GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cation_efflux - Cation efflux family
Pfam: PF01545 (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: CL0184
Length: 284
Sequences: 5150
Seq/Len: 18.13
HH_delta: 0.065 (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
240_I276_I0.640762.974
168_W173_V0.622152.888
224_H241_H0.621652.886
86_I176_L0.574862.668
214_I260_I0.531822.469
184_Y188_P0.531512.467
214_I240_I0.517752.403
56_D63_Y0.51192.376
195_R200_A0.502612.333
211_R215_E0.472122.192
254_H277_H0.471432.188
213_I267_K0.469362.179
19_G28_L0.45572.115
75_S190_I0.448492.082
59_Y63_Y0.445032.066
16_I31_G0.4372.029
242_V260_I0.43162.003
87_V91_Q0.431162.001
160_L170_A0.428751.990
66_L198_L0.428711.990
18_A108_V0.41771.939
209_K267_K0.412381.914
238_V271_I0.40861.897
85_L175_S0.396121.839
262_K266_E0.391591.818
213_I268_F0.391461.817
107_I111_V0.390161.811
221_I245_D0.388721.804
208_E212_R0.386191.793
217_V260_I0.379291.761
191_K195_R0.376941.750
252_E255_E0.364861.694
110_L114_I0.359561.669
106_L155_L0.356791.656
33_H143_H0.352591.637
160_L164_G0.351271.631
42_L46_F0.350971.629
180_L184_Y0.34781.614
16_I20_I0.34551.604
65_R199_D0.344661.600
153_A174_A0.342781.591
82_G183_L0.341071.583
213_I263_R0.339681.577
217_V263_R0.327821.522
176_L180_L0.327391.520
7_L115_V0.327371.520
212_R216_S0.322141.495
138_R192_E0.320611.488
86_I179_A0.319221.482
207_V228_V0.318971.481
159_L163_L0.318921.480
224_H279_E0.317511.474
15_K34_S0.315351.464
17_I21_I0.307951.429
228_V238_V0.305131.416
2_I6_I0.302041.402
61_F239_E0.300351.394
33_H37_D0.299271.389
89_S175_S0.298051.384
222_E243_Q0.297591.381
47_A70_A0.294161.365
250_V253_A0.293251.361
9_L38_A0.292351.357
263_R267_K0.290011.346
264_L271_I0.28921.342
83_L87_V0.2861.328
253_A278_I0.285231.324
56_D59_Y0.283751.317
140_D143_H0.283731.317
254_H280_P0.283391.315
244_V250_V0.28331.315
110_L155_L0.282611.312
159_L162_Y0.281371.306
11_L115_V0.280331.301
187_Y191_K0.279111.296
117_L121_W0.277961.290
206_L209_K0.277421.288
30_D151_S0.277221.287
217_V259_R0.275571.279
202_P228_V0.275191.277
255_E259_R0.275161.277
113_I155_L0.272871.267
259_R263_R0.272361.264
30_D33_H0.270931.258
124_R141_A0.269591.251
25_L89_S0.268941.248
90_I94_I0.268511.246
258_E262_K0.268451.246
199_D237_V0.26821.245
121_W125_R0.268181.245
49_R52_S0.266951.239
19_G31_G0.26661.238
68_P196_I0.265181.231
9_L13_V0.263061.221
69_L198_L0.261051.212
246_P251_E0.260881.211
91_Q95_S0.260271.208
58_R63_Y0.259591.205
251_E255_E0.258031.198
59_Y195_R0.255481.186
241_H279_E0.255051.184
227_R273_D0.253491.177
207_V211_R0.252421.172
199_D229_W0.250281.162
11_L15_K0.250061.161
203_D206_L0.245381.139
199_D231_V0.244581.135
217_V256_I0.243291.129
5_L38_A0.243111.129
88_E91_Q0.241941.123
106_L162_Y0.241111.119
258_E261_E0.239951.114
114_I118_L0.238851.109
19_G22_T0.23831.106
60_P201_S0.23821.106
12_A16_I0.23761.103
254_H279_E0.237271.101
12_A31_G0.237081.101
6_I10_I0.235931.095
212_R215_E0.234961.091
257_R278_I0.234611.089
226_L240_I0.234131.087
157_S174_A0.23411.087
2_I45_L0.232521.079
141_A145_L0.232361.079
143_H147_D0.232131.078
93_L176_L0.231971.077
257_R277_H0.231861.076
13_V17_I0.229571.066
12_A35_L0.228691.062
79_I186_G0.228231.059
152_L156_I0.227971.058
