GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CAT_RBD - CAT RNA binding domain
Pfam: PF03123 (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. )
Length: 59
Sequences: 699
Seq/Len: 11.85
HH_delta: 0.017 (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
7_L13_L0.630043.156
14_A22_V0.617793.095
33_K37_D0.49832.496
16_D20_Q0.429282.150
12_V30_G0.383591.921
3_I6_V0.371561.861
31_F45_E0.361791.812
46_K50_L0.316421.585
12_V24_V0.314851.577
5_K8_N0.311291.559
21_E46_K0.276781.386
4_K15_K0.275271.379
5_K21_E0.274971.377
7_L11_V0.273711.371
27_K30_G0.267441.340
40_D43_K0.264751.326
9_N46_K0.21631.083
18_N53_E0.215391.079
32_G55_D0.213551.070
44_I48_F0.204811.026
5_K25_M0.204681.025
22_V49_V0.202941.017
41_E44_I0.200811.006
9_N23_I0.200561.005
34_K37_D0.200061.002
24_V47_V0.200041.002
14_A24_V0.192750.966
3_I11_V0.190120.952
26_G40_D0.188330.943
6_V35_P0.186960.937
25_M58_R0.186360.934
52_D57_E0.178310.893
29_I59_F0.17780.891
13_L27_K0.176340.883
2_K38_E0.174830.876
32_G43_K0.174780.876
6_V34_K0.173730.870
23_I57_E0.173630.870
28_G31_F0.1730.867
11_V25_M0.171620.860
9_N31_F0.168180.842
1_M44_I0.166760.835
10_N25_M0.166350.833
5_K55_D0.165930.831
11_V23_I0.165310.828
52_D55_D0.165120.827
39_I42_S0.162350.813
54_E57_E0.161050.807
1_M24_V0.160840.806
36_G39_I0.158540.794
38_E45_E0.157340.788
45_E48_F0.157230.788
16_D48_F0.156760.785
2_K20_Q0.15540.778
52_D59_F0.155370.778
11_V27_K0.154820.776
7_L15_K0.153560.769
11_V48_F0.151560.759
32_G36_G0.151420.758
15_K32_G0.150030.752
6_V29_I0.149950.751
14_A30_G0.149530.749
45_E59_F0.14940.748
19_G41_E0.149190.747
31_F34_K0.148680.745
4_K32_G0.148160.742
20_Q38_E0.148090.742
17_D38_E0.147770.740
29_I49_V0.147330.738
24_V29_I0.146530.734
24_V39_I0.145830.730
23_I55_D0.144450.724
6_V12_V0.144210.722
10_N13_L0.142870.716
29_I45_E0.142690.715
24_V30_G0.142660.715
3_I59_F0.142260.713
3_I33_K0.141740.710
14_A47_V0.140140.702
23_I27_K0.139660.700
5_K9_N0.139350.698
2_K52_D0.139310.698
7_L49_V0.137840.690
13_L59_F0.136010.681
4_K23_I0.135610.679
14_A23_I0.13520.677
4_K13_L0.135130.677
26_G44_I0.134730.675
11_V21_E0.133690.670
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
3rioA199.80.017
1l1cA0.932299.70.05
1auuA0.932299.70.059
1ah9A0.949217.90.87
1svcP0.779712.50.879
1nfkA0.77978.20.888
2oqkA0.98317.90.889
1hr0W0.94927.40.89
1a3qA0.77976.50.893
4efzA16.30.893

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