GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SpoVAD - Stage V sporulation protein AD (SpoVAD)
Pfam: PF07451 (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: CL0046
Length: 329
Sequences: 4961
Seq/Len: 15.08
HH_delta: 0.196 (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
56_K94_D1.03314.120
127_Y170_S0.915963.653
14_I170_S0.86463.448
59_V129_L0.751582.997
116_A128_V0.698842.787
18_S288_L0.682642.722
91_A131_A0.65422.609
69_K72_D0.637712.543
288_L292_R0.631012.517
56_K91_A0.624542.491
55_Q91_A0.599422.391
57_E60_E0.597092.381
53_K94_D0.580992.317
219_S222_D0.57612.298
75_Y128_V0.562972.245
249_D252_E0.559912.233
112_S130_A0.554142.210
56_K60_E0.54882.189
62_A168_I0.539172.150
117_A121_D0.529162.110
74_D126_D0.520722.077
16_T288_L0.509352.031
212_H216_T0.505822.017
72_D127_Y0.495271.975
60_E64_K0.490011.954
59_V95_L0.485511.936
74_D127_Y0.480461.916
41_Y46_S0.476031.898
62_A66_A0.475311.896
27_G30_G0.469241.871
113_L169_L0.460031.835
65_K291_L0.450851.798
243_L250_I0.443711.770
25_G28_P0.440531.757
68_L127_Y0.438061.747
210_E214_K0.437871.746
51_E133_S0.436831.742
63_L70_K0.434321.732
20_V271_A0.426551.701
61_L65_K0.421491.681
120_V169_L0.419421.673
274_S284_C0.416461.661
47_W146_P0.416161.660
77_F116_A0.413841.650
75_Y119_L0.412241.644
61_L64_K0.409941.635
236_R240_R0.405971.619
19_V54_M0.402431.605
50_A53_K0.390281.556
77_F100_L0.387411.545
15_S65_K0.386861.543
79_G112_S0.377041.504
17_A62_A0.3731.488
218_R223_Y0.366471.462
40_D46_S0.366071.460
84_Q180_H0.362621.446
73_I97_I0.359351.433
28_P31_D0.358741.431
125_A128_V0.356031.420
135_H138_T0.351631.402
72_D126_D0.349011.392
73_I168_I0.344961.376
218_R222_D0.344771.375
107_S309_S0.342911.368
58_A166_A0.342611.366
118_M122_G0.342211.365
116_A130_A0.341891.363
65_K292_R0.341511.362
210_E220_P0.338841.351
239_L253_N0.338791.351
236_R255_N0.338661.351
68_L72_D0.338541.350
68_L168_I0.338041.348
73_I129_L0.337881.348
63_L73_I0.33621.341
254_Y286_Y0.333641.331
60_E70_K0.326271.301
63_L68_L0.32531.297
291_L296_L0.324661.295
78_A87_S0.323451.290
100_L115_L0.322781.287
36_I40_D0.32171.283
57_E61_L0.321511.282
33_F157_A0.321011.280
240_R250_I0.316731.263
24_E46_S0.316271.261
23_K28_P0.315951.260
118_M124_F0.315551.258
243_L253_N0.315151.257
120_V128_V0.314811.256
73_I127_Y0.31421.253
17_A61_L0.312111.245
74_D125_A0.310891.240
105_A306_A0.310861.240
39_D46_S0.310831.240
116_A169_L0.3071.224
22_P49_K0.303711.211
15_S66_A0.301891.204
36_I41_Y0.301741.203
24_E44_E0.301521.202
256_D289_P0.298161.189
195_N198_G0.294921.176
115_L119_L0.293781.172
18_S284_C0.292011.165
225_L290_K0.291661.163
56_K95_L0.291111.161
109_M167_A0.291061.161
58_A164_A0.28981.156
109_M283_L0.288481.150
76_L97_I0.287711.147
59_V131_A0.287691.147
120_V123_G0.285871.140
36_I39_D0.284611.135
15_S168_I0.284541.135
55_Q78_A0.283081.129
81_L105_A0.281581.123
224_D297_K0.281031.121
113_L283_L0.280971.121
59_V63_L0.280871.120
55_Q133_S0.277211.106
126_D171_K0.276371.102
146_P157_A0.276351.102
18_S292_R0.276211.102
213_F220_P0.275631.099
33_F36_I0.274591.095
225_L295_E0.273971.093
76_L92_A0.27191.084
254_Y290_K0.271041.081
