_L185_I0.531981.424
65_C78_Y0.530261.420
91_P125_D0.524751.405
8_I30_I0.523811.402
67_A129_L0.517121.384
7_I67_A0.515081.379
163_Q167_D0.513091.374
44_L79_A0.494321.323
134_L169_L0.488731.308
41_E45_E0.484791.298
137_A182_R0.480961.288
167_D171_E0.479141.283
33_L46_A0.477341.278
166_I187_V0.4761.274
40_P79_A0.471321.262
173_I185_I0.469351.256
160_L164_E0.467161.251
76_L127_L0.466421.249
10_G62_A0.464081.242
168_A172_A0.464031.242
48_N52_Y0.463941.242
24_A28_S0.461151.235
130_Y134_L0.457891.226
44_L64_A0.455261.219
11_D132_D0.446711.196
171_E175_R0.445081.191
153_L172_A0.43581.167
87_L130_Y0.430441.152
15_H19_A0.43031.152
139_N143_E0.429131.149
67_A127_L0.428941.148
65_C80_N0.425961.140
16_G20_A0.420021.124
67_A78_Y0.414391.109
29_A50_R0.41351.107
91_P122_E0.412921.105
174_D181_L0.412921.105
48_N51_L0.410731.100
46_A50_R0.408491.094
88_L125_D0.406441.088
167_D170_L0.403531.080
48_N107_G0.402991.079
9_V186_T0.397481.064
74_G120_Q0.392171.050
42_E45_E0.390831.046
95_E99_L0.387431.037
151_L155_D0.385061.031
121_L127_L0.384511.029
181_L184_D0.38391.028
168_A171_E0.38381.027
100_E103_G0.375791.006
12_V15_H0.374951.004
40_P44_L0.373711.000
80_N86_P0.37240.997
126_R165_I0.368590.987
103_G115_Q0.367250.983
32_E50_R0.366720.982
170_L173_I0.36650.981
8_I66_Y0.365570.979
107_G110_E0.364750.976
23_S27_A0.363910.974
97_E100_E0.363670.974
11_D183_D0.362030.969
25_A28_S0.360520.965
21_L25_A0.357450.957
34_L43_L0.356820.955
131_T184_D0.355720.952
13_S16_G0.355150.951
17_V21_L0.355140.951
152_E155_D0.353760.947
66_Y79_A0.353210.946
96_I99_L0.352050.942
126_R189_V0.351550.941
8_I64_A0.351330.941
164_E168_A0.347580.930
76_L121_L0.347250.930
127_L190_I0.346240.927
78_Y119_I0.346120.927
36_E46_A0.345870.926
45_E49_R0.342550.917
86_P129_L0.342210.916
10_G64_A0.341710.915
33_L36_E0.341320.914
99_L103_G0.337930.905
29_A32_E0.337090.902
8_I27_A0.334180.895
137_A181_L0.331450.887
29_A33_L0.330290.884
47_L51_L0.326490.874
27_A31_R0.326070.873
39_D42_E0.325810.872
81_A114_Y0.324580.869
44_L66_Y0.324220.868
98_Q104_P0.319890.856
9_V131_T0.317450.850
128_L154_L0.31570.845
153_L168_A0.313430.839
63_T132_D0.311920.835
49_R53_R0.310930.832
162_P191_R0.308510.826
73_T120_Q0.307020.822
16_G19_A0.305650.818
136_E144_F0.305650.818
52_Y55_L0.305080.817
79_A116_E0.304270.815
54_D58_D0.304120.814
165_I189_V0.304050.814
7_I188_L0.303180.812
12_V83_H0.303050.811
40_P66_Y0.302890.811
160_L168_A0.30280.811
138_L182_R0.300920.806
42_E46_A0.300910.806
94_R97_E0.300730.805
100_E104_P0.299980.803
99_L102_E0.298130.798
69_I76_L0.295960.792
95_E98_Q0.294850.789
79_A114_Y0.294160.787
80_N85_P0.293880.787
44_L48_N0.293630.786
