GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CutA1 - CutA1 divalent ion tolerance protein
Pfam: PF03091 (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: CL0089
Length: 102
Sequences: 1110
Seq/Len: 10.88
HH_delta: -0.06 (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
24_E69_R0.775112.860
13_E75_P0.772392.850
63_F67_E0.707832.611
89_G94_L0.672672.482
22_V39_I0.617872.279
15_E48_E0.614912.269
9_P75_P0.567252.093
62_R65_E0.553422.042
27_A56_I0.55042.031
30_V56_I0.549142.026
69_R73_L0.549082.026
19_R48_E0.493551.821
43_E77_E0.476621.758
17_I73_L0.474391.750
6_T70_I0.468151.727
20_A69_R0.439741.622
6_T56_I0.40971.511
59_T62_R0.398931.472
53_L80_E0.398171.469
11_R15_E0.397711.467
4_V66_L0.396941.464
18_A32_I0.391091.443
8_C54_L0.391081.443
71_R92_A0.390371.440
21_L56_I0.389251.436
32_I52_V0.374381.381
40_Y49_E0.370861.368
67_E71_R0.369611.364
9_P13_E0.365891.350
10_D13_E0.354811.309
25_R41_R0.35391.306
31_N53_L0.34981.291
37_T48_E0.347031.280
5_Y80_E0.346561.279
63_F83_A0.34011.255
19_R23_E0.333481.230
5_Y53_L0.333121.229
13_E16_R0.325291.200
33_I53_L0.322171.189
41_R46_I0.317381.171
32_I39_I0.31671.168
20_A24_E0.316511.168
36_I53_L0.314881.162
69_R72_E0.305061.125
82_I86_I0.302951.118
30_V54_L0.3011.110
78_V90_N0.29951.105
33_I55_L0.296891.095
20_A73_L0.295141.089
86_I89_G0.290551.072
31_N36_I0.289261.067
15_E37_T0.288351.064
5_Y31_N0.286661.058
58_T66_L0.277321.023
43_E47_E0.27491.014
8_C52_V0.272931.007
18_A30_V0.272561.006
27_A30_V0.271571.002
80_E93_Y0.265410.979
29_C38_S0.263190.971
16_R20_A0.254740.940
11_R50_E0.249570.921
29_C57_K0.24510.904
22_V27_A0.243140.897
71_R81_I0.242630.895
11_R37_T0.232060.856
22_V41_R0.232020.856
68_E72_E0.231780.855
6_T31_N0.22620.835
5_Y55_L0.216830.800
8_C75_P0.216390.798
21_L66_L0.215980.797
10_D52_V0.215440.795
63_F90_N0.214450.791
63_F81_I0.214010.790
67_E88_K0.211580.781
33_I36_I0.210890.778
7_T36_I0.20560.759
78_V92_A0.205250.757
5_Y84_L0.204460.754
14_A54_L0.204270.754
35_P52_V0.203280.750
21_L27_A0.201640.744
8_C17_I0.195810.722
7_T53_L0.194050.716
37_T50_E0.192580.710
3_L94_L0.19220.709
11_R34_P0.192130.709
18_A56_I0.189470.699
20_A23_E0.189360.699
64_D67_E0.189310.698
29_C76_Y0.187590.692
65_E68_E0.186880.689
3_L84_L0.183050.675
16_R72_E0.182830.675
86_I97_I0.180050.664
70_I81_I0.179640.663
16_R73_L0.17590.649
31_N80_E0.175360.647
89_G93_Y0.170740.630
14_A32_I0.169140.624
38_S57_K0.169050.624
14_A18_A0.167860.619
12_E16_R0.166810.615
42_W45_K0.165120.609
83_A87_D0.164870.608
24_E97_I0.16370.604
18_A62_R0.163210.602
14_A52_V0.162980.601
67_E90_N0.160850.593
57_K80_E0.159960.590
58_T63_F0.15980.590
91_P95_E0.159690.589
4_V81_I0.159490.588
35_P53_L0.158040.583
58_T62_R0.157890.582
39_I46_I0.15770.582
21_L69_R0.156840.579
3_L55_L0.156690.578
17_I69_R0.156090.576
64_D68_E0.155580.574
56_I80_E0.15520.573
3_L80_E0.154970.572
28_A57_K0.153940.568
8_C13_E0.153540.566
24_E95_E0.152650.563
6_T54_L0.151730.560
6_T35_P0.151110.557
56_I70_I0.150630.556
61_S68_E0.148180.547
11_R52_V0.147470.544
85_P94_L0.147370.544
42_W93_Y0.147280.543
85_P89_G0.147190.543
42_W89_G0.146320.540
15_E39_I0.145790.538
78_V97_I0.145470.537
60_A85_P0.145090.535
77_E84_L0.144790.534
48_E92_A0.144680.534
21_L29_C0.144370.533
11_R16_R0.14350.529
38_S80_E0.142690.526
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
4e98A1100-0.06
2zfhA1100-0.058
2nuhA1100-0.051
3gsdA1100-0.046
1naqA1100-0.043
3ahpA1100-0.04
2zomA1100-0.04
1nzaA1100-0.039
1oscA1100-0.037
1kr4A0.9902100-0.036

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