67_E134_S0.227861.058
244_V256_I0.227491.056
208_E211_R0.225481.047
50_I53_K0.225361.046
50_I66_L0.224951.044
210_I228_V0.224571.042
224_H243_Q0.224031.040
209_K212_R0.222921.035
261_E277_H0.222881.035
209_K213_I0.222411.032
225_D273_D0.22191.030
43_I70_A0.220751.025
118_L121_W0.220721.025
93_L168_W0.220251.022
261_E265_R0.219621.019
117_L145_L0.219041.017
188_P191_K0.217961.012
238_V274_V0.217391.009
16_I28_L0.216831.007
196_I230_Q0.216021.003
75_S189_L0.214390.995
44_S136_A0.2130.989
25_L92_R0.21260.987
7_L119_L0.211670.983
4_S119_L0.2110.979
210_I264_L0.207720.964
48_L136_A0.207470.963
120_A141_A0.207120.961
8_N34_S0.207110.961
126_V130_L0.206690.959
46_F50_I0.206610.959
5_L45_L0.205770.955
170_A174_A0.205730.955
84_F87_V0.204340.949
204_P208_E0.203890.946
88_E92_R0.203130.943
5_L42_L0.202970.942
4_S123_L0.202620.941
118_L122_Y0.201450.935
160_L163_L0.201360.935
220_V242_V0.201110.934
119_L144_S0.200790.932
173_V177_L0.200730.932
61_F229_W0.200280.930
215_E222_E0.200180.929
11_L119_L0.199450.926
14_V111_V0.198510.921
116_N144_S0.197560.917
64_G235_K0.196950.914
219_G252_E0.19610.910
219_G259_R0.195970.910
44_S139_A0.194840.904
216_S263_R0.194430.903
17_I20_I0.193320.897
76_I80_F0.192890.895
257_R276_I0.192590.894
257_R261_E0.191920.891
213_I217_V0.191810.890
219_G256_I0.191540.889
16_I35_L0.191230.888
106_L158_L0.190790.886
79_I187_Y0.189830.881
96_P99_P0.189680.880
3_I122_Y0.189350.879
259_R262_K0.188770.876
105_V108_V0.188590.875
20_I31_G0.187340.870
93_L172_P0.187320.870
121_W124_R0.187220.869
89_S176_L0.186280.865
116_N123_L0.185380.861
116_N143_H0.185240.860
250_V278_I0.185050.859
58_R200_A0.184960.859
103_G107_I0.184290.855
4_S8_N0.184230.855
161_A164_G0.183550.852
109_A155_L0.182440.847
116_N147_D0.182090.845
223_V240_I0.18150.843
263_R266_E0.181090.841
225_D241_H0.181070.841
215_E223_V0.180930.840
123_L140_D0.180830.839
260_I276_I0.180770.839
244_V253_A0.180290.837
102_P162_Y0.179930.835
8_N37_D0.179430.833
30_D109_A0.179430.833
46_F49_R0.179250.832
25_L175_S0.178880.830
244_V278_I0.178660.829
209_K268_F0.177980.826
79_I83_L0.17730.823
4_S140_D0.176640.820
29_A37_D0.176390.819
139_A189_L0.176040.817
71_A136_A0.175780.816
12_A38_A0.175710.816
15_K30_D0.175570.815
248_M252_E0.175390.814
214_I226_L0.174990.812
277_H280_P0.174980.812
75_S193_S0.174830.812
93_L173_V0.174420.810
33_H78_L0.174310.809
213_I216_S0.173490.805
90_I176_L0.173350.805
248_M256_I0.173080.803
119_L123_L0.171970.798
256_I260_I0.171850.798
24_S171_D0.171390.796
214_I264_L0.171130.794
123_L144_S0.170070.789
86_I90_I0.16840.782
243_Q281_D0.167610.778
23_G97_H0.166730.774
20_I28_L0.166250.772
243_Q279_E0.166140.771
80_F87_V0.165820.770
65_R229_W0.165750.769
142_L145_L0.165630.769
151_S154_V0.165550.768
26_A174_A0.165140.767
92_R99_P0.165140.767
22_T105_V0.164540.764
33_H116_N0.163290.758
79_I183_L0.163060.757
22_T28_L0.162810.756
254_H257_R0.162390.754
78_L144_S0.162370.754
51_A67_E0.161890.751
71_A135_P0.160570.745
232_G237_V0.160530.745
201_S207_V0.160430.745
150_S153_A0.1590.738
148_V151_S0.158770.737
34_S150_S0.158370.735
202_P236_Y0.158150.734
116_N119_L0.157930.733
15_K112_S0.157870.733
8_N144_S0.157190.730
5_L41_L0.156590.727
181_F185_S0.156020.724
72_L190_I0.155970.724
