GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DsbD_2 - Cytochrome C biogenesis protein transmembrane region
Pfam: PF13386 (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: CL0549
Length: 199
Sequences: 3288
Seq/Len: 16.52
HH_delta: 0.905 (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
44_L122_F0.940535.185
183_R187_R0.55523.061
3_F165_P0.501722.766
85_G194_I0.438242.416
47_T157_L0.414032.282
51_A153_A0.393872.171
41_G122_F0.385982.128
39_N164_L0.377562.081
4_L8_L0.375722.071
37_L118_P0.373182.057
184_R187_R0.350291.931
9_G159_F0.347161.914
117_G120_G0.341541.883
184_R188_L0.340331.876
85_G89_L0.337331.860
47_T160_G0.334311.843
78_G81_G0.332441.833
17_C20_I0.331391.827
78_G197_G0.328221.809
45_S126_F0.327061.803
35_H171_G0.326961.802
33_L172_L0.325871.796
36_L40_L0.308851.703
50_G152_G0.305161.682
81_G85_G0.304971.681
191_V195_I0.304931.681
43_I160_G0.304331.678
85_G190_G0.303791.675
82_L197_G0.287771.586
12_H15_G0.28451.568
89_L194_I0.279641.542
40_L122_F0.278141.533
54_G149_P0.268021.477
82_L194_I0.267861.477
41_G162_G0.266131.467
89_L190_G0.26551.464
34_R121_A0.265111.461
68_G71_R0.256041.411
6_G162_G0.250241.379
12_H17_C0.248131.368
68_G72_I0.241881.333
37_L121_A0.240471.326
74_G78_G0.240191.324
12_H16_M0.238921.317
150_L153_A0.238611.315
2_A155_L0.23221.280
21_A25_S0.229091.263
106_R109_Q0.228631.260
42_R163_T0.224681.239
3_F161_L0.224031.235
102_H106_R0.223551.232
52_L55_L0.218381.204
21_A24_L0.217641.200
187_R191_V0.215661.189
39_N168_L0.214461.182
103_G106_R0.213821.179
134_G137_Y0.213791.179
51_A149_P0.209011.152
78_G85_G0.207631.145
140_L156_M0.20551.133
2_A139_A0.204111.125
43_I47_T0.203581.122
86_L91_G0.203581.122
44_L126_F0.200921.108
38_Y128_N0.200081.103
153_A157_L0.198881.096
128_N131_L0.198541.094
190_G194_I0.197441.088
50_G57_G0.197331.088
148_S151_Y0.196571.084
75_I79_L0.195181.076
149_P152_G0.194441.072
83_F92_P0.193671.068
12_H18_G0.193541.067
45_S129_G0.193351.066
37_L122_F0.191511.056
146_S151_Y0.191231.054
20_I23_A0.18781.035
191_V194_I0.186851.030
37_L40_L0.1861.025
38_Y121_A0.18581.024
39_N43_I0.185241.021
166_A170_A0.185041.020
42_R45_S0.184971.020
82_L85_G0.184861.019
54_G57_G0.183611.012
10_S46_Y0.183591.012
15_G18_G0.182881.008
21_A167_L0.182731.007
73_I77_L0.18261.007
17_C42_R0.181220.999
147_G152_G0.179680.990
149_P153_A0.179020.987
69_L73_I0.178650.985
50_G54_G0.178030.981
189_A197_G0.177340.978
143_A156_M0.177140.976
33_L36_L0.175710.969
9_G135_P0.175660.968
166_A169_L0.174720.963
40_L157_L0.174570.962
46_Y137_Y0.173060.954
16_M167_L0.171890.948
79_L83_F0.17140.945
18_G163_T0.171360.945
109_Q113_R0.171090.943
90_G93_R0.170620.941
106_R110_P0.170310.939
178_S181_L0.169480.934
188_L191_V0.169440.934
122_F126_F0.169250.933
3_F162_G0.168730.930
75_I78_G0.168550.929
153_A156_M0.16770.924
54_G144_A0.167060.921
49_L140_L0.165590.913
157_L161_L0.164760.908
107_R110_P0.164690.908
5_L46_Y0.164040.904
43_I157_L0.164030.904
14_I132_P0.162440.895
54_G153_A0.162420.895
50_G156_M0.162280.895
58_S61_S0.16220.894
5_L8_L0.162030.893
38_Y46_Y0.161450.890
47_T153_A0.161220.889
103_G107_R0.160920.887
46_Y133_C0.159610.880
130_L134_G0.158610.874
39_N171_G0.158050.871
163_T167_L0.15680.864
42_R165_P0.156750.864
46_Y129_G0.156280.862
9_G16_M0.155930.860
85_G197_G0.155510.857
72_I75_I0.155340.856
16_M20_I0.155150.855
76_L154_L0.154680.853
185_L189_A0.1540.849
