GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VIT1 - VIT family
Pfam: PF01988 (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: 213
Sequences: 1145
Seq/Len: 5.38
HH_delta: 0.949 (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
175_F193_G0.38463.308
72_W76_N0.335322.884
67_R117_M0.319022.744
100_E104_E0.266922.296
90_R96_E0.248722.139
82_K104_E0.238452.051
77_N80_E0.230251.981
98_D101_E0.210541.811
102_I106_L0.209451.802
49_A135_A0.207021.781
19_L40_G0.206921.780
205_A209_L0.202111.739
52_E138_T0.200831.728
179_Y189_W0.20071.726
95_S105_E0.197471.699
73_E121_L0.19421.670
164_I168_A0.190791.641
136_L140_L0.188091.618
84_E120_E0.185621.597
41_L146_G0.185581.596
15_T40_G0.185571.596
50_V199_I0.184421.586
111_D114_D0.18431.585
116_M120_E0.181581.562
175_F197_L0.178941.539
7_F138_T0.178361.534
73_E120_E0.177021.523
13_L173_A0.176941.522
171_I197_L0.176131.515
82_K107_S0.175871.513
98_D105_E0.173971.496
168_A172_L0.173161.490
4_D52_E0.169831.461
81_E120_E0.167231.438
44_G142_F0.165361.422
13_L152_P0.164521.415
70_E73_E0.164431.414
89_Y102_I0.164311.413
87_E90_R0.163481.406
83_E87_E0.161591.390
98_D102_I0.160621.382
101_E104_E0.159731.374
89_Y119_E0.152311.310
17_F204_A0.143911.238
86_V96_E0.143381.233
165_A168_A0.142671.227
181_K192_S0.14251.226
79_E97_E0.142241.224
118_R122_G0.141941.221
81_E116_M0.141751.219
82_K86_V0.141361.216
174_L200_G0.141321.216
83_E100_E0.140991.213
56_V59_E0.140931.212
73_E81_E0.140541.209
70_E81_E0.139861.203
183_R189_W0.139491.200
171_I201_L0.139441.199
28_V36_A0.138291.190
52_E55_S0.138131.188
68_E71_E0.137911.186
74_L113_L0.137441.182
161_E164_I0.137351.181
50_V203_A0.136231.172
44_G138_T0.136051.170
52_E134_A0.135571.166
201_L205_A0.133861.151
15_T44_G0.13371.150
86_V100_E0.133151.145
181_K193_G0.133071.145
66_E69_R0.132671.141
79_E83_E0.131991.135
56_V195_E0.131671.133
15_T142_F0.131631.132
46_I50_V0.131171.128
32_V36_A0.130251.120
88_I119_E0.12971.116
70_E84_E0.12891.109
67_R71_E0.128641.107
37_G150_L0.127311.095
82_K100_E0.126881.091
14_V203_A0.123921.066
86_V90_R0.123651.064
89_Y92_K0.123281.060
8_G48_M0.122671.055
138_T195_E0.122541.054
69_R73_E0.121071.041
73_E84_E0.120921.040
67_R113_L0.119781.030
140_L201_L0.119721.030
152_P169_V0.119491.028
156_L165_A0.119181.025
115_F119_E0.118931.023
49_A134_A0.118351.018
69_R121_L0.117551.011
4_D10_N0.11661.003
76_N83_E0.11610.999
44_G145_G0.115930.997
3_R10_N0.11590.997
41_L143_I0.115720.995
52_E142_F0.115570.994
15_T138_T0.115450.993
48_M51_G0.115080.990
15_T174_L0.114530.985
31_S209_L0.114410.984
83_E96_E0.114260.983
97_E104_E0.113890.980
164_I173_A0.113660.978
40_G142_F0.113630.977
81_E84_E0.11360.977
134_A138_T0.113580.977
4_D138_T0.113510.976
16_T146_G0.113110.973
85_L116_M0.11310.973
71_E75_E0.112910.971
4_D7_F0.11290.971
38_L150_L0.112870.971
187_Q191_R0.112770.970
54_L59_E0.112740.970
45_A52_E0.111540.959
70_E116_M0.11060.951
7_F45_A0.110550.951
25_G43_A0.110490.950
48_M55_S0.110370.949
17_F170_T0.110320.949
29_S32_V0.110050.947
57_K60_R0.10960.943
160_S168_A0.109350.941
94_L106_L0.108830.936
172_L176_I0.108680.935
5_A141_S0.108470.933
3_R145_G0.108220.931
155_F212_Y0.10690.920
9_A142_F0.106330.915
44_G174_L0.106050.912
140_L144_L0.106020.912
72_W75_E0.105840.910
96_E100_E0.105830.910
66_E121_L0.105660.909
101_E205_A0.105470.907
181_K196_M0.105380.906
37_G149_P0.1050.903
11_D48_M0.104870.902
70_E121_L0.104810.902
4_D134_A0.104210.896
25_G208_Y0.104180.896
189_W193_G0.103930.894
87_E91_A0.10310.887
137_A141_S0.103080.887
92_K103_A0.102770.884
60_R128_E0.102480.882
92_K119_E0.102120.878
17_F153_Y0.10210.878
104_E168_A0.101640.874
38_L143_I0.101520.873
153_Y162_A0.101090.870
148_I169_V0.100770.867
57_K181_K0.100720.866
51_G55_S0.100680.866