133_S164_A0.269241.074
78_A131_A0.269151.073
15_S62_A0.261751.044
102_L115_L0.261321.042
227_V286_Y0.256761.024
232_G273_G0.25671.024
129_L168_I0.256441.023
81_L103_Y0.255871.020
213_F216_T0.254691.016
223_Y300_L0.254671.016
207_D211_Q0.254541.015
61_L288_L0.251431.003
77_F102_L0.250941.001
191_I194_P0.250420.999
77_F128_V0.247670.988
14_I127_Y0.247210.986
60_E95_L0.245050.977
21_G24_E0.24380.972
111_E115_L0.240160.958
211_Q214_K0.239660.956
289_P293_K0.239480.955
27_G31_D0.239090.954
35_K39_D0.236080.942
49_K53_K0.235760.940
17_A58_A0.235690.940
52_S87_S0.234760.936
213_F218_R0.234440.935
70_K97_I0.234440.935
211_Q215_D0.23320.930
223_Y226_I0.231090.922
227_V287_L0.229250.914
62_A129_L0.228140.910
132_T279_S0.227550.907
49_K57_E0.22670.904
130_A169_L0.225160.898
60_E94_D0.223550.892
53_K57_E0.22340.891
248_Y252_E0.223260.890
16_T167_A0.222490.887
165_G283_L0.221030.881
208_T211_Q0.220420.879
90_F94_D0.219970.877
107_S304_T0.219620.876
87_S90_F0.218220.870
107_S110_M0.216430.863
52_S91_A0.21580.861
179_T215_D0.213620.852
120_V171_K0.212450.847
79_G279_S0.212330.847
86_I89_S0.21190.845
199_A202_A0.211070.842
55_Q59_V0.210960.841
120_V125_A0.210280.839
54_M135_H0.209760.837
220_P226_I0.209250.835
119_L125_A0.208370.831
290_K293_K0.207980.829
63_L67_G0.207330.827
289_P292_R0.205090.818
290_K295_E0.204780.817
88_S99_F0.203940.813
209_I228_T0.203570.812
136_F275_G0.202990.810
241_D245_E0.202920.809
110_M303_A0.202570.808
78_A91_A0.202460.807
55_Q131_A0.201960.805
226_I253_N0.201640.804
114_A118_M0.199380.795
78_A133_S0.199340.795
25_G44_E0.199090.794
35_K40_D0.198490.792
104_G309_S0.198270.791
218_R298_R0.197870.789
54_M164_A0.197070.786
119_L124_F0.196570.784
201_M207_D0.196210.783
254_Y293_K0.195010.778
118_M121_D0.194390.775
58_A62_A0.194190.774
35_K41_Y0.193590.772
91_A95_L0.192160.766
76_L129_L0.192110.766
286_Y290_K0.191970.766
90_F93_R0.191890.765
16_T292_R0.191580.764
115_L118_M0.190830.761
92_A184_G0.190210.759
214_K219_S0.189950.758
210_E245_E0.18980.757
59_V91_A0.188350.751
213_F223_Y0.187520.748
114_A124_F0.187250.747
80_D83_N0.187240.747
228_T254_Y0.187220.747
77_F115_L0.186840.745
22_P25_G0.185470.740
43_G46_S0.18390.733
40_D43_G0.183850.733
116_A125_A0.183250.731
282_V301_F0.182080.726
212_H215_D0.181770.725
29_L47_W0.181660.724
24_E28_P0.181580.724
290_K296_L0.180550.720
271_A284_C0.179280.715
148_E156_T0.179170.715
52_S94_D0.178980.714
284_C289_P0.178840.713
110_M282_V0.178760.713
225_L296_L0.178390.711
106_C232_G0.178310.711
36_I46_S0.178040.710
52_S90_F0.177260.707
163_G280_A0.176810.705
18_S61_L0.176770.705
33_F41_Y0.175310.699
225_L254_Y0.17520.699
59_V62_A0.175120.698
161_V166_A0.174950.698
39_D43_G0.174780.697
304_T308_L0.174590.696
225_L255_N0.174450.696
167_A287_L0.174420.696
256_D286_Y0.173970.694
221_D224_D0.173250.691
197_M201_M0.173210.691
79_G132_T0.172410.688
206_A245_E0.171960.686
82_L143_F0.171940.686
53_K56_K0.171370.683
64_K67_G0.171310.683
232_G281_V0.170770.681
304_T309_S0.17070.681
209_I213_F0.170450.680
66_A70_K0.17010.678
92_A97_I0.169530.676
35_K46_S0.169440.676
85_I90_F0.168490.672
