GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SRP54 - SRP54-type protein GTPase domain
Pfam: PF00448 (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: CL0023
Length: 196
Sequences: 18206
Seq/Len: 92.89
HH_delta: 0.046 (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
5_A157_G1.458263.433
78_K82_K1.065862.510
108_L142_I1.035792.439
52_A59_F1.02592.415
134_L138_E0.929042.187
31_K38_D0.923932.175
50_T53_E0.826691.946
44_A47_Q0.793911.869
135_A139_A0.792091.865
103_E106_K0.789571.859
69_A73_R0.779321.835
23_A27_L0.769571.812
33_A84_Y0.765911.803
70_E74_E0.751161.769
24_R28_K0.74991.766
99_E103_E0.739241.741
135_A138_E0.711691.676
23_A56_G0.708341.668
46_E49_K0.704971.660
49_K53_E0.70211.653
42_I47_Q0.699111.646
71_I108_L0.685921.615
30_K86_L0.675131.590
106_K139_A0.667841.572
49_K61_V0.663571.562
6_L18_I0.646631.522
40_Y44_A0.63951.506
43_G47_Q0.634031.493
18_I88_L0.631911.488
73_R77_E0.6311.486
124_T128_E0.630911.485
25_L86_L0.618181.455
20_K32_V0.606451.428
31_K84_Y0.600071.413
71_I74_E0.599751.412
77_E82_K0.599311.411
74_E78_K0.596311.404
132_Q135_A0.596241.404
4_I161_S0.59551.402
23_A26_K0.58381.375
3_V89_I0.570171.342
108_L140_F0.569671.341
67_D71_I0.566191.333
131_E155_R0.560351.319
67_D70_E0.559641.318
71_I75_A0.559191.317
66_S70_E0.555931.309
68_P72_A0.551011.297
58_P61_V0.549791.294
6_L17_T0.547151.288
43_G46_E0.543831.280
52_A73_R0.543351.279
21_L145_L0.539981.271
148_T153_T0.538621.268
86_L90_D0.534221.258
30_K85_D0.533371.256
20_K27_L0.522341.230
116_E143_D0.521891.229
128_E132_Q0.50781.196
19_A25_L0.50681.193
74_E77_E0.495731.167
134_L137_Y0.49571.167
52_A56_G0.487761.148
18_I22_A0.480661.132
35_I75_A0.478251.126
109_L141_G0.473671.115
42_I46_E0.47271.113
77_E81_K0.468711.104
126_G152_E0.468581.103
18_I34_L0.466521.098
70_E73_R0.465811.097
131_E134_L0.459021.081
26_K56_G0.458671.080
35_I110_E0.457281.077
87_V90_D0.448731.057
118_H144_G0.448481.056
75_A78_K0.445781.050
68_P71_I0.445341.049
136_F139_A0.444291.046
77_E80_R0.443161.043
35_I87_V0.440751.038
62_A74_E0.440321.037
118_H146_I0.438651.033
124_T127_Q0.436851.029
31_K85_D0.436061.027
124_T136_F0.435621.026
104_E112_L0.432021.017
137_Y141_G0.430791.014
53_E56_G0.430561.014
51_Y54_I0.425831.003
76_L80_R0.416680.981
35_I39_T0.414890.977
3_V76_L0.414130.975
58_P84_Y0.41260.971
33_A60_Y0.412080.970
147_L159_L0.407550.960
33_A79_F0.406690.958
137_Y142_I0.403120.949
50_T54_I0.402550.948
52_A55_L0.402320.947
9_P12_V0.39970.941
103_E107_K0.399120.940
123_A147_L0.39460.929
78_K81_K0.394520.929
130_L134_L0.393780.927
20_K23_A0.392490.924
40_Y43_G0.389130.916
131_E135_A0.386850.911
122_S149_K0.38620.909
126_G130_L0.386020.909
43_G96_P0.378830.892
100_E103_E0.378430.891
5_A102_L0.378280.891
125_M129_D0.377980.890
8_G13_G0.37520.883
137_Y140_F0.373770.880
75_A79_F0.37330.879
33_A38_D0.37250.877
129_D133_A0.369450.870
60_Y74_E0.36510.860