75_E110_K0.10060.865
41_L203_A0.100480.864
148_I164_I0.100370.863
106_L112_A0.100240.862
13_L177_L0.100040.861
70_E120_E0.099950.860
4_D195_E0.099930.860
21_A150_L0.099810.859
21_A173_A0.099590.857
40_G44_G0.099580.857
75_E83_E0.099180.853
132_W136_L0.099020.852
85_L115_F0.0990.852
33_V37_G0.098940.851
178_G193_G0.098840.850
116_M121_L0.098530.848
206_V209_L0.098190.845
9_A145_G0.0980.843
52_E56_V0.097940.842
188_S191_R0.097820.841
42_I139_F0.097670.840
17_F202_I0.097660.840
166_S173_A0.097560.839
30_S33_V0.097460.838
47_S51_G0.097410.838
18_G203_A0.097360.837
152_P162_A0.097250.837
107_S110_K0.097070.835
199_I203_A0.0970.834
20_V166_S0.096930.834
44_G207_T0.096460.830
114_D127_E0.096450.830
114_D126_E0.09630.828
168_A190_W0.096210.828
83_E123_L0.096170.827
162_A166_S0.095560.822
7_F52_E0.095540.822
138_T142_F0.095490.821
124_S127_E0.095480.821
7_F10_N0.095450.821
136_L172_L0.095090.818
18_G177_L0.095040.818
139_F196_M0.09490.816
42_I50_V0.094350.812
104_E108_K0.094210.810
49_A56_V0.094170.810
18_G207_T0.094020.809
165_A210_I0.093950.808
176_I191_R0.093860.807
78_P82_K0.093550.805
84_E121_L0.093470.804
21_A163_F0.093330.803
181_K204_A0.093250.802
108_K112_A0.093160.801
25_G153_Y0.093060.800
161_E176_I0.0930.800
15_T24_A0.092880.799
4_D142_F0.092860.799
23_V142_F0.092840.799
114_D118_R0.092590.796
70_E113_L0.092530.796
152_P166_S0.092390.795
10_N15_T0.092380.795
56_V138_T0.092080.792
76_N80_E0.092010.791
8_G12_G0.091980.791
4_D181_K0.091810.790
188_S206_V0.091780.789
15_T146_G0.091750.789
15_T150_L0.091550.788
18_G204_A0.091520.787
59_E134_A0.09150.787
93_G102_I0.091480.787
36_A40_G0.091460.787
147_L151_L0.091370.786
97_E101_E0.091310.785
75_E127_E0.091240.785
82_K90_R0.091230.785
170_T177_L0.090960.782
79_E194_L0.090940.782
171_I202_I0.090790.781
57_K61_D0.090780.781
142_F174_L0.090640.780
61_D64_E0.090640.780
105_E117_M0.090580.779
152_P193_G0.090450.778
10_N13_L0.089840.773
182_A189_W0.089840.773
95_S102_I0.089820.773
188_S192_S0.089630.771
56_V134_A0.089530.770
171_I198_L0.08940.769
86_V117_M0.089390.769
107_S111_D0.089340.768
16_T152_P0.089220.767
55_S99_A0.089120.767
19_L45_A0.088970.765
173_A208_Y0.088960.765
17_F181_K0.088850.764
114_D167_I0.088790.764
14_V40_G0.088730.763
75_E82_K0.088640.762
40_G138_T0.088570.762
84_E88_I0.088360.760
148_I173_A0.088150.758
58_S129_E0.088150.758
99_A103_A0.08810.758
69_R168_A0.088010.757
176_I180_F0.087950.757
86_V104_E0.087810.755
13_L166_S0.087690.754
190_W193_G0.087560.753
9_A15_T0.087320.751
24_A106_L0.087290.751
44_G48_M0.087240.750
15_T52_E0.087150.750
31_S35_L0.086790.747
25_G45_A0.086130.741
40_G43_A0.086080.740
134_A145_G0.086020.740
61_D143_I0.0860.740
23_V26_A0.085930.739
10_N18_G0.085920.739
65_A70_E0.085650.737
138_T207_T0.085540.736
64_E151_L0.085530.736
69_R72_W0.085360.734
201_L209_L0.085360.734
182_A185_S0.085330.734
137_A181_K0.085150.732
88_I92_K0.08510.732
151_L161_E0.084860.730
13_L44_G0.084790.729
20_V170_T0.084630.728
93_G103_A0.084490.727
193_G196_M0.084470.727
14_V166_S0.08430.725
140_L205_A0.083940.722
13_L203_A0.083740.720
79_E176_I0.083550.719
101_E117_M0.083540.719
22_G47_S0.083420.718
94_L102_I0.083180.716
43_A129_E0.083150.715
195_E207_T0.083120.715
4_D55_S0.083070.715
48_M149_P0.083040.714
66_E70_E0.082910.713
20_V206_V0.082760.712
104_E194_L0.082680.711
208_Y212_Y0.082650.711
108_K113_L0.08260.711
43_A204_A0.082590.710
4_D56_V0.082570.710
94_L105_E0.082310.708
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
3viqB0.375635.60.949
4f4cA0.694829.80.951
4jr9A0.5775200.954
3qe7A0.436619.10.955
4j05A0.539918.50.955
3d31C0.4789180.955
4gw3A0.300517.90.955
1pw4A0.50717.10.956
4iu9B0.55414.30.957
1r31A0.483613.50.957
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