GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Spore_permease - Spore germination protein
Pfam: PF03845 (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: CL0062
Length: 320
Sequences: 19655
Seq/Len: 61.42
HH_delta: 0.3 (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
203_D206_K0.942713.364
206_K209_K0.766052.734
69_E74_K0.761272.717
42_G219_G0.755022.695
69_E77_G0.736552.629
126_Y130_K0.668682.386
133_E137_R0.636592.272
4_P8_F0.622762.223
247_E250_R0.621492.218
6_Q140_E0.619772.212
209_K213_I0.605522.161
144_P148_I0.576652.058
5_R9_F0.57112.038
4_P213_I0.5612.002
7_L201_V0.560542.000
163_W166_L0.55611.985
148_I152_L0.553751.976
138_V142_L0.551671.969
12_I217_I0.547481.954
124_A277_I0.541751.933
6_Q136_A0.536061.913
165_N168_P0.508551.815
151_L155_L0.499731.783
155_L159_P0.497871.777
8_F217_I0.497731.776
234_G237_L0.49231.757
8_F213_I0.490471.750
247_E251_S0.479861.713
61_G70_K0.479541.711
115_V119_L0.452161.614
74_K78_K0.443561.583
164_D167_L0.430391.536
125_A129_R0.430081.535
84_Y88_F0.424661.516
212_L216_L0.418891.495
260_R264_I0.417341.489
59_F70_K0.415851.484
205_K209_K0.413261.475
43_L47_L0.412141.471
147_L151_L0.402621.437
263_S267_L0.402241.436
124_A281_L0.393761.405
75_W79_I0.390841.395
118_L122_L0.390721.394
112_P115_V0.38191.363
126_Y129_R0.381621.362
85_I288_L0.376491.344
66_E70_K0.376131.342
56_L67_I0.374681.337
72_F76_L0.372891.331
216_L220_L0.371891.327
14_S279_L0.371771.327
209_K212_L0.371341.325
200_F286_E0.369631.319
4_P209_K0.369011.317
237_L251_S0.367811.313
173_G176_P0.367721.312
123_V274_F0.365941.306
73_G76_L0.364321.300
68_S76_L0.363541.297
204_K208_K0.360331.286
243_Y246_L0.357281.275
13_S143_F0.354741.266
50_L212_L0.351471.254
255_G260_R0.351451.254
137_R140_E0.351161.253
24_P27_L0.350121.250
15_I218_S0.349321.247
220_L224_F0.349191.246
68_S80_I0.347751.241
103_I116_I0.347611.241
35_W227_F0.345541.233
163_W167_L0.344841.231
281_L285_S0.344661.230
27_L31_A0.342821.223
61_G66_E0.34191.220
36_I39_L0.341891.220
213_I216_L0.341281.218
114_W118_L0.338031.206
9_F140_E0.335381.197
26_I30_Q0.334621.194
208_K211_L0.334551.194
139_A275_I0.3331.188
11_L214_A0.332691.187
79_I83_L0.331911.185
189_G192_E0.331111.182
96_L277_I0.330741.180
53_Y56_L0.329381.175
101_E105_T0.328221.171
88_F280_Y0.326951.167
134_V137_R0.325221.161
114_W117_I0.323831.156
272_G275_I0.322941.153
192_E196_F0.321641.148
139_A146_F0.321511.147
78_K82_L0.32051.144
179_K183_V0.31871.137
20_I218_S0.318171.135
111_T115_V0.315551.126
226_I229_T0.314781.123
122_L126_Y0.312941.117
49_A211_L0.312351.115
33_D177_I0.311771.113
130_K134_V0.31091.110
4_P206_K0.310671.109
20_I24_P0.310461.108
275_I279_L0.310011.106
127_A278_S0.309221.104
241_L244_P0.309061.103
68_S71_L0.307641.098
63_T66_E0.30681.095
5_R140_E0.306721.095
101_E104_K0.306471.094
162_D165_N0.305541.090
110_E113_I0.303561.083
168_P171_E0.302771.081
152_L156_L0.30231.079
37_S180_G0.301491.076
104_K113_I0.301021.074
22_F98_E0.298941.067
183_V187_P0.298521.065
53_Y57_K0.297811.063
120_F277_I0.29671.059
230_I233_F0.296231.057
91_I94_L0.296141.057
116_I119_L0.295121.053
26_I29_E0.294651.052
47_L51_L0.294511.051
99_F120_F0.292591.044
99_F273_I0.291761.041
138_V278_S0.291651.041
115_V118_L0.291581.041
12_I16_I0.289851.034
6_Q137_R0.289751.034
267_L271_I0.289451.033
137_R141_I0.28941.033