20_K24_R0.36110.850
129_D132_Q0.360080.848
63_R66_S0.357740.842
123_A127_Q0.355780.838
33_A82_K0.355490.837
52_A72_A0.355350.837
4_I86_L0.355170.836
156_L160_L0.351690.828
88_L91_T0.351510.828
4_I159_L0.351440.827
19_A22_A0.351160.827
8_G12_V0.349780.824
76_L81_K0.349450.823
19_A51_Y0.346520.816
26_K32_V0.344810.812
97_R119_L0.344430.811
121_L147_L0.343420.809
17_T21_L0.343160.808
46_E50_T0.343150.808
117_V120_V0.342870.807
3_V115_D0.342620.807
97_R100_E0.340970.803
40_Y47_Q0.340290.801
40_Y46_E0.337390.794
35_I111_A0.33310.784
24_R27_L0.332410.783
153_T156_L0.332190.782
17_T146_I0.331910.781
56_G68_P0.330890.779
64_T67_D0.330780.779
145_L148_T0.330430.778
11_G16_T0.329840.777
5_A98_D0.328670.774
46_E63_R0.328620.774
137_Y143_D0.327080.770
48_L52_A0.325420.766
98_D102_L0.322150.758
132_Q136_F0.320610.755
47_Q51_Y0.320260.754
153_T157_G0.318260.749
34_L39_T0.315830.744
109_L112_L0.31470.741
54_I57_V0.313780.739
7_V98_D0.309670.729
158_A161_S0.309330.728
119_L122_S0.307930.725
79_F102_L0.305830.720
32_V88_L0.305130.718
122_S125_M0.304970.718
42_I96_P0.30420.716
74_E79_F0.304060.716
17_T148_T0.303890.715
7_V117_V0.303690.715
48_L51_Y0.301840.711
5_A89_I0.300780.708
41_R47_Q0.298520.703
37_A89_I0.296950.699
36_S39_T0.296320.698
8_G14_K0.29580.696
62_A66_S0.29510.695
72_A89_I0.294050.692
60_Y63_R0.293380.691
42_I45_V0.291040.685
81_K86_L0.290590.684
5_A108_L0.290540.684
49_K59_F0.289680.682
109_L117_V0.289320.681
122_S126_G0.289150.681
107_K110_E0.288440.679
22_A32_V0.287950.678
41_R44_A0.287220.676
93_G126_G0.285730.673
65_E69_A0.285120.671
80_R83_G0.285090.671
7_V150_L0.284660.670
67_D107_K0.281990.664
114_P146_I0.280660.661
104_E107_K0.280270.660
60_Y75_A0.278950.657
128_E136_F0.27890.657
8_G11_G0.27860.656
20_K28_K0.277140.653
93_G130_L0.276010.650
6_L21_L0.275750.649
78_K84_Y0.274560.646
119_L123_A0.274120.645
49_K60_Y0.272950.643
46_E54_I0.272810.642
6_L145_L0.272730.642
41_R45_V0.271770.640
95_S98_D0.271690.640
121_L129_D0.271050.638
157_G161_S0.270950.638
34_L52_A0.27050.637
16_T20_K0.269980.636
59_F62_A0.269970.636
125_M153_T0.269360.634
105_L109_L0.266040.626
59_F107_K0.265890.626
12_V120_V0.26280.619
6_L147_L0.262640.618
95_S122_S0.261330.615
15_T93_G0.260880.614
114_P144_G0.259750.612
23_A55_L0.259650.611
101_L129_D0.259360.611
133_A144_G0.259320.611
9_P124_T0.258060.608
4_I25_L0.257660.607
100_E104_E0.257520.606
138_E141_G0.256370.604
48_L58_P0.256340.604
26_K57_V0.256230.603
69_A72_A0.255710.602
159_L162_L0.254720.600
25_L28_K0.254070.598
37_A98_D0.253970.598
35_I89_I0.253820.598
16_T149_K0.253650.597
66_S74_E0.253570.597
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
3dm5A11000.046
3kl4A11000.09
2ffhA199.90.134
2xxaA199.90.144
1j8mF199.90.146
1vmaA199.90.149
1zu4A199.90.152
1ls1A199.90.153
2j37W199.90.173
2v3cC0.989899.90.174

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