GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Rad51 - Rad51
Pfam: PF08423 (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: CL0023
Length: 256
Sequences: 5914
Seq/Len: 23.1
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
73_G135_K0.814633.259
74_K135_K0.775073.100
55_C184_T0.750233.001
21_S28_D0.747512.990
59_A138_V0.741962.968
22_T35_I0.724812.899
35_I58_L0.68592.744
227_E244_S0.663232.653
218_L230_A0.625822.503
59_A75_V0.601712.407
23_G28_D0.597162.389
190_K193_S0.576642.307
62_V136_L0.572962.292
37_T178_N0.521122.084
122_L137_I0.520152.081
41_T180_A0.518292.073
41_T216_T0.515572.062
99_D106_N0.510792.043
88_R92_I0.509992.040
189_T208_H0.509052.036
174_A181_V0.504652.019
35_I180_A0.497851.991
26_S29_E0.484381.938
22_T28_D0.480381.922
31_L216_T0.468071.872
27_L218_L0.462461.850
55_C138_V0.458391.834
40_I171_K0.455651.823
37_T135_K0.450081.800
25_K29_E0.431311.725
108_F132_S0.417571.670
137_I181_V0.41051.642
229_V242_S0.408141.633
62_V75_V0.405181.621
88_R91_Q0.402491.610
42_E214_V0.401461.606
76_V134_I0.383991.536
58_L136_L0.382971.532
136_L180_A0.381781.527
206_L217_R0.38151.526
59_A77_Y0.368281.473
173_L177_Y0.366751.467
81_E186_Q0.356181.425
63_Q107_I0.351951.408
220_L230_A0.351031.404
45_G220_L0.348361.393
219_F233_V0.344761.379
35_I182_V0.334331.337
18_S37_T0.332861.331
36_P39_S0.325251.301
20_I180_A0.324841.299
61_N64_L0.3221.288
172_R176_K0.32161.286
235_S238_L0.32141.286
136_L182_V0.314141.257
75_V136_L0.313221.253
55_C77_Y0.31191.248
27_L31_L0.311121.244
167_A213_A0.309521.238
137_I179_I0.307721.231
216_T235_S0.306141.225
74_K133_K0.305441.222
110_I121_L0.302921.212
54_L220_L0.302251.209
117_E120_E0.299481.198
173_L179_I0.295451.182
133_K177_Y0.294231.177
224_R227_E0.287251.149
74_K106_N0.286461.146
231_T242_S0.284841.139
187_V219_F0.283481.134
174_A180_A0.280121.120
72_G106_N0.279171.117
48_G237_S0.277151.109
223_G229_V0.276091.104
77_Y138_V0.275191.101
42_E217_R0.274791.099
170_L181_V0.272681.091
114_D117_E0.272041.088
214_V217_R0.271681.087
53_Q88_R0.270231.081
48_G234_K0.268891.076
138_V182_V0.265581.062
167_A183_V0.265281.061
38_G178_N0.264261.057
63_Q75_V0.263271.053
130_S177_Y0.263051.052
59_A63_Q0.261571.046
37_T73_G0.26151.046
19_R33_G0.259251.037
123_E173_L0.257931.032
93_A96_F0.255791.023
78_I137_I0.253651.015
173_L181_V0.253341.013
40_I167_A0.252751.011
113_F121_L0.2480.992
85_S88_R0.246560.986
170_L174_A0.245370.981
235_S239_P0.240540.962
39_S237_S0.239490.958
56_L89_L0.23930.957
62_V73_G0.238170.953
54_L58_L0.238060.952
114_D148_S0.237790.951
82_G236_P0.236640.947
43_I182_V0.236530.946
74_K108_F0.235970.944
218_L232_I0.235070.940
30_L243_A0.233640.935
171_K213_A0.233410.934
55_C182_V0.232870.931
45_G51_K0.232030.928
31_L34_G0.231940.928
42_E210_W0.231810.927
169_I172_R0.230920.924
113_F117_E0.228930.916
40_I170_L0.228660.915
30_L241_G0.228020.912
44_V219_F0.227620.910
57_Q61_N0.225890.904
45_G49_S0.224540.898
46_E219_F0.224340.897
36_P216_T0.223490.894
74_K132_S0.222790.891
76_V137_I0.220270.881
87_E91_Q0.218870.875
171_K215_T0.217480.870
55_C59_A0.217340.869
120_E123_E0.216760.867
26_S243_A0.215640.863
142_I210_W0.215110.860
167_A210_W0.215110.860
78_I122_L0.214790.859
215_T236_P0.214190.857
220_L228_R0.214080.856
223_G227_E0.212760.851
43_I218_L0.212410.850
119_L169_I0.211540.846
160_Q164_A0.210550.842
117_E121_L0.210040.840
137_I173_L0.209850.839
46_E49_S0.20980.839
192_D219_F0.206220.825
158_E162_M0.205390.822
112_V115_L0.203620.814
86_P90_Q0.203290.813
74_K134_I0.202920.812
