GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SSB - Single-strand binding protein family
Pfam: PF00436 (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: CL0021
Length: 104
Sequences: 3578
Seq/Len: 34.4
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
11_G49_W1.558113.057
84_E90_K1.48212.908
85_D89_Q1.453992.853
52_V98_A1.401392.750
18_Y24_P1.331292.612
10_L66_L1.175212.306
81_R95_E1.108372.175
85_D91_R1.067222.094
82_T90_K1.062172.084
3_K75_E1.048842.058
23_T56_G1.034192.029
13_D67_K0.936061.837
54_A62_V0.926191.817
12_K29_S0.899331.764
28_F52_V0.890651.747
62_V66_L0.844151.656
81_R93_R0.840881.650
28_F54_A0.83961.647
9_R71_R0.810911.591
32_V50_I0.796751.563
53_V95_E0.764481.500
19_T25_V0.742231.456
19_T55_W0.739351.451
16_L26_A0.736961.446
4_V96_I0.710231.393
7_I73_Y0.701211.376
80_T94_V0.696331.366
57_K60_E0.695651.365
83_Y93_R0.691381.356
29_S51_N0.679961.334
16_L63_A0.674271.323
98_A101_I0.663581.302
34_R77_R0.649481.274
14_P26_A0.648491.272
77_R99_D0.643811.263
67_K70_D0.616281.209
34_R46_K0.60281.183
66_L72_V0.599761.177
11_G29_S0.580061.138
31_A49_W0.577481.133
79_R97_I0.574761.128
31_A47_T0.573421.125
75_E100_N0.568781.116
71_R102_E0.556431.092
38_D42_E0.556081.091
37_K43_G0.55451.088
24_P60_E0.553861.087
34_R48_D0.552171.083
65_Y103_F0.546341.072
54_A98_A0.543741.067
7_I71_R0.534571.049
6_L30_L0.527671.035
46_K79_R0.512441.005
38_D44_D0.51031.001
30_L72_V0.50930.999
13_D68_K0.50150.984
9_R31_A0.498280.978
54_A58_L0.492270.966
77_R97_I0.486890.955
19_T23_T0.486140.954
55_W97_I0.481460.945
50_I96_I0.477570.937
83_Y91_R0.47490.932
36_F44_D0.474690.931
51_N93_R0.473620.929
61_N103_F0.466280.915
6_L96_I0.456020.895
9_R33_N0.453560.890
38_D43_G0.449730.882
76_G96_I0.444060.871
60_E64_E0.443070.869
35_R45_E0.438780.861
80_T92_Y0.43730.858
53_V81_R0.436920.857
24_P63_A0.43660.857
4_V78_L0.43640.856
54_A101_I0.435510.854
48_D80_T0.431810.847
5_T73_Y0.426220.836
70_D103_F0.417550.819
61_N101_I0.411740.808
17_R27_R0.410230.805
10_L14_P0.404860.794
25_V55_W0.403530.792
62_V101_I0.400350.785
19_T22_G0.398570.782
33_N47_T0.389320.764
12_K15_E0.388640.763
6_L32_V0.387950.761
50_I80_T0.378780.743
27_R51_N0.372950.732
57_K61_N0.370710.727
33_N45_E0.370240.726
36_F43_G0.370130.726
35_R43_G0.368360.723
16_L24_P0.363750.714
58_L61_N0.361970.710
78_L96_I0.353980.695
6_L78_L0.351980.691
4_V76_G0.349780.686
32_V48_D0.334610.657
17_R25_V0.331590.651
61_N65_Y0.329630.647
10_L72_V0.326210.640
30_L74_V0.324060.636
53_V97_I0.313570.615
73_Y102_E0.313520.615
25_V53_V0.31090.610
18_Y60_E0.306650.602
23_T55_W0.304940.598
61_N64_E0.303080.595
84_E88_G0.30160.592
28_F98_A0.300890.590
38_D46_K0.300250.589
12_K51_N0.299740.588
7_I102_E0.299080.587
83_Y92_Y0.298350.585
86_K89_Q0.297810.584
82_T92_Y0.294460.578
26_A63_A0.293580.576
2_N78_L0.292330.574
41_G44_D0.291230.571
27_R53_V0.288030.565
5_T75_E0.287270.564
26_A62_V0.287180.563
14_P62_V0.285270.560
16_L59_A0.283590.556
5_T102_E0.283360.556
56_G59_A0.283080.555
14_P28_F0.281840.553
52_V74_V0.280740.551
56_G97_I0.280650.551
54_A74_V0.278170.546
48_D79_R0.277630.545
37_K42_E0.276910.543
37_K41_G0.274750.539
11_G31_A0.270260.530
58_L101_I0.265790.521
18_Y22_G0.264760.519
78_L94_V0.2620.514
74_V96_I0.259230.509
28_F74_V0.258710.508
27_R81_R0.258350.507
9_R68_K0.255490.501
66_L101_I0.252670.496
51_N92_Y0.252220.495
36_F42_E0.246740.484
56_G60_E0.245850.482
10_L13_D0.244070.479
3_K99_D0.239860.471
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
3tqyA199.9-0.046
2vw9A199.9-0.042
1z9fA0.990499.9-0.036
1eqqA199.9-0.035
1se8A199.9-0.033
3pgzA199.9-0.031
1qvcA199.9-0.028
3ullA199.9-0.024
1se8A0.990499.9-0.024
3vdyA0.980899.9-0.024

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