GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DsbD - Cytochrome C biogenesis protein transmembrane region
Pfam: PF02683 (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: 211
Sequences: 6780
Seq/Len: 32.13
HH_delta: 0.913 (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
53_L121_F1.551265.729
88_G203_I0.967653.574
81_G206_G0.723972.674
192_R196_R0.686972.537
193_W196_R0.681072.515
85_I206_G0.678242.505
88_G199_G0.678112.504
85_I203_I0.630652.329
81_G210_L0.557052.057
74_P77_Y0.535561.978
78_I82_V0.533271.969
54_V125_L0.52141.926
88_G206_G0.520721.923
49_L121_F0.518531.915
200_I204_A0.512011.891
46_A117_L0.508631.878
193_W197_I0.507041.873
43_L120_A0.480161.773
92_L203_I0.468221.729
78_I210_L0.466191.722
92_L199_G0.461261.704
75_W78_I0.456071.684
50_G121_F0.455321.682
46_A120_A0.454161.677
75_W79_I0.450331.663
66_G69_F0.437471.616
44_G174_G0.410581.516
41_L175_L0.409851.514
121_F125_L0.403371.490
86_L89_L0.401941.484
89_L93_G0.401821.484
92_L196_R0.389081.437
72_I75_W0.374151.382
116_G119_G0.372561.376
52_A163_G0.370291.368
153_L156_L0.368891.362
47_F124_G0.356651.317
44_G48_V0.355071.311
166_F170_L0.342151.264
88_G92_L0.338291.249
118_L122_L0.335761.240
73_S77_Y0.335541.239
51_F55_F0.333411.231
85_I89_L0.329961.219
74_P78_I0.329541.217
59_G159_L0.327651.210
78_I81_G0.32551.202
56_A160_L0.325231.201
196_R200_I0.323431.194
83_L86_L0.321271.187
57_L125_L0.321161.186
48_V167_G0.310921.148
58_L128_G0.308231.138
48_V52_A0.304681.125
53_L57_L0.303341.120
149_S154_Q0.300881.111
199_G203_I0.300831.111
172_L176_F0.295671.092
128_G135_T0.292461.080
127_F130_V0.291931.078
110_K114_G0.291291.076
162_Y165_G0.289181.068
132_S137_P0.288811.067
59_G155_G0.287051.060
55_F135_T0.287041.060
61_G64_A0.286731.059
55_F128_G0.28531.054
46_A49_L0.284381.050
170_L177_S0.282611.044
179_S182_R0.279811.033
50_G124_G0.278941.030
139_L162_Y0.27731.024
93_G96_E0.277161.024
81_G85_I0.275711.018
179_S183_R0.275151.016
67_S70_G0.27261.007
48_V51_F0.27071.000
156_L159_L0.270330.998
47_F127_F0.269920.997
51_F166_F0.269780.996
55_F124_G0.26860.992
48_V174_G0.267380.987
169_P172_L0.266250.983
47_F120_A0.265010.979
86_L90_S0.263270.972
60_L156_L0.259320.958
82_V86_L0.258980.956
55_F59_G0.25670.948
75_W208_Y0.254070.938
162_Y166_F0.251230.928
49_L53_L0.250710.926
169_P173_I0.249530.922
45_L49_L0.248160.916
174_G178_G0.247320.913
46_A50_G0.247150.913
190_W193_W0.245690.907
42_L117_L0.244860.904
183_R186_K0.243880.901
152_V155_G0.243690.900
177_S180_L0.242860.897
158_L162_Y0.242240.895
51_F135_T0.24190.893
204_A208_Y0.24140.892
141_A144_A0.240440.888
203_I206_G0.238190.880
156_L160_L0.237560.877
182_R186_K0.235460.870
186_K189_R0.235320.869
185_R190_W0.234810.867
128_G170_L0.234340.865
71_Q74_P0.234280.865
186_K190_W0.234230.865
104_R114_G0.23370.863
76_L80_A0.233170.861
51_F54_V0.23290.860
56_A167_G0.232260.858
56_A163_G0.231450.855
45_L48_V0.231140.854
119_G122_L0.231090.853
55_F58_L0.230460.851
101_S104_R0.229940.849
53_L125_L0.229550.848
51_F136_G0.228970.846
43_L46_A0.228860.845
181_L185_R0.227120.839
