GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SecD_SecF - Protein export membrane protein
Pfam: PF02355 (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: CL0322
Length: 189
Sequences: 20329
Seq/Len: 107.56
HH_delta: 0.165 (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
119_S122_E1.93293.733
118_K126_I1.84223.558
74_I166_I1.50452.906
111_E118_K1.482052.862
121_R184_Y1.400982.706
111_E126_I1.244622.404
109_R113_R1.152872.226
143_L165_I1.150892.223
70_I170_I1.144592.210
124_I184_Y1.115972.155
111_E130_Q1.092322.110
31_K35_I1.079242.084
107_R130_Q1.075172.076
56_F109_R1.07092.068
35_I39_I1.058122.043
38_I42_I1.056882.041
122_E126_I1.054282.036
121_R125_N1.049542.027
139_S172_T1.003341.938
143_L169_I0.989221.910
107_R111_E0.984041.900
78_F162_L0.957911.850
111_E114_A0.938251.812
126_I129_K0.922911.782
100_D139_S0.922311.781
31_K34_L0.919341.775
118_K122_E0.895521.729
93_I167_G0.819421.582
45_L57_A0.812451.569
97_S171_G0.811011.566
34_L38_I0.806361.557
107_R110_E0.773011.493
45_L61_I0.770461.488
125_N129_K0.766041.479
42_I46_I0.764711.477
73_G76_S0.757011.462
104_I128_I0.731931.414
78_F166_I0.728911.408
49_F57_A0.716161.383
150_F165_I0.714051.379
114_A118_K0.704271.360
155_G158_K0.700251.352
75_F163_T0.695061.342
110_E114_A0.692551.337
57_A60_A0.682561.318
136_I172_T0.676391.306
108_I127_S0.671211.296
150_F162_L0.656061.267
35_I38_I0.652381.260
181_P185_W0.651311.258
126_I130_Q0.649281.254
181_P184_Y0.646391.248
108_I124_I0.643361.242
32_S35_I0.641951.240
80_I162_L0.638471.233
83_T86_S0.633881.224
82_L86_S0.631731.220
75_F80_I0.630871.218
117_G123_A0.629051.215
146_A165_I0.617431.192
122_E125_N0.607141.173
112_L120_L0.602851.164
120_L124_I0.602781.164
132_L136_I0.597811.154
172_T176_L0.595241.150
75_F86_S0.594031.147
80_I159_G0.586931.133
158_K162_L0.586771.133
108_I183_L0.584751.129
142_T168_V0.560951.083
100_D138_T0.556671.075
28_D31_K0.544481.052
49_F53_R0.537491.038
83_T159_G0.532391.028
44_I98_V0.531611.027
135_T172_T0.526181.016
66_H174_S0.511640.988
112_L183_L0.510630.986
74_I78_F0.510470.986
45_L49_F0.509910.985
46_I50_L0.50660.978
110_E113_R0.499170.964
39_I43_A0.49790.962
66_H178_I0.496430.959
120_L184_Y0.49610.958
138_T172_T0.495470.957
59_A182_L0.494240.954
39_I42_I0.486130.939
40_A44_I0.485680.938
165_I169_I0.483010.933
136_I140_L0.477930.923
169_I173_Y0.475020.917
150_F161_A0.472930.913
59_A186_L0.471510.911
150_F158_K0.469850.907
112_L117_G0.469670.907
174_S179_A0.457560.884
162_L166_I0.457110.883
118_K123_A0.457060.883
139_S168_V0.456730.882
30_L34_L0.45360.876
114_A126_I0.451980.873
177_F181_P0.450740.870
113_R117_G0.447690.865
173_Y177_F0.446890.863
147_L165_I0.445680.861
124_I128_I0.44410.858
30_L87_I0.439650.849
59_A179_A0.438190.846
128_I132_L0.432520.835
71_T167_G0.430510.831
109_R112_L0.428670.828
114_A117_G0.428210.827
171_G175_S0.427530.826
112_L123_A0.42530.821
120_L123_A0.424210.819
74_I162_L0.423920.819
80_I158_K0.423750.818
