GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_Mu_F - Phage Mu protein F like protein
Pfam: PF04233 (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: 112
Sequences: 981
Seq/Len: 8.76
HH_delta: 0.869 (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
71_A77_T0.747563.825
74_D108_R0.63753.262
15_K23_R0.56652.898
78_R109_C0.534822.736
78_R81_C0.510532.612
81_C104_H0.479172.452
74_D77_T0.415662.127
69_W103_E0.404452.069
72_T77_T0.381441.952
73_L77_T0.379991.944
41_R106_N0.379951.944
35_R39_I0.378561.937
68_R88_I0.377741.933
90_P93_D0.348381.782
69_W109_C0.339411.736
10_G20_I0.317451.624
78_R104_H0.31321.602
38_R42_T0.307751.575
35_R38_R0.294791.508
6_A20_I0.286271.465
15_K19_E0.282741.447
38_R106_N0.273761.401
84_L89_F0.267211.367
71_A74_D0.267191.367
43_E46_R0.259231.326
53_W67_W0.257331.317
71_A85_D0.252571.292
6_A23_R0.248651.272
37_E41_R0.248541.272
70_S110_T0.24831.270
76_R108_R0.245841.258
33_R37_E0.245281.255
79_P83_A0.239261.224
23_R26_D0.235851.207
72_T108_R0.235241.204
17_P21_A0.232381.189
77_T108_R0.23141.184
9_Q13_R0.228081.167
95_F99_N0.226231.157
16_S19_E0.222621.139
65_Y90_P0.222421.138
56_Y111_V0.220851.130
22_K25_R0.220681.129
83_A86_G0.21111.080
60_K63_G0.210241.076
20_I40_A0.207631.062
73_L82_R0.205551.052
56_Y67_W0.204211.045
67_W91_L0.196611.006
4_R8_T0.196031.003
7_V40_A0.1930.987
39_I43_E0.19250.985
91_L95_F0.191540.980
34_Y38_R0.18850.964
60_K91_L0.187920.961
74_D78_R0.187560.960
7_V10_G0.186930.956
89_F95_F0.185050.947
73_L85_D0.18490.946
38_R43_E0.182160.932
84_L99_N0.181860.930
81_C103_E0.17760.909
21_A37_E0.176640.904
26_D29_G0.175410.897
74_D109_C0.174470.893
69_W99_N0.172530.883
81_C109_C0.172480.882
81_C105_P0.171950.880
78_R82_R0.166770.853
53_W57_Q0.166440.852
103_E109_C0.165450.846
30_V36_A0.165220.845
50_A54_Q0.163920.839
57_Q60_K0.162680.832
54_Q57_Q0.162470.831
78_R105_P0.160410.821
18_Q22_K0.159170.814
6_A10_G0.157720.807
38_R105_P0.157240.804
6_A27_R0.15620.799
3_I36_A0.155520.796
78_R103_E0.153710.786
80_I104_H0.152570.781
7_V11_I0.151970.778
54_Q61_G0.151560.775
24_L27_R0.151210.774
71_A108_R0.151080.773
27_R34_Y0.149340.764
75_S82_R0.149140.763
67_W111_V0.149070.763
94_P100_Y0.148580.760
30_V34_Y0.147890.757
32_S36_A0.147360.754
100_Y111_V0.146470.749
52_R110_T0.145280.743
42_T46_R0.145020.742
71_A76_R0.144730.740
87_K90_P0.143970.737
21_A25_R0.143720.735
60_K67_W0.143540.734
10_G15_K0.143280.733
42_T105_P0.143010.732
39_I47_A0.142380.728
101_P111_V0.139560.714
6_A15_K0.138680.710
5_Q9_Q0.138180.707
69_W102_P0.13670.699
81_C102_P0.135940.695
65_Y88_I0.135760.695
77_T82_R0.135310.692
41_R76_R0.134540.688
50_A53_W0.133710.684
8_T12_E0.133550.683
52_R56_Y0.132070.676
20_I44_T0.132010.675
71_A82_R0.13120.671
69_W95_F0.130990.670
41_R45_A0.130790.669
37_E106_N0.130280.667
95_F100_Y0.12890.659
72_T85_D0.126760.649
69_W81_C0.126020.645
19_E98_S0.125930.644
24_L40_A0.125310.641
20_I24_L0.124950.639
80_I85_D0.124870.639
52_R55_Q0.124160.635
40_A69_W0.123420.631
71_A109_C0.12250.627
13_R19_E0.122320.626
48_Y52_R0.122080.625
80_I83_A0.121710.623
25_R32_S0.121430.621
84_L103_E0.120950.619
18_Q23_R0.120790.618
102_P111_V0.119560.612
45_A102_P0.119430.611
9_Q15_K0.119410.611
36_A40_A0.118640.607
60_K90_P0.11860.607
84_L98_S0.117970.604
69_W84_L0.117380.601
16_S72_T0.117240.600
80_I109_C0.117160.599
103_E111_V0.116850.598
41_R108_R0.116790.598
70_S85_D0.116340.595
29_G37_E0.116220.595
49_N60_K0.116140.594
30_V35_R0.115970.593
79_P82_R0.115920.593
84_L109_C0.115540.591
14_G51_A0.114590.586
7_V17_P0.114150.584
72_T75_S0.114140.584
9_Q21_A0.113990.583
84_L95_F0.113930.583
68_R86_G0.11370.582
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
3ob4A0.794672.60.869
3i3vA0.348228.60.899
2hl7A0.348219.60.906
2kw0A0.428615.10.911
2xd3A0.339313.30.913
1p90A0.410712.30.914
4ad9A0.562512.20.914
4b3nA0.87510.50.917
4aq4A0.36619.70.918
3kw2A0.61619.10.919
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