GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CbiM - Cobalt uptake substrate-specific transmembrane region
Pfam: PF01891 (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: CL0315
Length: 205
Sequences: 963
Seq/Len: 4.7
HH_delta: 0.859 (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
111_N157_V0.28673.048
140_F188_G0.281562.994
19_A110_L0.242032.573
87_A109_A0.235512.504
135_I199_V0.206962.200
115_P153_A0.199232.118
73_L82_A0.181961.935
23_L87_A0.174681.857
15_A110_L0.171161.820
139_G192_G0.168971.796
12_L16_W0.167581.782
86_M113_G0.16571.762
19_A109_A0.15991.700
181_L185_F0.157791.678
119_V149_L0.156791.667
169_W173_V0.155541.654
72_L191_T0.152071.617
22_L114_V0.151931.615
23_L109_A0.151871.615
136_F192_G0.151291.609
122_L126_L0.143781.529
110_L115_P0.14361.527
189_F193_M0.138471.472
91_L105_L0.138061.468
25_L80_W0.136791.454
19_A23_L0.1361.446
72_L194_V0.135211.438
56_N99_D0.13511.436
62_G69_G0.133511.419
65_V183_L0.13251.409
14_A17_V0.131611.399
178_P182_L0.130221.384
123_L141_L0.129481.377
171_A174_Q0.128761.369
19_A27_L0.126191.342
105_L109_A0.125481.334
28_R32_W0.125411.333
25_L29_R0.12511.330
20_A23_L0.124911.328
9_P13_I0.124491.324
134_N137_V0.123971.318
49_V73_L0.122761.305
10_W13_I0.122031.297
186_P190_L0.120961.286
144_F181_L0.120141.277
13_I17_V0.120141.277
90_L93_Q0.118291.258
52_A67_L0.116431.238
194_V197_F0.115851.232
65_V180_H0.115681.230
125_R129_R0.115541.228
154_V157_V0.115271.226
4_D188_G0.113821.210
140_F190_L0.113221.204
15_A107_A0.113061.202
157_V160_L0.11291.200
8_P11_W0.112651.198
68_L150_A0.111741.188
143_G188_G0.11041.174
43_A135_I0.109261.162
63_L175_A0.108831.157
75_L139_G0.108031.149
49_V82_A0.107991.148
125_R128_R0.107241.140
142_A146_S0.105961.127
127_L141_L0.104111.107
80_W118_L0.103321.098
8_P161_S0.103151.097
121_Y124_F0.101371.078
179_S183_L0.101121.075
101_G112_M0.100961.073
28_R31_R0.100021.063
42_L139_G0.099481.058
126_L130_K0.099441.057
140_F189_F0.098731.050
26_A84_L0.098611.048
53_W99_D0.098311.045
156_L160_L0.097731.039
127_L138_A0.097711.039
50_F93_Q0.09761.038
45_L73_L0.096431.025
69_G89_V0.096161.022
93_Q100_G0.095491.015
193_M196_T0.095351.014
83_A87_A0.095141.012
87_A91_L0.094671.007
133_R137_V0.094311.003
82_A116_P0.094291.002
30_L84_L0.093840.998
46_A85_A0.092640.985
185_F189_F0.092410.982
192_G199_V0.092310.981
148_L177_L0.092190.980
61_G172_L0.091910.977
63_L172_L0.091820.976
195_V201_Y0.091540.973
53_W93_Q0.091260.970
16_W20_A0.091230.970
152_L177_L0.09120.970
56_N180_H0.091040.968
92_L96_L0.090390.961
128_R189_F0.090210.959
110_L114_V0.090120.958
17_V24_A0.090020.957
144_F185_F0.089930.956
128_R137_V0.089620.953
24_A27_L0.089550.952
33_R38_P0.08930.949
88_I92_L0.088960.946
119_V168_P0.08860.942
115_P149_L0.088510.941
54_L161_S0.088310.939
76_M118_L0.088250.938
16_W102_W0.087970.935
200_V203_P0.087920.935
123_L183_L0.087860.934
134_N189_F0.087760.933
127_L132_P0.087370.929
11_W161_S0.087350.929
120_S201_Y0.087230.927
49_V178_P0.087020.925
75_L124_F0.086960.925
47_A51_L0.086940.924
17_V193_M0.08680.923
93_Q101_G0.08660.921
56_N150_A0.086350.918
129_R132_P0.086190.916
186_P200_V0.085970.914
64_S104_A0.085950.914
15_A114_V0.085910.913
152_L156_L0.085820.912
176_Y180_H0.085610.910
78_G143_G0.085580.910
26_A30_L0.08550.909
29_R32_W0.085390.908
119_V153_A0.085350.907
112_M150_A0.085280.907
20_A178_P0.085050.904
122_L125_R0.084950.903
31_R189_F0.084790.901
70_L120_S0.084760.901
58_P93_Q0.084740.901
27_L142_A0.084730.901
137_V140_F0.084660.900
93_Q97_F0.084660.900
82_A192_G0.084530.899
7_L192_G0.084460.898
45_L86_M0.084440.898
8_P12_L0.084440.898