141_I144_P0.288781.031
10_L197_L0.288561.030
176_P179_K0.288561.030
22_F25_A0.288071.028
140_E143_F0.284431.015
39_L43_L0.283981.013
210_S214_A0.283391.011
143_F146_F0.282941.010
50_L54_Y0.281841.006
243_Y247_E0.28141.004
132_I200_F0.280931.003
46_L212_L0.279840.999
139_A142_L0.279730.998
167_L171_E0.279480.997
16_I19_G0.277810.991
124_A274_F0.277630.991
202_K206_K0.275730.984
286_E289_S0.275680.984
97_R101_E0.27550.983
28_A34_A0.275190.982
35_W39_L0.274740.980
249_A252_I0.274270.979
143_F147_L0.273380.976
121_L125_A0.272360.972
12_I221_F0.27230.972
8_F11_L0.272270.972
142_L271_I0.272190.971
46_L50_L0.270170.964
92_S96_L0.269040.960
166_L169_V0.268470.958
226_I230_I0.267630.955
224_F228_I0.26710.953
132_I136_A0.266220.950
241_L247_E0.26580.949
55_L67_I0.265060.946
74_K77_G0.264040.942
205_K208_K0.262670.937
52_I56_L0.262660.937
27_L34_A0.262010.935
225_I229_T0.261780.934
145_I149_L0.260850.931
140_E144_P0.260460.930
164_D168_P0.26020.929
207_L211_L0.260040.928
118_L121_L0.259710.927
127_A274_F0.259290.925
203_D209_K0.259040.924
139_A143_F0.258330.922
227_F231_G0.257430.919
275_I278_S0.256220.914
69_E78_K0.255910.913
67_I71_L0.255040.910
181_S185_S0.254110.907
219_G223_L0.253970.906
91_I280_Y0.253430.904
225_I228_I0.253250.904
154_L224_F0.253160.903
242_T245_V0.253160.903
229_T233_F0.252760.902
111_T116_I0.251810.899
17_G186_F0.251220.897
154_L157_S0.251140.896
218_S222_L0.25070.895
165_N169_V0.249970.892
4_P210_S0.249480.890
103_I107_L0.249070.889
24_P28_A0.248890.888
20_I225_I0.247920.885
10_L13_S0.247350.883
86_L90_L0.247140.882
92_S277_I0.246780.881
65_V81_N0.24640.879
41_G184_I0.245710.877
142_L275_I0.244890.874
37_S40_L0.244550.873
254_I260_R0.243560.869
265_F268_I0.243030.867
19_G222_L0.24260.866
99_F103_I0.241730.863
136_A140_E0.241560.862
25_A29_E0.240290.858
49_A53_Y0.240250.857
102_F107_L0.239850.856
177_I181_S0.239780.856
161_I165_N0.237480.848
250_R262_D0.237370.847
153_I157_S0.237170.846
51_L54_Y0.237060.846
151_L154_L0.236860.845
58_R204_K0.236850.845
12_I143_F0.236640.845
196_F199_P0.236460.844
285_S289_S0.236140.843
260_R263_S0.234860.838
42_G188_F0.234670.837
43_L46_L0.234110.835
117_I121_L0.232370.829
284_A288_L0.232340.829
119_L123_V0.232110.828
196_F283_A0.231980.828
149_L268_I0.231660.827
152_L155_L0.231420.826
272_G276_K0.231360.826
157_S228_I0.230310.822
12_I218_S0.230270.822
96_L121_L0.230.821
159_P162_D0.229610.819
146_F150_L0.229140.818
11_L14_S0.22910.818
203_D208_K0.227690.813
165_N231_G0.227490.812
229_T232_V0.227360.811
24_P226_I0.227340.811
274_F278_S0.227030.810
156_L160_N0.226960.810
83_L86_L0.226870.810
25_A28_A0.225890.806
156_L261_L0.225210.804
34_A226_I0.224780.802
211_L214_A0.224340.801
236_E239_K0.224190.800
96_L100_S0.224090.800
278_S281_L0.223760.799
200_F204_K0.22360.798
34_A37_S0.223180.796
87_Y91_I0.222890.795
54_Y57_K0.222860.795
236_E240_K0.222730.795
90_L94_L0.222510.794
85_I284_A0.222360.794
167_L170_L0.222320.793
175_K178_L0.222310.793
99_F270_I0.222190.793
183_V186_F0.222170.793
54_Y58_R0.222160.793
120_F124_A0.2220.792
7_L210_S0.221540.791
231_G235_P0.221270.790
131_G134_V0.220790.788
127_A131_G0.220470.787
146_F275_I0.219930.785
174_I178_L0.219570.784
11_L15_I0.219480.783
198_F207_L0.219170.782
53_Y214_A0.219090.782
13_S139_A0.219050.782
113_I117_I0.218530.780
17_G20_I0.218370.779
8_F210_S0.217840.777
