GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AP_endonuc_2_N - AP endonuclease family 2 C terminus
Pfam: PF07582 (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: 55
Sequences: 2363
Seq/Len: 42.96
HH_delta: 0.289 (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
37_A41_R1.335033.001
1_D4_R1.31632.959
34_R38_A1.012922.277
8_A11_E0.828021.861
8_A12_I0.817271.837
20_I36_A0.798421.795
39_F43_L0.761741.712
3_K7_S0.75981.708
38_A42_K0.748161.682
23_E32_G0.624611.404
4_R8_A0.610721.373
31_E35_E0.600051.349
7_S11_E0.58911.324
9_L14_Y0.579521.303
3_K43_L0.568231.277
28_D31_E0.565011.270
38_A41_R0.511011.149
34_R37_A0.506821.139
6_F44_L0.496951.117
20_I40_L0.496661.116
22_H32_G0.465931.047
9_L12_I0.464571.044
33_A36_A0.451551.015
35_E38_A0.425870.957
24_D27_M0.412450.927
10_R44_L0.389830.876
17_W22_H0.385330.866
6_F40_L0.38060.856
3_K42_K0.380320.855
10_R15_D0.373750.840
27_M35_E0.363390.817
23_E29_P0.363360.817
39_F42_K0.352890.793
31_E34_R0.350720.788
26_L32_G0.344650.775
22_H26_L0.344410.774
2_W22_H0.338450.761
22_H36_A0.329860.741
36_A40_L0.326790.735
2_W6_F0.31490.708
27_M32_G0.313520.705
32_G35_E0.312730.703
32_G36_A0.312630.703
27_M31_E0.311460.700
23_E33_A0.311110.699
19_S23_E0.308510.693
10_R18_L0.305220.686
2_W40_L0.298960.672
6_F18_L0.290240.652
4_R7_S0.280.629
36_A39_F0.27750.624
5_I22_H0.276610.622
6_F43_L0.27630.621
22_H33_A0.275080.618
10_R35_E0.273820.616
20_I33_A0.27330.614
14_Y18_L0.272740.613
22_H25_A0.269820.607
25_A36_A0.26480.595
19_S30_E0.264520.595
35_E39_F0.261850.589
30_E34_R0.256090.576
33_A37_A0.252860.568
3_K35_E0.252310.567
2_W39_F0.247420.556
23_E36_A0.235570.530
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
2zdsA198.10.289
3lmzA0.8545980.313
3kwsA0.8364980.319
2qw5A0.8909980.321
3p6lA0.872797.90.333
3qc0A0.897.90.338
3u0hA0.890997.80.348
2hk0A0.836497.80.348
2zvrA0.854597.80.351
3tvaA0.909197.80.354

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