78_G82_L0.152250.839
128_N132_P0.152170.839
84_L193_L0.151510.835
42_R160_G0.151290.834
56_L59_G0.150940.832
164_L167_L0.149630.825
12_H39_N0.149510.824
175_G179_R0.149430.824
51_A54_G0.147740.814
10_S166_A0.147570.813
180_R184_R0.147490.813
50_G140_L0.146850.810
10_S16_M0.146350.807
51_A148_S0.145280.801
3_F158_A0.14440.796
167_L171_G0.144290.795
183_R186_L0.144290.795
138_F193_L0.14420.795
87_R90_G0.1440.794
5_L135_P0.143840.793
25_S167_L0.142390.785
49_L80_L0.142360.785
2_A158_A0.142020.783
63_S68_G0.141780.782
16_M164_L0.141690.781
11_L14_I0.141130.778
109_Q112_L0.141030.777
121_A128_N0.14080.776
16_M128_N0.14030.773
43_I88_L0.139960.772
174_A178_S0.139960.772
39_N42_R0.13960.770
41_G126_F0.139520.769
42_R46_Y0.138860.765
21_A131_L0.138550.764
50_G158_A0.138520.764
41_G125_G0.138430.763
125_G133_C0.138310.762
60_L64_G0.138190.762
28_Q31_R0.138150.762
50_G160_G0.137880.760
40_L44_L0.137560.758
186_L193_L0.137340.757
58_S62_L0.137190.756
135_P138_F0.136380.752
136_V156_M0.135680.748
10_S163_T0.135610.748
46_Y131_L0.135570.747
74_G81_G0.135290.746
177_L195_I0.135120.745
84_L87_R0.134820.743
88_L158_A0.134360.741
16_M132_P0.134320.740
119_W195_I0.133950.738
110_P113_R0.133690.737
161_L168_L0.133620.737
17_C46_Y0.133230.734
17_C131_L0.133130.734
36_L168_L0.132950.733
56_L166_A0.132930.733
154_L157_L0.13290.733
150_L154_L0.13270.732
100_L103_G0.13230.729
74_G77_L0.132120.728
134_G142_L0.131660.726
87_R92_P0.131420.724
138_F142_L0.131150.723
10_S167_L0.131020.722
144_A156_M0.130990.722
7_L10_S0.130690.720
80_L141_A0.13020.718
22_L26_L0.129880.716
12_H163_T0.129360.713
70_R74_G0.129240.712
116_K120_G0.129110.712
59_G63_S0.128940.711
189_A193_L0.128890.711
184_R198_I0.128350.708
82_L86_L0.128280.707
3_F7_L0.127840.705
24_L113_R0.127590.703
16_M46_Y0.127540.703
140_L144_A0.127510.703
87_R91_G0.127170.701
70_R73_I0.126790.699
21_A26_L0.126690.698
88_L189_A0.126030.695
176_K179_R0.125920.694
70_R141_A0.12580.693
9_G12_H0.125350.691
126_F173_L0.124920.689
126_F129_G0.124620.687
16_M163_T0.124430.686
77_L81_G0.124420.686
139_A143_A0.124340.685
138_F144_A0.124180.685
54_G147_G0.124110.684
23_A27_S0.124020.684
14_I18_G0.123030.678
125_G162_G0.122880.677
10_S21_A0.122490.675
171_G175_G0.122480.675
71_R75_I0.122250.674
16_M21_A0.122240.674
182_R186_L0.122190.674
35_H39_N0.122020.673
45_S63_S0.121740.671
37_L41_G0.121690.671
154_L158_A0.121180.668
12_H42_R0.121150.668
167_L174_A0.120930.667
87_R130_L0.120760.666
39_N165_P0.12050.664
5_L139_A0.120320.663
26_L32_W0.120020.662
34_R37_L0.119980.661
17_C163_T0.119970.661
143_A147_G0.11990.661
173_L177_L0.119770.660
17_C21_A0.119610.659
10_S38_Y0.11920.657
129_G159_F0.119120.657
128_N167_L0.118880.655
119_W123_L0.118640.654
156_M160_G0.118250.652
173_L176_K0.118210.652
43_I164_L0.118140.651
192_L196_L0.118010.651
10_S193_L0.117940.650
2_A9_G0.117680.649
123_L126_F0.117370.647
55_L110_P0.117230.646
52_L56_L0.117040.645
56_L141_A0.116720.643
139_A142_L0.116440.642
133_C159_F0.11620.641
20_I132_P0.115880.639
6_G139_A0.115780.638
40_L47_T0.115770.638
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
2gfpA0.899561.80.905
3o7qA0.949754.20.909
4jr9A0.909532.90.919
4iu9B0.909532.10.92
4j05A0.959829.30.921
1pw4A0.929628.80.922
4gc0A0.969823.40.925
4apsA0.929610.60.935
2cfqA0.41716.80.94
2l2tA0.17596.70.94
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