GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CbiQ - Cobalt transport protein
Pfam: PF02361 (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: 224
Sequences: 2694
Seq/Len: 12.03
HH_delta: 0.104 (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
13_K125_T0.571314.245
161_E202_R0.433863.224
13_K124_T0.413163.070
85_P99_E0.296872.206
165_I169_Q0.295672.197
8_L12_T0.293372.180
138_R141_Y0.291092.163
126_S129_D0.290052.155
17_L121_F0.280932.087
180_G183_N0.269051.999
163_K167_E0.267221.986
158_L199_A0.248821.849
165_I195_L0.247891.842
11_R133_A0.233921.738
166_R170_R0.233231.733
134_L138_R0.220261.637
146_L215_F0.217111.613
135_R145_A0.214911.597
210_M215_F0.209081.554
137_L140_P0.206651.535
156_P194_P0.206531.535
182_R186_R0.202381.504
171_L212_A0.201121.494
152_L156_P0.198721.477
146_L150_L0.198541.475
83_P97_T0.197741.469
24_V36_I0.19731.466
173_G194_P0.195021.449
33_L113_A0.194351.444
86_F97_T0.188331.399
32_F35_L0.183821.366
86_F95_S0.182951.359
62_W65_F0.181641.350
85_P98_Q0.180141.338
161_E164_R0.178361.325
150_L206_L0.175961.307
108_A112_L0.175161.301
9_D133_A0.17461.297
18_I22_V0.174311.295
207_A211_E0.173951.292
40_V117_A0.170051.264
102_I106_L0.169221.257
5_L8_L0.168311.251
169_Q187_S0.165171.227
184_R187_S0.163991.218
147_M151_T0.162841.210
102_I105_A0.161271.198
211_E214_G0.161141.197
181_I185_L0.159061.182
111_I115_L0.158951.181
167_E208_E0.158931.181
157_L206_L0.158411.177
16_F20_L0.15841.177
63_L66_I0.158241.176
135_R141_Y0.157841.173
28_N33_L0.157091.167
20_L117_A0.15691.166
164_R198_R0.155921.159
167_E170_R0.154181.146
87_V97_T0.153221.138
207_A210_M0.151751.128
98_Q102_I0.151621.127
171_L209_A0.151571.126
161_E198_R0.150991.122
134_L145_A0.150721.120
17_L117_A0.149871.114
151_T210_M0.148681.105
14_L133_A0.1481.100
145_A156_P0.14741.095
56_I59_R0.146651.090
157_L202_R0.146441.088
34_A37_L0.14611.086
153_R157_L0.145711.083
17_L118_S0.145191.079
156_P207_A0.145111.078
162_F166_R0.144781.076
29_N32_F0.144491.074
6_H13_K0.144431.073
14_L121_F0.143041.063
153_R161_E0.142921.062
201_R205_E0.142881.062
194_P207_A0.142791.061
55_R58_L0.142641.060
154_F206_L0.142581.059
146_L169_Q0.142051.055
37_L109_L0.142031.055
158_L162_F0.142021.055
71_I108_A0.141911.054
134_L139_L0.141641.052
83_P99_E0.14141.051
189_G207_A0.140541.044
27_T32_F0.139461.036
147_M202_R0.138681.030
138_R145_A0.138671.030
15_I137_L0.138551.029
154_F207_A0.138081.026
180_G184_R0.137311.020
20_L24_V0.137081.019
201_R208_E0.137011.018
71_I74_F0.136971.018
21_S25_F0.136821.017
162_F195_L0.135641.008
38_A102_I0.134781.001
35_L38_A0.13330.990
131_I145_A0.132760.986
26_L34_A0.132170.982
45_L102_I0.131290.976
169_Q194_P0.130260.968
160_E163_K0.129990.966
63_L109_L0.129840.965
106_L214_G0.129620.963
5_L43_I0.128830.957
141_Y216_G0.128640.956
38_A42_L0.128590.955
114_I151_T0.127980.951
83_P98_Q0.127550.948
49_L123_L0.127380.946
34_A38_A0.125650.934
147_M169_Q0.125620.933
7_R16_F0.125460.932
31_V35_L0.123720.919
11_R14_L0.12350.918
111_I194_P0.123370.917
109_L113_A0.123130.915
87_V99_E0.122630.911
29_N41_L0.122590.911
120_L124_T0.122130.907
45_L48_R0.122090.907
23_I27_T0.121920.906
19_L23_I0.121030.899
147_M206_L0.120440.895
114_I118_S0.12040.895
9_D12_T0.119440.887
160_E164_R0.119090.885
30_P106_L0.119010.884
171_L190_P0.118730.882
193_V206_L0.118530.881
125_T130_L0.118190.878
26_L150_L0.117960.876
169_Q190_P0.117470.873
121_F130_L0.117270.871
144_I147_M0.116250.864
154_F161_E0.115960.862
161_E195_L0.115380.857
183_N199_A0.115140.856
166_R191_L0.115050.855
