GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_rep_O - Bacteriophage replication protein O
Pfam: PF04492 (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: 100
Sequences: 2625
Seq/Len: 26.25
HH_delta: 0.399 (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
57_N72_S0.831572.999
30_L66_L0.789472.847
85_I92_G0.654852.361
79_I86_R0.580722.094
69_D73_K0.560782.022
15_T18_A0.53911.944
30_L70_H0.527081.901
29_D32_G0.515171.858
79_I85_I0.493631.780
76_N80_R0.478491.725
31_S77_E0.472351.703
52_M90_R0.465461.678
77_E81_R0.447741.615
35_L78_L0.446921.612
18_A22_L0.430841.554
42_I93_V0.429071.547
34_Q74_A0.413521.491
68_R72_S0.410391.480
37_I60_I0.3981.435
57_N68_R0.396621.430
64_T71_V0.378581.365
31_S81_R0.377161.360
31_S74_A0.374051.349
58_S68_R0.370351.336
24_A36_K0.369991.334
66_L71_V0.357451.289
58_S62_E0.35211.270
76_N79_I0.350831.265
78_L83_V0.346241.249
37_I64_T0.344581.243
24_A40_A0.339511.224
35_L39_L0.337721.218
37_I63_M0.33551.210
74_A77_E0.331811.197
22_L25_L0.328511.185
28_A36_K0.313741.131
60_I71_V0.296711.070
48_W51_K0.287031.035
34_Q64_T0.282541.019
75_L86_R0.280021.010
23_D26_L0.276850.998
86_R91_I0.272310.982
34_Q60_I0.268520.968
37_I55_I0.25040.903
57_N76_N0.246940.890
87_D90_R0.246070.887
57_N71_V0.245620.886
20_E40_A0.240740.868
66_L70_H0.239770.865
19_N23_D0.237370.856
67_S70_H0.235750.850
19_N59_Q0.235220.848
68_R71_V0.235190.848
16_R19_N0.234570.846
35_L83_V0.232330.838
41_I45_T0.231240.834
70_H73_K0.228730.825
77_E80_R0.225870.815
28_A65_G0.224630.810
74_A78_L0.221430.798
48_W52_M0.220570.795
57_N73_K0.220520.795
30_L74_A0.219960.793
56_S59_Q0.218990.790
38_L91_I0.217950.786
72_S76_N0.21490.775
61_A66_L0.214240.773
46_Y51_K0.210660.760
31_S34_Q0.209880.757
31_S78_L0.208540.752
35_L67_S0.208040.750
73_K88_G0.207250.747
87_D92_G0.204460.737
50_K85_I0.200550.723
45_T50_K0.199610.720
76_N86_R0.197830.713
32_G35_L0.195970.707
21_L40_A0.193970.699
23_D62_E0.193560.698
69_D72_S0.193160.697
55_I63_M0.192470.694
15_T19_N0.190850.688
53_D75_L0.186990.674
50_K90_R0.184880.667
24_A33_R0.184260.664
59_Q62_E0.183760.663
57_N69_D0.181870.656
41_I53_D0.180430.651
23_D27_R0.179960.649
82_G85_I0.179740.648
54_R82_G0.179580.648
46_Y49_N0.179230.646
52_M92_G0.179180.646
58_S89_K0.178860.645
21_L24_A0.177040.638
79_I89_K0.175470.633
24_A28_A0.173670.626
23_D29_D0.17290.623
24_A27_R0.172670.623
25_L88_G0.171250.618
28_A58_S0.171020.617
34_Q37_I0.170860.616
36_K40_A0.170320.614
58_S88_G0.170280.614
40_A79_I0.169580.612
26_L50_K0.169510.611
67_S74_A0.167680.605
34_Q71_V0.165270.596
42_I59_Q0.164630.594
56_S89_K0.164380.593
40_A44_K0.16390.591
32_G38_L0.163750.590
45_T48_W0.163230.589
38_L41_I0.163190.588
35_L65_G0.162610.586
46_Y78_L0.162310.585
34_Q78_L0.16140.582
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
3iwzA0.9698.90.399
3la7A0.9998.90.41
2gauA0.9998.90.417
3kccA0.9698.90.417
3rypA0.9698.90.419
2bgcA0.9998.80.422
4i2oA0.9998.80.422
2oz6A0.9698.80.423
1o5lA0.9798.80.425
3d0sA0.9998.80.43

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