71_T75_F0.420220.812
55_R59_A0.413940.799
104_I175_S0.413440.798
28_D32_S0.410460.793
70_I174_S0.407850.788
46_I49_F0.406920.786
121_R124_I0.402970.778
36_A40_A0.40250.777
96_Y100_D0.40070.774
85_P156_S0.400040.773
99_D103_V0.39910.771
101_N179_A0.398720.770
69_L73_G0.398480.770
100_D103_V0.395840.764
62_I178_I0.395390.764
108_I120_L0.394140.761
73_G77_L0.384740.743
63_A174_S0.384440.742
86_S159_G0.382230.738
151_F154_G0.38140.737
54_W58_L0.381260.736
155_G159_G0.380930.736
146_A164_L0.379660.733
56_F59_A0.378350.731
89_A159_G0.375930.726
119_S123_A0.375820.726
63_A101_N0.374620.723
58_L62_I0.370340.715
103_V135_T0.365470.706
96_Y99_D0.363790.703
135_T139_S0.363470.702
62_I182_L0.358820.693
74_I170_I0.357760.691
108_I112_L0.355970.687
174_S178_I0.355180.686
52_F60_A0.353080.682
63_A179_A0.350290.676
104_I135_T0.349320.675
96_Y138_T0.349090.674
107_R131_T0.348860.674
50_L53_R0.348670.673
107_R127_S0.344720.666
145_A148_I0.344440.665
123_A127_S0.341230.659
131_T139_S0.341220.659
39_I46_I0.339170.655
178_I182_L0.338180.653
71_T90_L0.337890.653
41_L45_L0.335640.648
96_Y142_T0.332690.642
60_A105_F0.332530.642
80_I150_F0.330770.639
166_I170_I0.330220.638
60_A98_V0.329890.637
112_L118_K0.329570.636
133_S137_D0.329490.636
149_L161_A0.328050.634
182_L185_W0.328010.633
29_L33_A0.32620.630
127_S135_T0.324460.627
163_T167_G0.324240.626
127_S131_T0.32370.625
168_V172_T0.322750.623
36_A39_I0.321460.621
100_D171_G0.321450.621
48_I61_I0.318980.616
138_T149_L0.318680.615
104_I176_L0.318450.615
99_D141_T0.317810.614
76_S80_I0.317710.614
48_I137_D0.314390.607
60_A101_N0.307550.594
67_D97_S0.307320.594
112_L119_S0.306990.593
29_L84_L0.306960.593
96_Y168_V0.306920.593
55_R58_L0.305870.591
47_Y51_R0.305720.590
71_T163_T0.304870.589
60_A64_L0.304550.588
61_I65_I0.304480.588
71_T93_I0.304350.588
64_L94_I0.304050.587
157_L161_A0.303150.585
67_D71_T0.302510.584
43_A46_I0.301030.581
133_S136_I0.299340.578
131_T134_R0.299240.578
124_I180_R0.296980.574
41_L94_I0.296320.572
118_K121_R0.295720.571
147_L151_F0.295640.571
58_L61_I0.295480.571
42_I49_F0.295220.570
76_S79_G0.295130.570
30_L33_A0.294550.569
41_L61_I0.294280.568
71_T166_I0.294070.568
91_L94_I0.293970.568
47_Y99_D0.293450.567
89_A163_T0.293070.566
111_E117_G0.292640.565
51_R106_D0.292140.564
161_A165_I0.291130.562
88_A91_L0.290250.561
90_L95_G0.289750.560
132_L176_L0.289510.559
108_I111_E0.28930.559
179_A182_L0.2880.556
51_R57_A0.287590.555
86_S163_T0.286960.554
100_D175_S0.286770.554
147_L150_F0.286550.553
57_A61_I0.285520.551
52_F137_D0.282240.545
93_I163_T0.282110.545
65_I68_V0.282010.545
42_I50_L0.280660.542
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
3aqpA0.989499.90.165
3aqpA0.994799.90.192
2v50A0.973599.90.192
3w9iA0.978899.90.201
4dx5A0.978899.90.203
4dx5A0.968399.90.218
2v50A0.968399.90.22
3w9iA0.968399.90.226
3ne5A0.984199.90.237
3ne5A0.978899.90.246

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