221_S231_T0.202110.808
176_K180_A0.197970.792
30_L235_S0.197410.790
20_I62_V0.197290.789
58_L62_V0.197270.789
115_L119_L0.196760.787
73_G136_L0.196240.785
60_V64_L0.196110.784
56_L77_Y0.194470.778
40_I183_V0.194210.777
109_V112_V0.193890.776
104_L107_I0.193430.774
89_L92_I0.192950.772
141_S212_H0.192730.771
108_F111_R0.189920.760
73_G133_K0.189130.757
141_S184_T0.188620.754
168_R171_K0.18830.753
32_G123_E0.187650.751
39_S216_T0.186910.748
26_S30_L0.186410.746
80_T144_A0.185690.743
58_L182_V0.185620.742
58_L61_N0.185320.741
205_A208_H0.183860.735
60_V92_I0.182830.731
43_I54_L0.182750.731
48_G235_S0.182480.730
27_L232_I0.182280.729
187_V208_H0.182120.728
44_V233_V0.182020.728
53_Q57_Q0.181490.726
52_T56_L0.180550.722
90_Q94_E0.179510.718
47_S211_S0.178690.715
21_S25_K0.176270.705
118_L139_I0.176040.704
115_L121_L0.1760.704
81_E236_P0.175750.703
188_T191_I0.175050.700
23_G61_N0.17470.699
49_S220_L0.173140.693
157_A161_R0.172880.692
164_A209_S0.172160.689
24_C28_D0.172120.688
118_L145_L0.172010.688
75_V138_V0.171860.687
160_Q209_S0.170950.684
171_K174_A0.170230.681
79_D82_G0.170140.681
35_I62_V0.169670.679
184_T189_T0.169660.679
185_N207_G0.169350.677
54_L230_A0.168150.673
217_R236_P0.168140.673
19_R36_P0.168070.672
48_G52_T0.167470.670
38_G175_R0.167420.670
81_E206_L0.166790.667
119_L122_L0.166720.667
49_S228_R0.165620.662
162_M167_A0.165530.662
219_F223_G0.165440.662
116_E148_S0.164230.657
221_S229_V0.163470.654
39_S215_T0.161730.647
229_V244_S0.16130.645
31_L232_I0.161150.645
35_I136_L0.160780.643
77_Y185_N0.160470.642
51_K140_D0.160360.641
209_S213_A0.159520.638
115_L169_I0.158420.634
143_A185_N0.158040.632
28_D34_G0.157590.630
168_R172_R0.157370.629
189_T211_S0.157240.629
112_V117_E0.157060.628
119_L123_E0.156740.627
20_I37_T0.15650.626
107_I116_E0.155830.623
55_C58_L0.15540.622
36_P235_S0.155350.621
145_L166_L0.155340.621
159_R162_M0.155110.620
92_I96_F0.1550.620
171_K175_R0.154850.619
24_C58_L0.154720.619
108_F121_L0.154720.619
142_I187_V0.154550.618
191_I208_H0.154440.618
142_I166_L0.153350.613
211_S217_R0.153130.613
19_R238_L0.152970.612
30_L240_E0.152830.611
46_E187_V0.152830.611
230_A243_A0.152660.611
211_S215_T0.15260.610
25_K64_L0.151840.607
234_K238_L0.151750.607
117_E122_L0.151730.607
171_K181_V0.151460.606
20_I136_L0.151440.606
93_A97_G0.151170.605
59_A136_L0.150960.604
226_S241_G0.150770.603
19_R32_G0.150720.603
46_E208_H0.150220.601
79_D185_N0.149510.598
38_G83_T0.149440.598
186_Q189_T0.149420.598
93_A242_S0.149370.597
165_R169_I0.14930.597
210_W217_R0.149060.596
143_A212_H0.149040.596
44_V143_A0.148830.595
38_G237_S0.148210.593
232_I235_S0.148140.593
141_S144_A0.147410.590
140_D234_K0.147330.589
119_L166_L0.147220.589
47_S234_K0.147120.588
21_S61_N0.147020.588
79_D92_I0.14680.587
24_C61_N0.146710.587
18_S21_S0.146660.587
30_L232_I0.146590.586
212_H215_T0.146330.585
25_K61_N0.145510.582
86_P100_P0.145470.582
47_S189_T0.145230.581
78_I110_I0.145110.580
24_C54_L0.145050.580
144_A217_R0.145020.580
60_V98_L0.144960.580
18_S36_P0.144530.578
116_E119_L0.144410.578
210_W214_V0.144220.577
111_R114_D0.1440.576
17_W21_S0.14380.575
99_D131_E0.143280.573
39_S235_S0.143140.573
21_S73_G0.143030.572
109_V114_D0.142960.572
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
1v5wA11000.192
2z43A0.98831000.208
2i1qA0.98051000.22
3ldaA11000.22
4hyyA0.99221000.268
1pznA0.98051000.304
1n0wA0.94531000.322
4b3bA0.88281000.377
1q57A0.94531000.38
3cmwA0.92191000.387

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