5_L120_L0.114560.851
203_A207_A0.114450.850
172_R209_A0.11440.850
10_P133_A0.114340.850
203_A213_R0.113990.847
15_I139_L0.113940.847
81_T84_G0.113770.845
157_L205_E0.113740.845
161_E204_E0.113580.844
154_F210_M0.112760.838
140_P143_K0.11270.837
171_L213_R0.112520.836
164_R205_E0.112470.836
125_T204_E0.112330.835
55_R59_R0.112230.834
151_T211_E0.112220.834
148_I163_K0.111650.830
111_I156_P0.111490.828
165_I194_P0.111490.828
17_L21_S0.111130.826
171_L200_L0.11110.826
100_G197_I0.111090.825
5_L47_A0.110830.823
116_L120_L0.110680.822
115_L193_V0.110630.822
153_R206_L0.110120.818
47_A124_T0.110050.818
117_A214_G0.110010.817
214_G217_G0.109990.817
71_I191_L0.109890.817
202_R206_L0.109770.816
37_L45_L0.10970.815
208_E211_E0.109380.813
6_H125_T0.109120.811
110_R162_F0.108910.809
17_L217_G0.108890.809
135_R138_R0.108510.806
7_R15_I0.108320.805
23_I40_V0.10820.804
175_G184_R0.1080.802
46_I115_L0.107640.800
31_V46_I0.107620.800
42_L46_I0.107590.799
37_L112_L0.107340.798
19_L86_F0.107240.797
42_L163_K0.107230.797
127_P156_P0.107040.795
70_I74_F0.106910.794
154_F197_I0.106530.792
167_E171_L0.10640.791
62_W74_F0.106110.788
100_G104_A0.105820.786
23_I107_L0.105730.786
165_I207_A0.105730.786
13_K129_D0.105510.784
151_T155_I0.105190.782
146_L152_L0.104820.779
136_K139_L0.104780.779
182_R185_L0.104760.778
168_A171_L0.104690.778
149_S167_E0.104640.778
53_F57_W0.104510.777
20_L202_R0.104210.774
191_L198_R0.103890.772
202_R210_M0.103890.772
37_L113_A0.103740.771
10_P121_F0.103680.770
24_V113_A0.103650.770
99_E134_L0.10360.770
99_E103_Y0.103580.770
31_V34_A0.103530.769
118_S155_I0.103140.766
33_L109_L0.10290.765
66_I101_L0.10270.763
17_L113_A0.102470.761
49_L124_T0.102430.761
137_L144_I0.102140.759
35_L148_I0.101960.758
23_I117_A0.101860.757
21_S114_I0.101620.755
202_R205_E0.101620.755
150_L189_G0.101520.754
20_L36_I0.101460.754
62_W137_L0.101340.753
155_I165_I0.101210.752
146_L156_P0.101030.751
67_L216_G0.10060.747
127_P152_L0.100470.747
111_I147_M0.100420.746
156_P193_V0.100190.744
128_S132_S0.099850.742
54_K58_L0.099830.742
127_P158_L0.099780.741
134_L148_I0.099610.740
12_T39_L0.09940.739
148_I217_G0.099390.738
43_I68_G0.099360.738
87_V101_L0.099190.737
35_L105_A0.099090.736
115_L170_R0.099080.736
130_L180_G0.099030.736
15_I34_A0.09890.735
17_L40_V0.098890.735
64_L216_G0.098840.734
116_L181_I0.098730.734
95_S144_I0.098390.731
135_R150_L0.09790.727
169_Q211_E0.097840.727
140_P158_L0.097620.725
25_F149_S0.097620.725
37_L42_L0.097510.725
40_V116_L0.096850.720
49_L54_K0.096740.719
103_Y107_L0.096590.718
56_I196_L0.096570.718
209_A213_R0.096460.717
58_L62_W0.096460.717
154_F193_V0.096390.716
195_L201_R0.096310.716
208_E212_A0.096130.714
54_K116_L0.095980.713
46_I218_G0.095930.713
105_A109_L0.09580.712
199_A210_M0.095580.710
15_I18_I0.095560.710
164_R202_R0.095510.710
35_L55_R0.095380.709
21_S118_S0.095040.706
21_S145_A0.094780.704
139_L144_I0.094650.703
206_L210_M0.094490.702
153_R202_R0.094270.700
164_R215_F0.094220.700
29_N196_L0.094190.700
67_L70_I0.094160.700
47_A50_P0.094120.699
34_A132_S0.094110.699
74_F193_V0.093860.697
187_S217_G0.093550.695
45_L95_S0.093450.694
11_R137_L0.093230.693
16_F24_V0.0930.691
154_F204_E0.092990.691
74_F107_L0.092930.690
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
4huqT0.97321000.104
4ehxA0.36165.60.948
2l0eA0.14734.60.95
2wwbC0.16074.20.951
2ww9C0.16073.40.953
2fz1A0.26793.40.953
1rh5C0.14733.40.953
3dfeA0.20092.70.955
1lbjA0.11162.20.957
3tqkA0.37951.90.958

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