GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SecA_PP_bind - SecA preprotein cross-linking domain
Pfam: PF01043 (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. )
Length: 113
Sequences: 1595
Seq/Len: 14.12
HH_delta: 0.052 (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
104_W112_I1.021714.331
23_D42_K0.998864.234
89_V98_I0.80123.396
90_I104_W0.760383.223
24_Y73_H0.672622.851
16_K72_H0.660182.798
12_D72_H0.549962.331
82_I98_I0.546792.318
11_A65_I0.53092.250
82_I91_V0.488962.073
12_D16_K0.445551.889
89_V100_P0.408031.729
54_Y62_Y0.407291.726
17_Q46_L0.402961.708
76_K79_V0.39621.679
84_R98_I0.389481.651
27_D30_Q0.385381.633
6_N10_E0.3721.577
51_D55_D0.361571.533
31_R80_D0.359581.524
10_E13_K0.35541.506
35_L65_I0.354421.502
25_E36_T0.337851.432
26_V73_H0.330261.400
14_F47_L0.323181.370
91_V98_I0.316951.343
42_K46_L0.314481.333
41_E45_K0.307331.303
103_R113_E0.30331.286
14_F43_A0.302761.283
40_I62_Y0.297681.262
26_V74_L0.293941.246
43_A65_I0.292971.242
83_V88_V0.292011.238
6_N9_R0.290071.229
19_K22_E0.285091.208
33_V74_L0.278811.182
75_F104_W0.273171.158
90_I109_H0.270571.147
42_K45_K0.265551.126
14_F18_L0.264141.120
29_K93_E0.26341.116
23_D38_K0.261161.107
14_F17_Q0.255741.084
69_L105_S0.245741.042
28_E93_E0.245411.040
63_H67_Q0.244851.038
89_V99_M0.244051.034
14_F46_L0.243951.034
15_A72_H0.243011.030
31_R79_V0.239551.015
33_V73_H0.238361.010
7_L64_H0.236121.001
11_A43_A0.232190.984
87_E101_G0.229880.974
70_K108_L0.229290.972
47_L53_L0.22840.968
7_L61_L0.226730.961
22_E38_K0.223930.949
11_A47_L0.221930.941
87_E100_P0.22160.939
84_R100_P0.221370.938
49_I58_N0.219330.930
67_Q108_L0.217750.923
15_A73_H0.215610.914
63_H106_D0.21550.913
25_E34_E0.213680.906
35_L43_A0.212720.902
9_R13_K0.208730.885
55_D94_F0.20720.878
75_F105_S0.206260.874
60_E64_H0.204340.866
13_K16_K0.201670.855
18_L42_K0.200750.851
15_A43_A0.200290.849
63_H108_L0.197190.836
95_T102_R0.19650.833
49_I52_N0.193920.822
40_I60_E0.192820.817
31_R74_L0.191780.813
14_F65_I0.191090.810
11_A15_A0.190880.809
94_F102_R0.190830.809
17_Q48_G0.188710.800
41_E55_D0.186960.792
54_Y75_F0.185120.785
43_A46_L0.184770.783
58_N61_L0.177860.754
75_F112_I0.177520.752
90_I95_T0.177440.752
20_E73_H0.175940.746
37_E69_L0.175250.743
29_K103_R0.175010.742
84_R89_V0.173770.737
109_H113_E0.173720.736
63_H105_S0.173530.736
70_K75_F0.168540.714
2_E5_S0.167970.712
26_V33_V0.167550.710
38_K42_K0.167340.709
35_L57_E0.164850.699
41_E98_I0.164680.698
93_E102_R0.164070.695
38_K41_E0.16390.695
62_Y66_N0.163830.694
61_L66_N0.163570.693
22_E42_K0.163480.693
92_D95_T0.163170.692
40_I52_N0.162370.688
44_E47_L0.161310.684
18_L46_L0.159470.676
107_G110_Q0.158080.670
70_K101_G0.157820.669
30_Q56_E0.157380.667
4_S7_L0.156940.665
6_N78_D0.156060.661
19_K38_K0.15540.659
41_E57_E0.154790.656
35_L69_L0.154410.654
102_R105_S0.15440.654
101_G107_G0.153990.653
30_Q74_L0.153250.650
45_K51_D0.152830.648
92_D101_G0.152490.646
29_K90_I0.151240.641
55_D58_N0.150460.638
96_G110_Q0.149560.634
99_M102_R0.148920.631
51_D58_N0.147660.626
6_N13_K0.147310.624
32_T73_H0.147180.624
44_E53_L0.147140.624
70_K106_D0.146930.623
101_G109_H0.146780.622
24_Y72_H0.145080.615
103_R106_D0.143430.608
5_S9_R0.143410.608
75_F109_H0.143250.607
3_D25_E0.143160.607
102_R106_D0.142770.605
90_I102_R0.141830.601
64_H68_A0.141210.599
31_R76_K0.140870.597
12_D73_H0.140680.596
19_K30_Q0.140040.594
14_F42_K0.139670.592
78_D82_I0.139480.591
8_Y103_R0.139330.591
101_G105_S0.139080.590
30_Q34_E0.138340.586
46_L76_K0.137390.582
69_L91_V0.136550.579
24_Y64_H0.136140.577
4_S79_V0.135760.575
57_E77_R0.134440.570
89_V109_H0.134150.569
34_E59_S0.133710.567
4_S112_I0.13360.566
25_E32_T0.133230.565
36_T113_E0.132610.562
97_R113_E0.132380.561
24_Y28_E0.132320.561
52_N62_Y0.132160.560
90_I93_E0.131570.558
18_L23_D0.131490.557
12_D52_N0.131350.557
3_D75_F0.131340.557
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
3juxA0.99121000.052
2ipcA0.99121000.092
1nktA0.99121000.19
1tf5A0.99121000.226
2fsfA11000.245
1ni3A0.840770.10.909
1jalA0.8319460.921
2dbyA0.8407400.924
2qvoA0.495636.70.925
4fn5A0.858430.20.928

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