GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VWA_CoxE - VWA domain containing CoxE-like protein
Pfam: PF05762 (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: CL0128
Length: 222
Sequences: 1372
Seq/Len: 6.18
HH_delta: 0.699 (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
173_R177_R0.235052.498
36_A48_V0.217322.309
136_L168_L0.217172.308
137_R171_E0.207392.204
160_W199_V0.192792.049
140_L175_L0.189722.016
153_V182_V0.188662.005
153_V175_L0.185291.969
63_L139_F0.183571.951
160_W188_L0.173381.842
172_L176_R0.170061.807
176_R182_V0.168941.795
32_R48_V0.166181.766
66_V95_V0.164711.750
169_A173_R0.16461.749
133_G167_P0.1611.711
62_V81_L0.156441.662
95_V103_V0.151961.615
96_F132_I0.148651.580
92_R102_E0.144461.535
130_T133_G0.14381.528
159_G184_W0.141011.498
94_F139_F0.140531.493
188_L196_Y0.138431.471
166_E170_E0.136731.453
32_R36_A0.136651.452
100_L175_L0.132811.411
43_E157_S0.131051.393
170_E173_R0.127691.357
136_L153_V0.125471.333
37_S40_T0.124021.318
59_R90_R0.123411.311
27_R51_R0.123361.311
19_R22_R0.122291.299
106_L112_P0.122191.298
95_V132_I0.120051.276
141_R170_E0.119361.268
98_T132_I0.119231.267
10_R152_T0.11821.256
63_L153_V0.115611.228
170_E174_R0.115261.225
21_R63_L0.114861.221
72_G191_A0.114631.218
137_R174_R0.113851.210
144_A178_R0.112611.197
57_P151_T0.111331.183
90_R104_T0.111211.182
167_P170_E0.108861.157
152_T165_P0.10851.153
45_L51_R0.107561.143
69_S158_D0.106811.135
132_I168_L0.106621.133
157_S168_L0.106171.128
19_R50_R0.105991.126
20_R27_R0.104231.108
9_A13_A0.102511.089
46_R112_P0.102491.089
140_L171_E0.101971.084
136_L172_L0.101941.083
89_R152_T0.101871.082
18_R22_R0.100961.073
134_Q141_R0.100741.070
53_R173_R0.100321.066
18_R169_A0.11.063
75_E81_L0.099961.062
103_V129_G0.09991.062
16_R166_E0.099381.056
18_R141_R0.099141.053
134_Q167_P0.098951.051
188_L191_A0.098931.051
132_I196_Y0.098811.050
126_F129_G0.09861.048
92_R142_Q0.098551.047
111_D128_G0.097271.034
194_P197_D0.096911.030
111_D178_R0.09691.030
35_R39_R0.096561.026
60_L87_Q0.09621.022
192_G196_Y0.095861.019
41_G78_L0.095841.018
63_L94_F0.095711.017
70_M161_D0.095541.015
25_R131_D0.09521.012
163_N168_L0.094821.008
19_R28_L0.094741.007
184_W187_P0.094371.003
28_L47_L0.093830.997
79_A82_Y0.09290.987
113_E191_A0.092610.984
68_G71_A0.092120.979
93_V96_F0.091390.971
20_R81_L0.09110.968
113_E153_V0.090990.967
26_G39_R0.090590.963
89_R167_P0.090550.962
33_T48_V0.090530.962
100_L153_V0.090520.962
77_M156_I0.089940.956
188_L192_G0.089510.951
39_R127_G0.089360.950
140_L174_R0.088970.945
57_P80_F0.088840.944
79_A150_R0.08840.939
68_G97_S0.088260.938
155_I178_R0.087790.933
153_V176_R0.087540.930
98_T129_G0.087070.925
25_R178_R0.086780.922
134_Q138_E0.08660.920
20_R25_R0.086580.920
73_Y97_S0.086360.918
159_G186_N0.086060.914
153_V178_R0.085940.913
45_L108_R0.085850.912
28_L167_P0.085650.910
10_R63_L0.085640.910
111_D192_G0.085360.907
49_R77_M0.085020.903
143_Y151_T0.084450.897
70_M132_I0.084320.896
23_R33_T0.08430.896
36_A84_L0.0840.893
79_A83_A0.083970.892
156_I183_I0.083930.892
66_V187_P0.083930.892
53_R166_E0.083890.891
96_F130_T0.083710.890
131_D134_Q0.083690.889
63_L107_L0.08360.888
23_R45_L0.083530.888
152_T181_R0.083460.887
25_R159_G0.083190.884
85_Q149_R0.082980.882
40_T43_E0.082920.881