59_G63_G0.226570.837
83_L134_C0.226260.836
158_L161_A0.225190.832
153_L157_L0.223850.827
138_I142_I0.222720.823
79_I83_L0.222280.821
157_L160_L0.220630.815
151_S154_Q0.220230.813
84_L206_G0.220070.813
47_F55_F0.218340.806
90_S93_G0.217350.803
205_L208_Y0.215730.797
57_L60_L0.2150.794
159_L162_Y0.213810.790
194_I198_S0.212230.784
101_S105_L0.211830.782
92_L200_I0.211670.782
100_L103_P0.211520.781
124_G128_G0.211030.779
87_F202_L0.210440.777
191_S195_K0.210360.777
59_G163_G0.209290.773
115_G119_G0.208740.771
170_L174_G0.208110.769
161_A165_G0.207560.767
142_I162_Y0.206580.763
58_L129_L0.206570.763
197_I200_I0.20570.760
45_L171_L0.205430.759
86_L93_G0.204780.756
54_V128_G0.204140.754
58_L62_A0.203180.750
71_Q75_W0.203140.750
55_F134_C0.202340.747
42_L45_L0.202140.747
84_L205_L0.201830.745
61_G65_L0.200940.742
134_C137_P0.200050.739
75_W80_A0.19980.738
162_Y170_L0.199780.738
58_L162_Y0.19930.736
55_F139_L0.197740.730
63_G159_L0.196170.724
46_A121_F0.195680.723
143_L147_A0.195560.722
141_A205_L0.194650.719
51_F128_G0.193850.716
189_R192_R0.193320.714
60_L64_A0.193090.713
157_L161_A0.193030.713
135_T166_F0.190380.703
150_G153_L0.18970.701
52_A56_A0.188890.698
167_G171_L0.188880.698
59_G143_L0.188380.696
47_F169_P0.188110.695
132_S139_L0.186820.690
144_A148_S0.186710.690
86_L134_C0.186440.689
154_Q157_L0.186220.688
89_L94_L0.186130.687
189_R193_W0.186030.687
80_A133_P0.18590.687
192_R195_K0.185240.684
41_L171_L0.185130.684
55_F127_F0.182980.676
84_L209_L0.182780.675
136_G139_L0.181860.672
176_F179_S0.181360.670
77_Y133_P0.180660.667
175_L179_S0.180320.666
91_L196_R0.179940.665
201_L208_Y0.179380.662
190_W194_I0.178980.661
144_A147_A0.178890.661
166_F173_I0.178560.659
160_L164_L0.178180.658
132_S140_A0.177970.657
198_S205_L0.177780.657
163_G170_L0.177680.656
62_A132_S0.177290.655
123_L202_L0.177210.654
185_R188_R0.176640.652
203_I207_L0.175990.650
41_L45_L0.17540.648
46_A118_L0.175360.648
123_L126_L0.175110.647
48_V170_L0.1750.646
51_F140_A0.174780.645
68_F80_A0.174250.644
56_A61_G0.174160.643
91_L198_S0.174070.643
44_G128_G0.172820.638
90_S94_L0.172780.638
124_G165_G0.172480.637
48_V171_L0.172420.637
137_P140_A0.17230.636
51_F163_G0.172220.636
127_F133_P0.172210.636
76_L140_A0.172110.636
50_G165_G0.172060.635
55_F163_G0.171660.634
51_F165_G0.171550.634
57_L61_G0.171380.633
127_F173_I0.170340.629
52_A170_L0.170140.628
79_I152_V0.169730.627
90_S141_A0.168770.623
198_S202_L0.168760.623
152_V156_L0.16870.623
80_A137_P0.168680.623
178_G182_R0.16850.622
134_C165_G0.16730.618
105_L110_K0.16690.616
122_L126_L0.166480.615
55_F165_G0.166110.613
52_A169_P0.166080.613
47_F123_L0.165670.612
180_L183_R0.165660.612
41_L44_G0.165030.609
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:
PDB Cov Prob HH_delta
4apsA0.919431.60.913
3o7qA0.886327.80.915
1pw4A0.905222.70.918
2gfpA0.857822.10.919
4humA0.857815.70.924
3l1lA0.81526.50.935
2m67A0.36975.90.936
4j05A0.53555.30.938
3mktA0.82465.20.938
4iu9B0.85314.60.939
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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