290_K294_G0.16840.672
210_E246_K0.168280.671
91_A94_D0.168160.671
208_T302_V0.167480.668
288_L291_L0.166980.666
163_G274_S0.166030.662
47_W137_A0.16590.662
63_L129_L0.165770.661
235_G238_I0.16520.659
88_S101_G0.165010.658
197_M308_L0.164810.657
179_T211_Q0.163810.653
63_L97_I0.163770.653
77_F119_L0.162250.647
66_A168_I0.161880.646
156_T160_T0.161650.645
93_R185_K0.161380.644
63_L69_K0.161250.643
29_L33_F0.160340.639
144_R148_E0.160330.639
19_V22_P0.160.638
202_A209_I0.159950.638
63_L66_A0.159930.638
68_L170_S0.159260.635
68_L73_I0.159060.634
206_A242_L0.158840.633
71_E98_P0.158460.632
148_E155_P0.158260.631
172_E175_G0.157980.630
214_K217_G0.157880.630
33_F39_D0.157850.630
136_F144_R0.157570.628
25_G29_L0.157190.627
16_T291_L0.157140.627
81_L134_S0.157090.626
66_A127_Y0.157010.626
74_D120_V0.156940.626
52_S84_Q0.156850.626
233_K281_V0.156850.626
202_A206_A0.156550.624
19_V57_E0.15650.624
213_F217_G0.156090.623
75_Y125_A0.155920.622
109_M165_G0.155780.621
179_T208_T0.15550.620
13_I16_T0.155460.620
89_S182_T0.155410.620
51_E87_S0.154930.618
132_T165_G0.154820.617
240_R243_L0.154630.617
220_P247_G0.154090.615
20_V25_G0.154060.614
154_P157_A0.153230.611
81_L279_S0.153140.611
134_S279_S0.152930.610
78_A88_S0.152740.609
124_F215_D0.152420.608
113_L301_F0.152280.607
209_I300_L0.152150.607
81_L107_S0.150950.602
95_L129_L0.150630.601
254_Y295_E0.150210.599
188_D194_P0.149930.598
242_L302_V0.149820.598
238_I308_L0.148740.593
28_P32_Y0.148420.592
51_E55_Q0.148160.591
244_K247_G0.147970.590
55_Q58_A0.147760.589
40_D44_E0.147670.589
163_G284_C0.147420.588
117_A178_I0.147240.587
161_V164_A0.14710.587
84_Q138_T0.146770.585
287_L299_V0.146580.585
100_L119_L0.146370.584
66_A97_I0.146110.583
303_A308_L0.145590.581
197_M303_A0.145380.580
104_G107_S0.145370.580
23_K32_Y0.145260.579
61_L129_L0.144820.578
165_G280_A0.144440.576
210_E213_F0.142870.570
27_G32_Y0.142660.569
254_Y284_C0.142460.568
178_I181_A0.142240.567
208_T212_H0.141950.566
32_Y35_K0.141660.565
127_Y171_K0.141610.565
126_D173_G0.141420.564
59_V168_I0.141250.563
31_D34_D0.141150.563
59_V76_L0.140880.562
190_G194_P0.140710.561
54_M133_S0.140690.561
244_K250_I0.140680.561
120_V124_F0.140630.561
69_K214_K0.14030.560
186_V197_M0.139470.556
26_E274_S0.139390.556
136_F143_F0.139250.555
281_V286_Y0.139080.555
129_L166_A0.138580.553
273_G281_V0.13850.552
62_A68_L0.138390.552
66_A129_L0.138380.552
67_G70_K0.138190.551
121_D124_F0.138010.550
109_M303_A0.137930.550
179_T216_T0.137890.550
45_K232_G0.137880.550
85_I180_H0.137720.549
81_L242_L0.137690.549
41_Y181_A0.137610.549
216_T223_Y0.137580.549
274_S280_A0.137560.549
27_G43_G0.137480.548
223_Y298_R0.137410.548
180_H216_T0.137280.547
84_Q179_T0.137250.547
81_L136_F0.137110.547
23_K26_E0.137060.547
77_F99_F0.137030.546
198_G201_M0.136360.544
102_L112_S0.136280.544
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
3lmaA0.9971000.196
4efiA0.90881000.356
3h78A0.91191000.363
3gwaA0.87841000.373
3s21A0.88451000.39
3ledA0.87541000.392
3ov2A0.92711000.392
4dfeA0.86931000.395
3oitA0.91491000.397
3il3A0.86631000.4

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