101_T104_T0.082890.881
73_Y186_N0.082620.878
75_E79_A0.082520.877
8_L15_R0.082020.872
107_L153_V0.081960.871
151_T174_R0.081840.870
98_T161_D0.081670.868
68_G73_Y0.08160.867
94_F104_T0.081570.867
79_A96_F0.081550.867
86_R127_G0.081280.864
41_G76_F0.081250.863
90_R164_D0.081160.862
69_S185_L0.081050.861
62_V154_V0.081020.861
56_K188_L0.080980.861
149_R155_I0.080650.857
139_F184_W0.080590.856
141_R178_R0.080580.856
144_A151_T0.080420.855
15_R144_A0.080380.854
135_A159_G0.080140.852
9_A118_R0.080020.850
194_P198_P0.07970.847
157_S184_W0.079680.847
141_R174_R0.079520.845
62_V194_P0.079520.845
160_W196_Y0.07940.844
41_G63_L0.079380.844
33_T44_P0.079350.843
96_F99_R0.079180.841
182_V191_A0.079170.841
15_R178_R0.079090.840
39_R108_R0.078660.836
68_G128_G0.078570.835
161_D168_L0.078440.834
39_R175_L0.078340.832
33_T38_L0.078270.832
24_R47_L0.078230.831
132_I157_S0.078210.831
66_V186_N0.078150.830
73_Y196_Y0.078090.830
32_R50_R0.078070.830
95_V117_A0.078040.829
66_V132_I0.077850.827
137_R140_L0.077770.826
133_G165_P0.07770.826
94_F172_L0.077620.825
34_I137_R0.077620.825
111_D144_A0.077270.821
70_M183_I0.077140.820
172_L184_W0.077020.818
78_L82_Y0.076980.818
19_R49_R0.076860.817
95_V106_L0.076830.816
133_G159_G0.076520.813
37_S42_G0.076490.813
177_R194_P0.076450.812
10_R53_R0.076110.809
98_T168_L0.075990.807
39_R90_R0.075910.807
77_M149_R0.075870.806
129_G188_L0.075790.805
14_L164_D0.075780.805
23_R38_L0.075750.805
8_L19_R0.07570.804
26_G50_R0.075420.801
61_V151_T0.075410.801
97_S157_S0.075060.798
166_E169_A0.075050.797
21_R88_F0.075020.797
129_G192_G0.074960.797
29_D172_L0.074660.793
36_A177_R0.074630.793
137_R166_E0.074540.792
73_Y149_R0.074440.791
59_R92_R0.074440.791
28_L44_P0.074370.790
126_F188_L0.074320.790
85_Q93_V0.074280.789
48_V62_V0.074180.788
27_R180_R0.074130.788
72_G80_F0.074130.788
98_T126_F0.073940.786
195_G198_P0.073710.783
191_A194_P0.073690.783
20_R89_R0.073650.783
181_R191_A0.07360.782
177_R183_I0.073560.782
41_G185_L0.073520.781
139_F143_Y0.07340.780
31_R64_C0.07340.780
22_R54_P0.073270.779
29_D164_D0.073220.778
62_V115_A0.073060.776
140_L144_A0.073040.776
131_D197_D0.073020.776
113_E154_V0.072890.775
126_F131_D0.072890.775
52_R114_E0.072720.773
88_F175_L0.072650.772
25_R167_P0.072650.772
97_S187_P0.072610.772
112_P120_S0.072530.771
109_R173_R0.072530.771
27_R153_V0.072490.770
12_L60_L0.072480.770
133_G197_D0.072480.770
64_C193_W0.072480.770
16_R31_R0.072420.770
93_V103_V0.072420.770
86_R109_R0.072340.769
139_F179_G0.072290.768
82_Y116_L0.072190.767
149_R178_R0.072180.767
67_S103_V0.072170.767
35_R42_G0.072160.767
137_R168_L0.072140.767
196_Y199_V0.072070.766
73_Y98_T0.071870.764
126_F162_T0.071580.761
94_F98_T0.071570.761
98_T163_N0.071480.760
70_M163_N0.071470.759
136_L175_L0.071420.759
14_L155_I0.071330.758
56_K90_R0.071060.755
59_R198_P0.071030.755
34_I174_R0.070990.754
29_D91_V0.070850.753
73_Y129_G0.070790.752
137_R154_V0.070760.752
136_L155_I0.070670.751
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
4hqoA0.797399.50.699
1yvrA0.927999.50.7
4hqfA0.810899.40.706
1mf7A0.761399.40.706
1n3yA0.779399.40.706
2x31A0.725299.40.707
1ijbA0.765899.40.713
3n2nF0.743299.40.713
1shuX0.738799.40.714
2odpA0.761399.40.715
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