GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPR_5 - Tetratrico peptide repeat
Pfam: PF12688 (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: 120
Sequences: 69736
Seq/Len: 581.13
HH_delta: -0.133 (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
78_R97_W4.123442.292
90_R93_E4.111822.286
16_R19_E4.065362.260
53_R56_E4.058772.256
4_L23_L3.939072.190
41_L60_L3.90392.170
81_L97_W3.691552.052
62_E81_L3.653342.031
45_A61_L3.513191.953
82_A98_L3.482031.936
44_L60_L3.342991.858
25_R44_L3.299971.834
8_A24_Y3.228211.794
7_L23_L3.197251.777
85_L97_W3.138251.744
11_H19_E3.062831.703
48_L56_E2.92991.629
48_L60_L2.910981.618
11_H23_L2.897071.610
85_L93_E2.712641.508
24_Y43_Q2.634531.464
58_L62_E2.489741.384
95_L99_L2.439141.356
21_I25_R2.405121.337
61_L80_F2.298811.278
21_I51_L2.261871.257
10_A14_L2.200631.223
48_L53_R2.193721.219
58_L88_L2.156831.199
28_L41_L2.113431.175
58_L85_L2.112631.174
85_L90_R2.111441.174
78_R100_E2.070641.151
21_I48_L2.005521.115
27_A40_A1.987531.105
41_L63_E1.961381.090
64_A77_L1.931451.074
46_S80_F1.916591.065
68_F74_N1.910671.062
4_L26_R1.900871.057
11_H16_R1.876591.043
17_E47_T1.861741.035
65_L78_R1.857141.032
54_Y84_A1.837281.021
21_I44_L1.764820.981
31_G34_G1.751870.974
9_W43_Q1.734750.964
7_L11_H1.724420.959
54_Y87_N1.701380.946
93_E96_E1.691290.940
81_L85_L1.680.934
78_R101_A1.672860.930
55_D88_L1.665270.926
82_A101_A1.652650.919
44_L48_L1.651030.918
75_A101_A1.649060.917
18_E51_L1.64480.914
58_L81_L1.643170.913
42_I80_F1.616040.898
74_N77_L1.613130.897
12_D43_Q1.609390.895
49_R84_A1.599650.889
56_E59_A1.59190.885
12_D47_T1.587850.883
38_R64_A1.567880.872
21_I47_T1.56340.869
8_A27_A1.559840.867
58_L84_A1.554190.864
38_R68_F1.547630.860
84_A88_L1.522530.846
49_R80_F1.521970.846
86_Y98_L1.514430.842
19_E22_P1.512360.841
79_V83_L1.501320.835
23_L26_R1.495310.831
63_E67_E1.485860.826
49_R87_N1.484870.825
9_W13_S1.479740.823
47_T51_L1.472280.818
26_R30_A1.468270.816
5_Y40_A1.468260.816
45_A64_A1.464530.814
5_Y43_Q1.463370.813
5_Y9_W1.452050.807
86_Y91_P1.451640.807
97_W100_E1.448830.805
17_E50_N1.446870.804
28_L40_A1.412370.785
100_E103_A1.399150.778
82_A94_A1.398180.777
60_L63_E1.397870.777
63_E66_E1.388140.772
83_L86_Y1.385870.770
54_Y88_L1.371950.763
65_L81_L1.371620.762
9_W12_D1.350040.750
28_L44_L1.344430.747
42_I77_L1.342350.746
45_A57_A1.329830.739
46_S50_N1.326560.737
83_L87_N1.325410.737
86_Y94_A1.298920.722
19_E23_L1.286760.715
7_L10_A1.285640.715
49_R57_A1.27870.711
27_A30_A1.27690.710
17_E51_L1.275390.709
65_L77_L1.274280.708
25_R60_L1.267730.705
46_S49_R1.267240.704
41_L67_E1.264180.703
12_D24_Y1.25940.700
39_R76_A1.258550.700
42_I46_S1.240260.689
41_L64_A1.232770.685
12_D50_N1.223890.680
49_R61_L1.214390.675
26_R29_A1.209490.672
21_I53_R1.203310.669
49_R54_Y1.200540.667
12_D17_E1.18180.657
58_L90_R1.177410.654
62_E97_W1.164310.647
80_F83_L1.163250.647
22_P26_R1.144670.636
8_A20_A1.137850.632
93_E97_W1.132710.630
57_A84_A1.119620.622
6_E10_A1.115860.620
57_A61_L1.099210.611
25_R29_A1.095790.609
24_Y47_T1.091160.607
79_V101_A1.0840.603
96_E100_E1.078070.599
91_P95_L1.072090.596
38_R74_N1.066240.593
4_L30_A1.058710.589
59_A63_E1.057870.588
54_Y58_L1.05680.587
43_Q46_S1.055360.587
56_E60_L1.051940.585
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
4gywA0.9599.4-0.133
4gywA0.9599.4-0.095
4i2zA0.966799.3-0.047
2h6fA0.9599.2-0.027
3gyzA0.941799.2-0.013
2pziA0.941799.2-0.007
2pl2A0.9599.20.008
3qkyA199.10.013
4ga2A0.941799.10.015
4abnA0.941799.10.015

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