GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sua5_yciO_yrdC - Telomere recombination
Pfam: PF01300 (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: 179
Sequences: 3652
Seq/Len: 20.4
HH_delta: 0.026 (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
2_I7_G1.491775.075
11_Y20_G1.031773.510
22_D25_N0.975853.320
7_G149_D0.935893.184
55_E67_R0.779642.652
1_E5_A0.736072.504
26_P90_P0.698082.375
6_G25_N0.662422.253
49_S53_Q0.64032.178
42_K129_S0.589772.006
11_Y110_L0.589122.004
22_D119_G0.58071.975
31_R34_K0.575881.959
26_P92_Y0.558511.900
131_E143_R0.543811.850
48_V54_L0.542581.846
20_G123_S0.528861.799
3_L117_L0.51691.758
50_S115_E0.516231.756
8_V35_I0.503051.711
2_I150_L0.493081.677
49_S114_L0.490231.668
10_I148_V0.484441.648
21_C28_A0.478911.629
23_A46_L0.477481.624
136_D139_E0.471451.604
128_L143_R0.469181.596
14_D107_H0.468111.592
141_I145_G0.467281.590
30_E34_K0.466331.586
137_F153_D0.456541.553
24_F119_G0.455991.551
63_S66_A0.447561.523
67_R71_E0.440951.500
112_E115_E0.437591.489
57_Y102_V0.424291.443
10_I140_I0.419771.428
26_P30_E0.419191.426
109_I152_V0.416981.419
7_G31_R0.41591.415
52_E55_E0.412131.402
109_I154_G0.411191.399
51_I71_E0.409531.393
99_T167_D0.401741.367
58_V100_I0.386711.316
53_Q56_E0.384691.309
2_I149_D0.383371.304
17_Y137_F0.383151.303
47_L123_S0.381181.297
58_V82_L0.379541.291
20_G121_L0.379171.290
49_S115_E0.374551.274
11_Y113_L0.371931.265
35_I147_K0.367931.252
25_N28_A0.366461.247
141_I151_I0.357061.215
38_R127_N0.35561.210
35_I144_F0.351971.197
11_Y123_S0.349991.191
140_I151_I0.349321.188
70_L80_L0.347381.182
31_R35_I0.347061.181
64_P67_R0.344391.172
54_L102_V0.343911.170
54_L62_V0.343391.168
50_S53_Q0.343051.167
58_V102_V0.342871.166
33_Y40_K0.338761.152
10_I137_F0.337491.148
108_P112_E0.337461.148
167_D170_N0.334661.138
168_L173_P0.32841.117
62_V70_L0.32821.116
128_L147_K0.327531.114
9_V150_L0.324981.106
167_D173_P0.323791.101
113_L152_V0.322661.098
104_I111_R0.320471.090
30_E92_Y0.319851.088
136_D156_E0.318681.084
51_I104_I0.317781.081
48_V57_Y0.311921.061
79_T101_G0.311011.058
112_E116_A0.31081.057
66_A82_L0.310641.057
138_E142_E0.307811.047
30_E40_K0.307021.044
37_Q128_L0.305451.039
21_C32_I0.305351.039
32_I122_I0.303461.032
126_A140_I0.302671.030
48_V104_I0.298731.016
84_A94_T0.298161.014
66_A70_L0.293570.999
134_A140_I0.290790.989
59_D83_P0.290060.987
81_I176_L0.286030.973
117_L120_P0.285480.971
24_F90_P0.281280.957
45_I101_G0.276330.940
1_E4_K0.275880.939
3_L121_L0.275690.938
27_E30_E0.273530.931
139_E143_R0.270170.919
48_V53_Q0.268620.914
47_L114_L0.268550.914
167_D174_K0.267740.911
10_I19_L0.266370.906
170_N174_K0.265470.903
38_R125_S0.265260.902
111_R115_E0.264340.899
31_R149_D0.263780.897
51_I67_R0.262860.894
58_V62_V0.262850.894
69_L73_F0.25970.883
36_K42_K0.2560.871
36_K129_S0.254850.867
8_V149_D0.252890.860
83_P98_G0.252240.858
29_V93_L0.249750.850
15_T163_S0.249040.847
22_D117_L0.248230.844
23_A29_V0.247060.840
81_I99_T0.245490.835
62_V67_R0.244490.832
137_F156_E0.244180.831
105_P111_R0.243350.828
80_L166_V0.242690.826
33_Y44_L0.241360.821
51_I70_L0.241110.820
37_Q147_K0.24060.818
27_E31_R0.239450.815
169_T173_P0.239430.815
