GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_S24 - Peptidase S24-like
Pfam: PF00717 (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: CL0299
Length: 70
Sequences: 7314
Seq/Len: 104.49
HH_delta: 0.064 (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
4_G13_D1.844922.909
12_K15_D1.750922.761
45_R58_S1.739522.743
5_D8_E1.399112.206
6_S44_K1.374312.167
2_V17_V1.347492.125
1_R16_I1.335862.106
8_E12_K1.178781.859
20_D23_S1.113941.756
11_I30_I1.079661.702
2_V11_I1.047381.651
19_V32_V0.960811.515
35_I38_D0.933691.472
35_I42_Y0.921981.454
49_E54_I0.915451.443
5_D13_D0.915051.443
47_V54_I0.903061.424
30_I45_R0.89831.416
27_D47_V0.816641.288
47_V56_I0.793921.252
49_E52_G0.784541.237
2_V43_I0.766381.208
9_P58_S0.745941.176
27_D49_E0.745031.175
17_V43_I0.730731.152
34_K41_L0.729491.150
32_V43_I0.728081.148
3_E13_D0.725871.144
33_V42_Y0.719931.135
42_Y57_S0.700811.105
25_P31_V0.688271.085
25_P46_V0.68771.084
4_G44_K0.686561.082
33_V44_K0.671521.059
9_P45_R0.669681.056
27_D48_G0.64471.016
31_V46_V0.623370.983
11_I43_I0.622570.982
10_T45_R0.621840.980
26_K29_D0.567810.895
8_E13_D0.514580.811
53_I57_S0.509670.804
7_M30_I0.500620.789
4_G11_I0.489990.773
48_G52_G0.488580.770
9_P12_K0.473330.746
27_D52_G0.466090.735
34_K37_G0.462760.730
1_R14_G0.452750.714
34_K38_D0.451830.712
17_V32_V0.44240.698
48_G51_G0.433590.684
19_V43_I0.424310.669
8_E58_S0.421910.665
5_D37_G0.415610.655
48_G53_I0.407680.643
54_I58_S0.401560.633
11_I15_D0.387410.611
10_T15_D0.385930.608
44_K58_S0.384830.607
46_V54_I0.371850.586
3_E11_I0.364160.574
27_D53_I0.342580.540
50_P53_I0.325380.513
10_T30_I0.324890.512
28_G56_I0.319130.503
7_M44_K0.314880.496
47_V57_S0.313870.495
16_I37_G0.309290.488
35_I41_L0.306560.483
33_V46_V0.305910.482
5_D28_G0.300560.474
4_G7_M0.298610.471
37_G41_L0.295660.466
24_E51_G0.294060.464
35_I55_L0.291470.460
49_E53_I0.291450.460
28_G47_V0.277940.438
13_D44_K0.277710.438
30_I36_D0.275940.435
16_I20_D0.25960.409
7_M10_T0.258490.408
19_V41_L0.255140.402
16_I41_L0.25390.400
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
3k2zA0.971499.30.064
1jhfA0.971499.20.078
3bdnA0.985799.20.081
1umuA0.957199.20.084
2hnfA0.985799.20.087
1kcaA0.985799.20.093
1b12A0.971498.80.248
4k8wA0.998.70.26
2fjrA0.928697.90.437
2ayiA0.957132.40.798

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