GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_M23 - Peptidase family M23
Pfam: PF01551 (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: CL0105
Length: 96
Sequences: 7488
Seq/Len: 78
HH_delta: -0.087 (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
41_H47_T2.588763.288
74_N78_S2.120862.694
52_L70_G2.046382.599
10_A72_V2.032462.581
27_V55_V1.957652.486
15_P68_V1.953262.481
68_V71_T1.922152.441
19_P85_F1.903732.418
33_Y50_G1.751492.225
56_S71_T1.731462.199
19_P49_Y1.682422.137
23_K62_R1.671952.124
21_D64_K1.638152.081
38_I46_I1.515411.925
25_V40_Q1.504321.911
16_V52_L1.415231.798
17_Y68_V1.359311.726
12_E81_P1.35141.716
25_V46_I1.305351.658
57_V61_D1.301551.653
38_I48_V1.279081.625
88_R93_Y1.275071.619
53_D71_T1.257791.598
58_K61_D1.239471.574
64_K67_Q1.233541.567
54_S71_T1.229731.562
7_D84_H1.211.537
29_E35_N1.114671.416
22_G39_I1.102251.400
18_A39_I1.096881.393
52_L55_V1.079741.371
12_E53_D1.057341.343
36_Y48_V1.044991.327
72_V81_P1.035121.315
37_V52_L1.025631.303
3_H7_D1.017571.292
21_D65_A1.01731.292
20_A65_A1.010151.283
47_T85_F0.969771.232
11_P14_T0.968231.230
45_Y89_K0.951841.209
10_A14_T0.938291.192
26_F36_Y0.926491.177
20_A41_H0.917381.165
23_K40_Q0.903241.147
40_Q46_I0.890151.131
4_N93_Y0.883321.122
7_D82_H0.866681.101
48_V86_E0.836611.063
19_P47_T0.826181.049
30_D36_Y0.820491.042
47_T87_V0.814541.035
15_P71_T0.806971.025
89_K94_V0.805721.023
4_N86_E0.790741.004
26_F30_D0.787891.001
56_S68_V0.781780.993
45_Y87_V0.743370.944
26_F38_I0.727770.924
57_V67_Q0.709510.901
27_V57_V0.708150.899
48_V88_R0.70320.893
86_E93_Y0.690540.877
6_I96_P0.68360.868
35_N75_T0.675370.858
35_N55_V0.673110.855
26_F59_V0.664630.844
12_E74_N0.663390.843
46_I88_R0.650930.827
18_A66_G0.646990.822
3_H82_H0.6270.796
33_Y48_V0.607260.771
51_H76_G0.604160.767
39_I69_I0.599420.761
24_V57_V0.595160.756
21_D62_R0.595120.756
40_Q44_G0.590660.750
16_V72_V0.590040.749
51_H82_H0.579230.736
24_V39_I0.57720.733
9_A80_G0.555090.705
61_D67_Q0.548120.696
13_G53_D0.52130.662
33_Y36_Y0.520440.661
20_A45_Y0.499990.635
29_E36_Y0.497850.632
32_G77_N0.497570.632
34_G73_G0.479680.609
14_T72_V0.478740.608
41_H49_Y0.477410.606
18_A63_V0.476620.605
33_Y38_I0.475810.604
52_L83_L0.472570.600
46_I91_G0.470580.598
49_Y83_L0.456690.580
3_H84_H0.441610.561
16_V83_L0.439280.558
13_G81_P0.437390.556
36_Y50_G0.434560.552
39_I63_V0.433970.551
7_D51_H0.433410.550
74_N81_P0.430140.546
87_V94_V0.425970.541
74_N79_T0.423780.538
48_V77_N0.423320.538
24_V27_V0.419310.533
27_V59_V0.409690.520
30_D38_I0.407680.518
4_N88_R0.405920.516
56_S59_V0.39070.496
42_G45_Y0.388040.493
13_G72_V0.3840.488
56_S70_G0.382460.486
20_A85_F0.381630.485
51_H75_T0.375170.477
89_K92_Q0.366220.465
49_Y69_I0.36080.458
37_V69_I0.356980.453
42_G62_R0.356820.453
72_V83_L0.356540.453
37_V70_G0.355420.451
35_N53_D0.352330.448
16_V69_I0.348920.443
23_K60_G0.347740.442
25_V59_V0.346860.441
5_G84_H0.344580.438
40_Q43_N0.343350.436
3_H51_H0.341240.433
52_L56_S0.3380.429
78_S82_H0.336790.428
50_G86_E0.335990.427
75_T78_S0.335740.426
32_G50_G0.335370.426
79_T82_H0.332550.422
33_Y88_R0.332170.422
30_D88_R0.329130.418
34_G75_T0.323070.410
36_Y88_R0.322740.410
7_D78_S0.315770.401
16_V70_G0.314940.400
52_L72_V0.314440.399
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
2gu1A199.9-0.087
2hsiA199.9-0.08
3sluA0.989699.9-0.078
3tufB199.9-0.066
1qwyA199.9-0.033
3nyyA199.9-0.029
3it5A0.947999.90.008
3csqA0.989699.90.043
1ax3A0.937596.80.729
2gprA0.937596.80.729

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