GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AhpC-TSA - AhpCTSA family
Pfam: PF00578 (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: CL0172
Length: 124
Sequences: 19174
Seq/Len: 154.63
HH_delta: -0.054 (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
27_P117_P3.098273.739
9_T17_T2.327642.809
26_K61_Q2.136422.578
12_D16_K2.016922.434
116_D120_K1.989142.400
116_D122_R1.928122.327
11_T17_T1.91892.316
49_N83_P1.843562.225
9_T19_S1.786652.156
5_A98_F1.756192.119
52_Y56_K1.748862.110
19_S22_D1.687752.037
115_I121_I1.543911.863
28_V61_Q1.490541.799
12_D18_V1.459761.762
51_L54_K1.447371.747
93_E97_A1.445851.745
34_P37_W1.399911.689
49_N53_K1.335061.611
7_D21_S1.334811.611
18_V23_L1.330331.605
7_D19_S1.262961.524
38_C41_C1.23851.495
27_P122_R1.206311.456
64_G84_F1.190931.437
74_K78_E1.176981.420
28_V119_G1.145611.382
31_F112_V1.14221.378
21_S24_K1.123281.355
33_W64_G1.105861.334
10_L87_L1.090171.316
52_Y83_P1.055581.274
13_S77_L1.051781.269
7_D20_L1.037291.252
73_I76_F1.021371.232
61_Q85_P1.019661.230
113_F121_I1.00471.212
53_K56_K0.982961.186
29_V114_L0.968731.169
46_P50_E0.934071.127
47_E51_L0.931751.124
89_D92_G0.913531.102
23_L28_V0.903991.091
42_Q80_Y0.880391.062
56_K61_Q0.876831.058
18_V22_D0.870271.050
93_E96_K0.866451.046
82_L85_P0.866131.045
8_F20_L0.865431.044
95_A101_E0.864561.043
67_T92_G0.859781.038
47_E50_E0.857891.035
27_P60_V0.847591.023
64_G86_V0.839811.013
32_F65_I0.837651.011
77_L86_V0.834991.008
13_S74_K0.832521.005
31_F44_E0.826410.997
44_E112_V0.819440.989
94_L98_F0.810550.978
5_A115_I0.80110.967
67_T95_A0.795670.960
45_L82_L0.787160.950
76_F80_Y0.780620.942
96_K101_E0.777380.938
75_Q78_E0.768950.928
14_D74_K0.756780.913
31_F45_L0.751310.907
49_N52_Y0.75070.906
23_L63_I0.745680.900
34_P38_C0.741330.895
27_P114_L0.741240.894
10_L94_L0.732110.883
38_C110_P0.729860.881
12_D87_L0.729520.880
30_L115_I0.726930.877
28_V63_I0.723090.873
54_K57_D0.721680.871
41_C44_E0.720470.869
53_K83_P0.707890.854
24_K28_V0.695330.839
29_V48_L0.694890.839
94_L97_A0.688970.831
92_G101_E0.68690.829
72_E75_Q0.684480.826
70_P88_S0.683580.825
114_L123_Y0.679650.820
75_Q79_E0.679280.820
29_V60_V0.670160.809
31_F48_L0.668470.807
37_W75_Q0.667630.806
28_V115_I0.666360.804
70_P74_K0.665440.803
51_L55_Y0.650570.785
52_Y62_V0.648010.782
66_S73_I0.646990.781
18_V87_L0.639240.771
46_P49_N0.637020.769
43_A46_P0.636860.769
49_N84_F0.63210.763
24_K119_G0.628340.758
31_F40_F0.62250.751
69_D72_E0.622070.751
12_D85_P0.621750.750
55_Y58_K0.617850.746
74_K77_L0.616640.744
48_L62_V0.611640.738
29_V112_V0.608380.734
56_K59_G0.604640.730
59_G117_P0.602460.727
35_T68_D0.601180.725
50_E54_K0.597720.721
42_Q76_F0.590680.713
53_K57_D0.588270.710
95_A108_A0.587610.709
63_I87_L0.579520.699
29_V62_V0.577020.696
33_W45_L0.571540.690
108_A111_A0.57150.690
91_D96_K0.571090.689
71_E75_Q0.560560.676
54_K58_K0.559140.675
92_G96_K0.559060.675
65_I94_L0.556170.671
37_W72_E0.543640.656
55_Y60_V0.542750.655
45_L64_G0.542360.654
43_A47_E0.541030.653
20_L28_V0.539130.651
100_I111_A0.530170.640
82_L86_V0.524510.633
23_L61_Q0.524410.633
27_P116_D0.520420.628
94_L100_I0.520230.628
92_G95_A0.515480.622
25_G119_G0.51450.621
25_G116_D0.514360.621
46_P80_Y0.511690.617
52_Y61_Q0.511190.617
65_I87_L0.507470.612
97_A100_I0.503740.608
33_W66_S0.499140.602
39_P43_A0.49650.599
32_F98_F0.496180.599
67_T108_A0.494340.597
50_E53_K0.491450.593
30_L65_I0.490330.592
27_P59_G0.484110.584
96_K99_G0.48250.582
32_F100_I0.481160.581
95_A100_I0.479530.579
78_E81_G0.478020.577
114_L122_R0.474190.572
10_L65_I0.472290.570
44_E48_L0.469930.567
91_D97_A0.467650.564
21_S119_G0.467330.564
5_A121_I0.467130.564
5_A20_L0.466460.563
27_P31_F0.46510.561
35_T72_E0.464530.561
60_V114_L0.461970.557
96_K100_I0.459210.554
20_L24_K0.457990.553
37_W80_Y0.4560.550
42_Q79_E0.454360.548
67_T101_E0.454140.548
33_W73_I0.453070.547
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
4g2eA199.8-0.054
4gqcA199.8-0.049
3qpmA199.8-0.008
2c0dA0.983999.8-0.007
3gknA199.8-0.005
3tjjA199.8-0.002
3u5rE0.943599.8-0.002
3drnA0.975899.8-0.001
3zrdA0.983999.80.001
3ixrA199.80.002

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