GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPR_19 - Tetratricopeptide repeat
Pfam: PF14559 (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: CL0020
Length: 68
Sequences: 59528
Seq/Len: 875.41
HH_delta: -0.192 (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
31_L47_L4.397032.386
6_D9_E4.330292.350
40_Q43_E4.317972.343
15_E31_L4.101422.225
28_R47_L4.098112.224
32_A48_L4.027512.185
14_L30_L3.94872.143
35_Y47_L3.539491.921
35_Y43_E3.452071.873
11_I38_Q3.092921.678
11_I35_Y2.990511.623
18_L28_R2.804731.522
11_I15_E2.724431.478
45_E49_E2.65731.442
17_A27_A2.488291.350
35_Y40_Q2.425981.316
7_Y34_C2.329951.264
28_R50_R2.303561.250
24_N27_A2.293061.244
58_N61_Y2.22011.205
21_N24_N2.149941.167
11_I31_L2.109931.145
29_L33_Q2.103691.141
25_P55_D2.073451.125
31_L35_Y2.056631.116
8_D38_Q2.010121.091
50_R54_Q2.001071.086
55_D58_N1.988921.079
13_L16_K1.948061.057
7_Y37_K1.887861.024
17_A20_R1.820890.988
18_L27_A1.810180.982
11_I34_C1.802690.978
9_E13_L1.75190.951
28_R51_L1.732590.940
51_L61_Y1.730910.939
33_Q37_K1.701270.923
16_K20_R1.687590.916
36_L41_Y1.677710.910
36_L44_A1.644820.893
50_R53_K1.641990.891
28_R54_Q1.626570.883
47_L50_R1.618750.878
9_E12_E1.616460.877
25_P51_L1.5910.863
30_L33_Q1.582810.859
52_L61_Y1.564150.849
32_A44_A1.55970.846
43_E46_E1.538410.835
34_C38_Q1.536140.834
7_Y38_Q1.506120.817
36_L48_L1.494520.811
33_Q36_L1.467550.796
32_A51_L1.464590.795
18_L31_L1.457030.791
16_K19_Q1.415810.768
11_I40_Q1.408030.764
25_P58_N1.384170.751
29_L61_Y1.294390.702
14_L34_C1.262310.685
49_E52_L1.250820.679
15_E35_Y1.242290.674
26_E30_L1.239920.673
41_Y45_E1.235770.671
51_L58_N1.224860.665
10_A14_L1.212260.658
10_A34_C1.199130.651
12_E16_K1.14610.622
29_L58_N1.13610.616
44_A48_L1.134080.615
33_Q48_L1.133890.615
49_E53_K1.127250.612
29_L51_L1.107770.601
13_L17_A1.105850.600
23_D54_Q1.072460.582
46_E50_R1.057280.574
8_D11_I1.052140.571
51_L54_Q1.05040.570
15_E19_Q1.046340.568
17_A24_N1.035980.562
46_E49_E1.005730.546
15_E47_L1.00410.545
12_E15_E1.002990.544
35_Y38_Q0.998370.542
17_A21_N0.993860.539
52_L56_P0.990060.537
7_Y10_A0.986910.536
42_D45_E0.986510.535
43_E47_L0.97760.530
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
4gywA198.4-0.192
3gyzA198.4-0.192
4i2zA198.4-0.183
4ga2A198.4-0.174
4gywA198.4-0.174
4i2zA198.3-0.155
3urzA198.2-0.14
2pziA198.2-0.136
2h6fA198.2-0.132
2vgxA198.2-0.128

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