108_P111_R0.239280.814
16_V162_P0.236870.806
65_K68_R0.235860.802
53_Q114_L0.235110.800
6_G22_D0.233890.796
48_V102_V0.233310.794
51_I55_E0.232960.792
142_E145_G0.232650.791
69_L78_L0.231060.786
84_A91_K0.231030.786
9_V20_G0.23040.784
36_K124_T0.229230.780
134_A139_E0.22750.774
106_D111_R0.226330.770
105_P110_L0.225460.767
127_N130_G0.225290.766
133_P162_P0.224770.765
8_V31_R0.223610.761
46_L93_L0.223460.760
114_L121_L0.22140.753
33_Y95_S0.219170.746
114_L118_G0.218710.744
66_A168_L0.217820.741
20_G113_L0.216910.738
32_I123_S0.216680.737
46_L57_Y0.216620.737
107_H110_L0.216520.737
10_I151_I0.215630.734
20_G110_L0.215460.733
175_I178_E0.21480.731
109_I112_E0.214780.731
41_N132_P0.214720.730
18_G103_R0.214670.730
3_L113_L0.214520.730
56_E85_K0.213460.726
137_F151_I0.213360.726
53_Q104_I0.212080.721
74_W78_L0.210960.718
106_D158_P0.210530.716
29_V92_Y0.209940.714
55_E85_K0.209380.712
29_V122_I0.208990.711
22_D28_A0.207310.705
144_F149_D0.206750.703
84_A98_G0.206480.702
21_C122_I0.205760.700
69_L168_L0.204580.696
63_S70_L0.203640.693
54_L82_L0.203570.693
99_T169_T0.203210.691
18_G106_D0.203030.691
64_P68_R0.2030.691
4_K116_A0.202740.690
128_L144_F0.202710.690
137_F140_I0.20250.689
134_A143_R0.201690.686
79_T103_R0.201640.686
103_R163_S0.201410.685
113_L121_L0.200830.683
126_A151_I0.198350.675
36_K127_N0.19820.674
70_L104_I0.197970.673
49_S118_G0.196830.670
53_Q120_P0.196090.667
56_E87_E0.195720.666
42_K95_S0.195490.665
54_L58_V0.195340.665
65_K171_G0.195240.664
73_F78_L0.195190.664
56_E118_G0.194630.662
21_C29_V0.194370.661
16_V163_S0.19420.661
58_V85_K0.193580.659
62_V66_A0.192880.656
65_K168_L0.192680.655
54_L57_Y0.192190.654
148_V151_I0.191920.653
128_L131_E0.191790.652
104_I114_L0.191290.651
4_K119_G0.190730.649
62_V81_I0.189550.645
89_L100_I0.189420.644
89_L92_Y0.18890.643
124_T127_N0.188840.642
29_V44_L0.187210.637
42_K124_T0.186280.634
140_I148_V0.186040.633
35_I149_D0.184820.629
17_Y154_G0.184370.627
82_L102_V0.18380.625
149_D152_V0.183630.625
91_K98_G0.182760.622
14_D47_L0.18260.621
46_L89_L0.180780.615
33_Y38_R0.179990.612
40_K92_Y0.179380.610
10_I144_F0.178790.608
3_L20_G0.178180.606
57_Y120_P0.177850.605
38_R124_T0.177510.604
166_V175_I0.176680.601
114_L117_L0.175980.599
44_L122_I0.175640.598
105_P114_L0.175580.597
38_R129_S0.175570.597
89_L93_L0.175470.597
135_T160_G0.174750.594
74_W101_G0.174040.592
169_T172_K0.173690.591
164_T179_G0.173570.590
17_Y155_G0.173280.589
16_V133_P0.172880.588
10_I20_G0.172340.586
135_T139_E0.172240.586
82_L166_V0.17170.584
16_V127_N0.17150.583
78_L164_T0.171450.583
37_Q40_K0.171410.583
16_V125_S0.170130.579
47_L110_L0.169880.578
133_P161_Q0.169520.577
126_A134_A0.169250.576
170_N173_P0.168020.572
4_K118_G0.167910.571
82_L168_L0.167030.568
59_D86_K0.167020.568
81_I168_L0.166680.567
74_W104_I0.166380.566
3_L22_D0.165720.564
33_Y42_K0.165460.563
78_L166_V0.164490.560
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
2eqaA0.98881000.026
1k7jA0.97771000.081
1jcuA0.96651000.082
3vthA0.97211000.105
1hruA0.96651000.113
3ttcA0.92741000.162
3l7vA0.97771000.192
4g9iA0.97771000.286
3venA0.83897.10.867
1dcuA0.335282.60.92

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