120_A124_R0.155960.724
231_V237_V0.155580.722
60_P227_R0.155530.722
4_S41_L0.154870.719
8_N148_V0.153620.713
262_K265_R0.153610.713
214_I220_V0.153360.712
54_P63_Y0.153340.712
86_I180_L0.153110.711
214_I223_V0.152970.710
219_G245_D0.152620.708
106_L159_L0.15240.707
58_R195_R0.152320.707
217_V276_I0.151680.704
221_I244_V0.150920.701
26_A112_S0.150410.698
16_I32_L0.150070.697
69_L73_I0.149860.696
220_V223_V0.149390.693
66_L70_A0.149350.693
218_P221_I0.148640.690
183_L187_Y0.146820.682
41_L140_D0.146050.678
72_L194_I0.145710.676
113_I117_L0.145660.676
25_L29_A0.145620.676
18_A21_I0.145610.676
120_A144_S0.145510.675
71_A189_L0.145460.675
4_S144_S0.145390.675
14_V17_I0.145270.674
83_L183_L0.145020.673
253_A256_I0.144450.671
38_A149_L0.144320.670
229_W239_E0.144270.670
89_S172_P0.143590.667
172_P175_S0.143530.666
143_H146_I0.143510.666
67_E232_G0.143510.666
221_I281_D0.143230.665
210_I268_F0.142280.660
264_L274_V0.142080.660
239_E275_T0.1420.659
74_V78_L0.141770.658
44_S48_L0.141730.658
29_A33_H0.141190.655
238_V276_I0.140410.652
231_V239_E0.139880.649
154_V157_S0.139490.648
112_S116_N0.139470.647
107_I110_L0.139220.646
144_S147_D0.139180.646
218_P259_R0.138960.645
116_N154_V0.138580.643
265_R274_V0.138580.643
25_L88_E0.138490.643
147_D151_S0.138330.642
15_K33_H0.13820.642
15_K31_G0.138120.641
247_D251_E0.1380.641
74_V139_A0.137990.641
75_S198_L0.137980.640
265_R272_Y0.137720.639
80_F84_F0.137560.639
271_I274_V0.13730.637
224_H277_H0.137120.637
100_S104_I0.136820.635
153_A157_S0.136470.633
168_W172_P0.136440.633
104_I107_I0.1360.631
223_V226_L0.135910.631
171_D175_S0.135870.631
184_Y187_Y0.135860.631
111_V115_V0.135480.629
33_H140_D0.135390.628
135_P196_I0.135180.627
36_A81_L0.135160.627
258_E279_E0.135090.627
157_S170_A0.135080.627
221_I243_Q0.134790.626
51_A54_P0.134320.624
8_N116_N0.134310.623
174_A177_L0.134240.623
45_L49_R0.134140.623
115_V119_L0.133850.621
106_L110_L0.133570.620
180_L215_E0.13320.618
99_P102_P0.133180.618
150_S181_F0.132810.616
65_R68_P0.132550.615
230_Q236_Y0.132450.615
147_D182_I0.132410.615
252_E259_R0.132360.614
122_Y126_V0.132280.614
28_L33_H0.131980.613
206_L236_Y0.131890.612
34_S189_L0.131510.610
64_G231_V0.131160.609
259_R266_E0.131060.608
160_L168_W0.130860.607
164_G170_A0.130790.607
41_L74_V0.130440.605
10_I121_W0.130250.605
241_H277_H0.130160.604
202_P206_L0.129830.603
253_A257_R0.129790.602
11_L112_S0.12960.602
12_A34_S0.12950.601
150_S154_V0.129280.600
124_R138_R0.129250.600
8_N32_L0.129090.599
8_N38_A0.12860.597
84_F88_E0.128380.596
227_R239_E0.128370.596
9_L18_A0.127870.594
119_L122_Y0.12770.593
219_G260_I0.127570.592
82_G186_G0.127430.592
56_D66_L0.127390.591
214_I242_V0.127280.591
27_L109_A0.127050.590
33_H36_A0.126970.589
117_L142_L0.126960.589
65_R158_L0.12640.587
230_Q233_R0.126350.587
26_A36_A0.12630.586
70_A153_A0.126030.585
75_S186_G0.125840.584
57_K207_V0.125680.583
253_A277_H0.125490.583
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
3h90A0.97891000.065
3j1zP0.97891000.076
3bypA0.306399.50.728
2zztA0.302899.40.734
3j1zP0.637396.10.896
3h90A0.595195.70.9
3lnoA0.320491.30.917
3cq1A0.306385.50.925
1uwdA0.309973.80.933
2kjwA0.2993560.94

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