172_S176_P0.21780.777
206_K210_S0.21770.777
138_V141_I0.217630.777
54_Y204_K0.217340.776
100_S103_I0.217090.775
56_L195_L0.217070.775
22_F26_I0.216940.774
100_S116_I0.216730.773
75_W78_K0.216660.773
246_L266_I0.215580.769
249_A253_E0.215290.768
234_G251_S0.214890.767
124_A278_S0.214520.766
232_V248_L0.213350.761
228_I231_G0.213020.760
227_F230_I0.213010.760
13_S16_I0.212880.760
69_E73_G0.212690.759
66_E69_E0.211960.756
17_G21_L0.211930.756
48_L191_I0.211810.756
23_L26_I0.211770.756
95_V277_I0.211670.755
140_E146_F0.211560.755
65_V69_E0.211350.754
241_L245_V0.211030.753
88_F91_I0.210870.753
182_L186_F0.21070.752
8_F12_I0.210630.752
49_A215_I0.209440.747
147_L221_F0.209260.747
161_I231_G0.20880.745
221_F224_F0.208720.745
133_E136_A0.208490.744
70_K74_K0.208350.744
170_L177_I0.208250.743
154_L225_I0.208070.743
163_W231_G0.207680.741
33_D170_L0.207490.740
210_S213_I0.207250.740
45_G49_A0.207130.739
47_L52_I0.207030.739
179_K182_L0.206930.738
9_F13_S0.20690.738
72_F75_W0.206680.738
242_T246_L0.206440.737
182_L185_S0.20630.736
18_T98_E0.206010.735
277_I280_Y0.205640.734
127_A138_V0.205510.733
85_I89_L0.205170.732
214_A218_S0.204920.731
65_V77_G0.204780.731
128_A278_S0.204730.731
14_S280_Y0.204310.729
157_S232_V0.204180.729
94_L98_E0.203690.727
201_V207_L0.203530.726
137_R142_L0.203130.725
238_A241_L0.203040.725
120_F274_F0.202960.724
180_G183_V0.202680.723
107_L110_E0.202120.721
181_S184_I0.2020.721
157_S168_P0.201950.721
202_K205_K0.201550.719
156_L161_I0.201350.719
52_I64_L0.201280.718
180_G184_I0.201150.718
208_K212_L0.201140.718
78_K81_N0.20110.718
38_V186_F0.20080.717
52_I55_L0.200560.716
112_P116_I0.200450.715
65_V287_G0.200230.715
55_L71_L0.200150.714
193_I283_A0.199950.714
268_I272_G0.199860.713
130_K133_E0.199630.712
142_L145_I0.19940.712
18_T273_I0.199340.711
20_I23_L0.199090.711
162_D166_L0.198830.710
104_K110_E0.19850.708
21_L24_P0.198320.708
40_L43_L0.198180.707
150_L157_S0.19810.707
248_L251_S0.19790.706
16_I218_S0.197480.705
170_L173_G0.197320.704
156_L159_P0.197060.703
18_T22_F0.196990.703
160_N163_W0.195920.699
146_F272_G0.195880.699
35_W38_V0.195870.699
37_S45_G0.19540.697
177_I180_G0.194610.695
92_S280_Y0.19440.694
248_L252_I0.194340.694
174_I177_I0.194190.693
212_L215_I0.193930.692
5_R209_K0.193720.691
84_Y287_G0.193630.691
80_I84_Y0.193380.690
188_F222_L0.192680.688
56_L60_P0.192460.687
140_E147_L0.192450.687
280_Y284_A0.192350.686
39_L223_L0.191530.684
119_L122_L0.191530.684
159_P163_W0.191460.683
38_V41_G0.190690.681
165_N234_G0.190680.680
232_V235_P0.19040.679
9_F143_F0.190340.679
44_I47_L0.189860.678
54_Y60_P0.189650.677
62_K65_V0.189280.676
52_I60_P0.189230.675
63_T286_E0.189230.675
170_L174_I0.189050.675
251_S254_I0.188750.674
89_L93_A0.188520.673
261_L265_F0.187770.670
59_F71_L0.187430.669
9_F139_A0.187420.669
39_L42_G0.187340.669
213_I217_I0.187290.668
222_L225_I0.187070.668
207_L210_S0.186890.667
146_F157_S0.18680.667
187_P191_I0.186740.666
136_A139_A0.186420.665
5_R137_R0.186290.665
42_G218_S0.185940.664
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
3l1lA0.98441000.3
3giaA0.987599.90.355
2xq2A0.978199.80.46
3dh4A0.978199.80.461
4djkA0.978199.80.466
2jlnA0.965699.70.54
2a65A0.984498.80.72
2wswA0.987596.80.84
4ainA0.978196.70.842
1zcdA0.19066.90.945

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