81_L149_L0.084430.898
99_D180_H0.084310.896
101_G113_G0.084250.896
68_L116_P0.084080.894
65_V179_S0.083980.893
16_W25_L0.083970.893
138_A141_L0.083880.892
197_F201_Y0.083360.886
151_A184_A0.083120.884
146_S194_V0.083040.883
19_A203_P0.082740.880
125_R133_R0.08190.871
135_I139_G0.081690.869
25_L203_P0.081690.869
137_V199_V0.081350.865
115_P154_V0.080960.861
154_V158_L0.080880.860
38_P82_A0.080480.856
25_L170_M0.080220.853
14_A83_A0.080040.851
48_A77_L0.079980.850
147_V158_L0.07990.849
11_W20_A0.079780.848
17_V189_F0.079770.848
59_I97_F0.079370.844
61_G171_A0.078990.840
50_F101_G0.078930.839
90_L108_N0.078650.836
127_L133_R0.078630.836
20_A141_L0.078490.834
56_N68_L0.078440.834
136_F200_V0.078380.833
128_R134_N0.078340.833
47_A189_F0.078140.831
27_L31_R0.078110.830
65_V104_A0.077980.829
18_V110_L0.077960.829
111_N153_A0.077920.828
82_A86_M0.077790.827
53_W100_G0.077570.825
144_F148_L0.077480.824
8_P14_A0.077350.822
2_I6_I0.077120.820
29_R81_L0.077030.819
101_G180_H0.076910.818
195_V198_L0.076890.817
123_L127_L0.076890.817
26_A155_S0.076840.817
132_P194_V0.076590.814
5_G38_P0.076540.814
185_F200_V0.076540.814
98_G179_S0.076480.813
6_I63_L0.076450.813
88_I181_L0.076430.813
99_D176_Y0.076360.812
44_V77_L0.076360.812
35_L114_V0.076240.811
47_A64_S0.076210.810
23_L73_L0.076090.809
77_L108_N0.076090.809
36_E75_L0.076080.809
71_T188_G0.076080.809
7_L107_A0.075860.807
83_A118_L0.075860.807
48_A65_V0.07580.806
31_R35_L0.075670.805
56_N176_Y0.075650.804
88_I127_L0.075530.803
87_A105_L0.075480.802
65_V184_A0.07530.801
146_S154_V0.075280.800
11_W14_A0.075220.800
150_A179_S0.075160.799
57_I183_L0.075080.798
31_R37_K0.074980.797
122_L146_S0.074950.797
55_W200_V0.074950.797
75_L129_R0.074770.795
38_P123_L0.074760.795
43_A119_V0.074590.793
78_G118_L0.074420.791
100_G108_N0.074410.791
20_A170_M0.074390.791
9_P200_V0.074250.789
68_L172_L0.074010.787
10_W29_R0.0740.787
3_P6_I0.073980.787
107_A124_F0.073980.787
96_L197_F0.073970.786
119_V201_Y0.073730.784
148_L181_L0.073650.783
140_F192_G0.07340.780
6_I55_W0.073390.780
174_Q178_P0.073380.780
111_N154_V0.07330.779
124_F142_A0.073230.779
6_I45_L0.073180.778
91_L95_L0.073140.778
21_G24_A0.072860.775
58_P101_G0.072530.771
154_V161_S0.072510.771
112_M128_R0.072470.770
195_V200_V0.072470.770
50_F97_F0.072370.769
18_V87_A0.072220.768
49_V86_M0.07220.768
145_L160_L0.072170.767
96_L103_T0.072170.767
23_L105_L0.072030.766
80_W170_M0.071920.765
121_Y138_A0.07190.764
65_V150_A0.071860.764
25_L123_L0.071840.764
4_D26_A0.071750.763
154_V176_Y0.071630.762
20_A198_L0.071610.761
43_A169_W0.071580.761
45_L76_M0.071460.760
152_L196_T0.071310.758
90_L98_G0.070960.754
100_G106_G0.070880.754
39_I196_T0.070810.753
178_P181_L0.070680.751
110_L139_G0.070480.749
44_V88_I0.070470.749
139_G203_P0.070440.749
126_L198_L0.070420.749
148_L172_L0.070370.748
114_V152_L0.070360.748
61_G161_S0.070350.748
189_F202_R0.070340.748
12_L17_V0.070310.748
52_A77_L0.070290.747
43_A54_L0.070260.747
175_A179_S0.070240.747
81_L118_L0.070190.746
55_W190_L0.069950.744
141_L156_L0.069940.744
55_W175_A0.06980.742
12_L54_L0.069770.742
20_A28_R0.069760.742
90_L101_G0.069750.742
7_L183_L0.069730.741
8_P15_A0.069670.741
36_E45_L0.069370.738
161_S191_T0.069360.737
56_N59_I0.069230.736
31_R143_G0.069020.734
65_V68_L0.0690.734
55_W86_M0.068960.733
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
3p5nA0.843997.50.859
4hzuS0.785497.20.868
3rlbA0.843996.50.881
4huqS0.896.40.883
4dveA0.8634830.92
1tg7A0.263480.956
3hd6A0.87324.90.96
3ejkA0.28292.50.965
4gc0A0.71712.40.965
2xw6A0.22.40.965
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