GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RecO_C - Recombination protein O C terminal
Pfam: PF02565 (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: 118
Sequences: 1605
Seq/Len: 13.6
HH_delta: 0.233 (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
12_Y56_E0.395882.724
13_I37_A0.392862.703
27_N62_L0.294982.030
16_L56_E0.292392.012
57_L77_L0.271931.871
92_P96_R0.262191.804
20_L63_L0.250371.723
17_L34_L0.250181.722
56_E60_L0.248061.707
17_L55_F0.246211.694
3_D6_R0.23411.611
12_Y52_L0.210051.445
17_L21_L0.208941.438
22_P25_E0.208791.437
21_L30_L0.208611.436
12_Y16_L0.202061.390
107_Q113_R0.201981.390
12_Y103_E0.194511.339
57_L102_L0.194181.336
46_D95_R0.190711.312
97_E104_Q0.19011.308
73_L90_L0.185921.279
81_D84_K0.184461.269
33_L36_A0.183791.265
29_E93_E0.182781.258
73_L77_L0.182171.254
19_R112_R0.180971.245
36_A40_A0.179821.237
56_E99_L0.178371.227
57_L67_P0.177441.221
98_L101_L0.175381.207
97_E100_R0.173561.194
103_E117_L0.173411.193
13_I34_L0.172981.190
13_I77_L0.17031.172
56_E103_E0.169941.169
29_E33_L0.166831.148
10_A41_L0.164211.130
35_L39_D0.162731.120
19_R111_G0.16251.118
33_L62_L0.162481.118
59_L63_L0.16121.109
29_E62_L0.160421.104
10_A15_E0.160221.103
65_F111_G0.159471.097
37_A50_L0.158371.090
30_L55_F0.153911.059
72_K76_Y0.15311.054
44_G96_R0.152691.051
14_A34_L0.152511.049
71_L74_L0.151441.042
17_L59_L0.151081.040
96_R100_R0.15061.036
15_E19_R0.148521.022
67_P74_L0.147551.015
53_I110_L0.147521.015
60_L73_L0.147391.014
38_L116_S0.147351.014
24_G27_N0.147141.013
70_S75_R0.147131.012
52_L56_E0.146861.011
58_K88_I0.146261.006
19_R114_L0.144390.994
4_L8_A0.142330.979
108_Y111_G0.141680.975
15_E103_E0.140810.969
7_L12_Y0.140220.965
32_D35_L0.140190.965
28_P32_D0.139780.962
20_L59_L0.139610.961
49_L90_L0.139220.958
21_L38_L0.138230.951
77_L98_L0.137140.944
12_Y117_L0.136450.939
49_L52_L0.135810.935
55_F63_L0.135420.932
30_L109_H0.134420.925
72_K75_R0.13330.917
70_S79_R0.132940.915
81_D93_E0.131780.907
34_L55_F0.131240.903
74_L102_L0.131230.903
86_E114_L0.131170.903
9_Y90_L0.131080.902
100_R104_Q0.129520.891
56_E117_L0.129490.891
26_P29_E0.129160.889
107_Q117_L0.12870.886
85_L89_S0.128480.884
58_K82_L0.128190.882
37_A55_F0.128120.882
37_A82_L0.128020.881
77_L81_D0.127490.877
3_D8_A0.127080.874
61_K66_G0.125960.867
79_R93_E0.125680.865
37_A41_L0.1250.860
46_D49_L0.124820.859
38_L50_L0.124660.858
48_W52_L0.124270.855
4_L7_L0.122790.845
34_L117_L0.122760.845
47_P51_L0.122640.844
30_L59_L0.122120.840
71_L80_N0.12150.836
18_D23_E0.121230.834
24_G47_P0.120810.831
55_F96_R0.120680.830
102_L106_L0.120510.829
45_E89_S0.120130.827
5_E31_F0.119640.823
25_E65_F0.119240.821
79_R84_K0.118620.816
49_L99_L0.118330.814
99_L103_E0.118130.813
43_E61_K0.117790.811
27_N30_L0.117370.808
103_E106_L0.117260.807
43_E86_E0.117120.806
7_L91_S0.116550.802
94_T97_E0.11610.799
44_G75_R0.115990.798
45_E93_E0.115270.793
74_L98_L0.115240.793
52_L55_F0.115150.792
23_E99_L0.114520.788
36_A39_D0.114270.786
79_R82_L0.113540.781
17_L30_L0.113380.780
10_A14_A0.113340.780
10_A18_D0.112490.774
69_L74_L0.112260.773
11_S59_L0.112240.772
53_I72_K0.111940.770
104_Q108_Y0.111640.768
13_I30_L0.111490.767
85_L90_L0.11120.765
88_I107_Q0.111110.765
90_L98_L0.111060.764
32_D36_A0.110660.762
39_D43_E0.110550.761
39_D87_R0.110490.760
75_R79_R0.110380.760
4_L88_I0.110090.758
20_L101_L0.109640.754
30_L102_L0.109490.753
8_A65_F0.109380.753
59_L99_L0.109250.752
78_L94_T0.108650.748
37_A40_A0.108130.744
12_Y106_L0.107930.743
80_N83_D0.107590.740
50_L95_R0.107570.740
11_S116_S0.107460.739
67_P102_L0.107090.737
8_A88_I0.106990.736
9_Y51_L0.10690.736
4_L10_A0.105920.729
19_R110_L0.105570.726
32_D85_L0.105530.726
57_L74_L0.105450.726
4_L14_A0.105390.725
8_A19_R0.105340.725
51_L95_R0.105120.723
9_Y50_L0.105110.723
84_K94_T0.104790.721
65_F105_Y0.104730.721
21_L27_N0.104580.720
17_L27_N0.104540.719
17_L110_L0.104370.718
12_Y99_L0.104260.717
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
1u5kA0.983199.60.233
3q8dA0.974699.40.353
3b0bC0.457619.40.881
4e45B0.508514.90.887
4draE0.516912.10.891
3i4zA0.85598.50.898
3huuA0.50858.30.899
4e0tA0.95765.50.906
3o2kA0.80515.10.907
3hmmA0.415350.908

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