23_S28_S0.293440.786
11_D63_T0.291580.781
7_I69_I0.29150.780
131_T186_T0.288430.772
99_L104_P0.288130.771
9_V65_C0.287890.771
140_E143_E0.287220.769
81_A112_I0.286650.767
84_P130_Y0.28640.767
101_S104_P0.284160.761
170_L174_D0.283660.759
133_G183_D0.283570.759
83_H130_Y0.28350.759
162_P165_I0.281960.755
96_I102_E0.281690.754
151_L154_L0.28140.753
43_L66_Y0.281120.753
164_E167_D0.278930.747
171_E174_D0.277470.743
134_L138_L0.275450.737
18_S21_L0.275340.737
19_A22_L0.275070.736
87_L151_L0.273190.731
134_L173_I0.272610.730
10_G27_A0.27140.727
170_L187_V0.27090.725
6_F43_L0.269550.722
40_P43_L0.268940.720
89_L154_L0.265680.711
46_A49_R0.2650.709
85_P135_F0.264880.709
89_L126_R0.261750.701
138_L144_F0.261720.701
90_R97_E0.261240.699
87_L154_L0.260580.698
21_L24_A0.259760.695
43_L47_L0.259390.694
48_N112_I0.25920.694
155_D159_G0.258540.692
99_L105_P0.257810.690
65_C84_P0.257570.690
50_R53_R0.257530.689
126_R162_P0.257210.689
166_I173_I0.25680.687
173_I181_L0.256230.686
102_E105_P0.25550.684
174_D184_D0.255490.684
15_H136_E0.255350.684
108_I111_D0.25410.680
63_T70_D0.25210.675
60_R64_A0.250390.670
14_G132_D0.249430.668
154_L165_I0.249260.667
34_L66_Y0.247190.662
166_I169_L0.246850.661
33_L47_L0.245370.657
165_I191_R0.24310.651
90_R96_I0.242910.650
183_D186_T0.241890.648
19_A26_L0.241680.647
48_N81_A0.240130.643
107_G111_D0.239520.641
15_H20_A0.238880.639
69_I190_I0.237590.636
48_N110_E0.236390.633
86_P127_L0.236380.633
104_P108_I0.235420.630
98_Q151_L0.235190.630
68_I77_T0.23490.629
22_L60_R0.234790.629
9_V129_L0.234640.628
96_I100_E0.233720.626
6_F40_P0.23350.625
17_V20_A0.23340.625
19_A27_A0.231870.621
80_N117_Q0.230240.616
130_Y187_V0.229960.616
18_S22_L0.228680.612
101_S117_Q0.227950.610
25_A29_A0.227390.609
89_L93_G0.227340.609
80_N84_P0.226850.607
29_A47_L0.226750.607
40_P48_N0.226740.607
120_Q123_P0.224610.601
83_H86_P0.22250.596
65_C83_H0.222190.595
89_L155_D0.219860.589
17_V28_S0.219790.588
10_G23_S0.219320.587
65_C129_L0.21870.585
169_L187_V0.217620.583
15_H18_S0.217070.581
139_N142_G0.216540.580
15_H184_D0.215940.578
109_F112_I0.215320.576
63_T84_P0.215020.576
61_Y108_I0.214440.574
166_I170_L0.214240.574
19_A34_L0.213160.571
70_D75_T0.213060.570
50_R54_D0.213030.570
64_A67_A0.21220.568
30_I43_L0.212060.568
139_N144_F0.211890.567
52_Y112_I0.211580.566
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
3pu9A0.97931000.106
3t91A0.96891000.117
3f79A0.953499.90.177
3eq2A0.953499.90.213
3ke6A0.963799.90.221
3rnrA0.911999.90.241
2j82A0.911999.90.251
2pk0A0.917199.90.263
3zt9A0.860199.90.265
2jfrA0.901699.90.295

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