GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SRPRB - Signal recognition particle receptor beta subunit
Pfam: PF09439 (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: 181
Sequences: 2932
Seq/Len: 16.2
HH_delta: 0.281 (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
85_S119_C0.457772.710
134_K138_E0.450992.669
17_T21_S0.41092.432
129_P132_K0.406192.404
19_L82_V0.397212.351
8_L20_F0.322261.907
130_P134_K0.310351.837
12_S59_H0.303711.798
84_D121_K0.295461.749
80_I118_A0.278271.647
132_K136_L0.27351.619
21_S25_N0.257261.523
146_K149_S0.251561.489
119_C122_Q0.236611.401
146_K151_S0.235051.391
125_F129_P0.233511.382
10_G15_G0.232961.379
86_S124_L0.228131.350
126_T129_P0.227911.349
11_P99_L0.225551.335
30_P33_T0.225111.332
92_L96_A0.224111.327
9_V55_D0.217141.285
30_P34_S0.216221.280
147_T150_K0.215011.273
129_P133_I0.213481.264
98_Y101_D0.212921.260
29_V32_V0.210881.248
126_T130_P0.206861.224
32_V35_M0.206381.222
56_I69_E0.203361.204
55_D58_G0.203191.203
132_K135_K0.19741.168
73_L76_A0.196891.165
101_D104_S0.196831.165
136_L139_K0.19441.151
80_I116_L0.191981.136
33_T41_Y0.18921.120
103_L115_I0.188341.115
54_V57_P0.187741.111
10_G16_K0.185991.101
90_K93_R0.185921.100
8_L80_I0.184961.095
90_K94_D0.184241.091
131_K135_K0.183241.085
14_S82_V0.183231.085
149_S152_L0.182371.079
93_R99_L0.180771.070
148_R151_S0.180391.068
120_N133_I0.179731.064
144_L152_L0.179531.063
148_R152_L0.179331.061
31_T35_M0.179131.060
125_F130_P0.177051.048
84_D120_N0.176981.048
5_T54_V0.176951.047
93_R96_A0.175471.039
128_K132_K0.175441.038
132_K138_E0.174981.036
59_H62_L0.174851.035
130_P143_K0.172681.022
12_S57_P0.172041.018
63_R66_L0.171591.016
28_T41_Y0.171221.013
29_V33_T0.169861.005
135_K139_K0.168881.000
31_T34_S0.168860.999
66_L69_E0.16840.997
7_L10_G0.167790.993
89_Q92_L0.166780.987
6_V51_L0.166710.987
139_K152_L0.165640.980
36_E39_I0.165480.979
147_T152_L0.164820.976
54_V79_I0.164160.972
146_K150_K0.163860.970
85_S122_Q0.162980.965
82_V120_N0.162560.962
100_Y104_S0.162420.961
21_S56_I0.162330.961
94_D97_E0.159660.945
94_D98_Y0.158840.940
118_A123_D0.158650.939
96_A100_Y0.157640.933
136_L140_E0.157640.933
122_Q125_F0.157520.932
11_P14_S0.156940.929
127_A138_E0.156810.928
145_R151_S0.156480.926
10_G13_G0.155980.923
21_S24_V0.155430.920
14_S83_V0.155420.920
21_S64_S0.154120.912
141_I149_S0.152680.904
122_Q130_P0.15250.903
84_D123_D0.152140.901
16_K19_L0.150590.891
7_L76_A0.150330.890
59_H66_L0.149850.887
27_K31_T0.149320.884
120_N123_D0.148990.882
5_T52_R0.148520.879
27_K32_V0.148180.877
142_D151_S0.147740.874
52_R74_S0.147670.874
54_V137_L0.146440.867
131_K148_R0.146250.866
28_T32_V0.145780.863
74_S139_K0.14510.859
30_P37_N0.144820.857
93_R97_E0.143890.852
14_S84_D0.143570.850
12_S21_S0.143510.849
95_V102_I0.14320.848
7_L56_I0.142890.846
67_L73_L0.142710.845
35_M115_I0.142380.843
92_L95_V0.142210.842
34_S38_N0.141830.839
49_K141_I0.141630.838
145_R150_K0.141620.838
118_A138_E0.141590.838
57_P61_R0.141460.837
65_K68_D0.14140.837
6_V48_G0.140860.834
56_I77_K0.140790.833
69_E73_L0.140690.833
91_E95_V0.139750.827
83_V120_N0.139620.826
131_K138_E0.139620.826
104_S126_T0.139340.825
131_K134_K0.139190.824
96_A99_L0.139110.823
62_L65_K0.139070.823
37_N40_A0.139050.823
49_K135_K0.138290.819
36_E40_A0.138250.818
55_D59_H0.138210.818
34_S65_K0.137320.813
56_I120_N0.136680.809
97_E100_Y0.136390.807
38_N52_R0.136330.807
7_L23_L0.136270.807
94_D99_L0.136070.805
138_E149_S0.135990.805
13_G25_N0.135180.800
39_I52_R0.134940.799
11_P81_F0.134790.798
9_V67_L0.134650.797
29_V37_N0.134560.796
142_D150_K0.134510.796
96_A144_L0.133730.792
127_A149_S0.133240.789
139_K150_K0.132350.783
29_V34_S0.132080.782
98_Y103_L0.131810.780
14_S31_T0.131610.779
18_A113_P0.131540.779
7_L13_G0.131230.777
49_K115_I0.130890.775
143_K147_T0.130840.774
91_E96_A0.130390.772
51_L55_D0.13020.771
125_F137_L0.129940.769
128_K133_I0.129590.767
90_K96_A0.129420.766
127_A131_K0.129350.766
27_K33_T0.129340.766
21_S31_T0.129260.765
33_T37_N0.127480.755
135_K138_E0.127440.754
54_V146_K0.126390.748
14_S58_G0.126250.747
76_A79_I0.12610.746
124_L132_K0.125870.745
56_I67_L0.125830.745
97_E101_D0.125730.744
57_P60_P0.125450.743
137_L144_L0.12540.742
30_P143_K0.125340.742
129_P136_L0.125320.742
142_D146_K0.125010.740
119_C130_P0.124870.739
24_V144_L0.124770.739
135_K149_S0.124570.737
8_L19_L0.123370.730
129_P140_E0.12330.730
125_F144_L0.123050.728
23_L26_G0.122620.726
135_K143_K0.122470.725
36_E68_D0.122350.724
95_V98_Y0.122340.724
27_K48_G0.122240.724
113_P117_I0.122230.723
83_V117_I0.12220.723
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
2fh5B0.98999.90.281
1nrjB0.961399.80.347
2gedA0.790199.80.377
3lvqE0.950399.80.383
1f6bA0.889599.80.384
3o47A0.906199.80.389
1m2oB0.88499.80.397
3r7wB0.933799.80.405
2b6hA0.900699.80.407
2h57A0.928299.80.408

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