GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAP2_3 - PAP2 superfamily
Pfam: PF14378 (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: CL0525
Length: 191
Sequences: 1168
Seq/Len: 6.12
HH_delta: 0.67 (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
128_F180_A0.297793.069
140_A160_N0.219742.265
74_G131_L0.177891.833
181_G185_A0.172951.782
133_V164_L0.170641.759
70_A134_A0.164061.691
74_G134_A0.157081.619
167_T172_Q0.155741.605
164_L167_T0.153641.583
133_V167_T0.15291.576
182_A186_L0.150961.556
86_P127_A0.150021.546
137_V182_A0.149841.544
125_V131_L0.148691.532
85_P172_Q0.147361.519
77_I184_L0.144071.485
133_V178_V0.143111.475
140_A157_L0.142041.464
150_R155_L0.141291.456
154_A158_A0.132741.368
140_A156_F0.131181.352
168_V175_V0.127961.319
150_R187_L0.127861.318
126_A172_Q0.126131.300
88_F178_V0.12531.291
20_Q126_A0.124481.283
167_T178_V0.122161.259
131_L134_A0.119181.228
78_Y184_L0.118411.220
51_L175_V0.115141.187
47_V139_C0.11511.186
104_G107_F0.114621.181
84_A127_A0.114061.175
18_S80_L0.11351.170
180_A183_A0.113081.165
71_L75_F0.112681.161
20_Q24_A0.112141.156
20_Q25_S0.111671.151
155_L187_L0.11161.150
87_R124_G0.111521.149
61_R74_G0.111131.145
59_R157_L0.109951.133
37_Y60_F0.106991.103
78_Y127_A0.105221.084
137_V160_N0.105211.084
85_P126_A0.105041.083
85_P127_A0.10491.081
33_L165_F0.104571.078
156_F161_V0.10371.069
59_R73_I0.103421.066
127_A168_V0.103231.064
78_Y126_A0.103051.062
144_W153_R0.102641.058
76_V158_A0.102181.053
68_L79_I0.102011.051
85_P167_T0.101961.051
28_W153_R0.101811.049
108_F112_A0.100531.036
67_L135_W0.100281.033
71_L131_L0.100241.033
43_Q160_N0.100141.032
151_W154_A0.100051.031
73_I76_V0.099481.025
48_V73_I0.099291.023
44_V150_R0.099251.023
83_A133_V0.098591.016
64_F67_L0.098331.013
126_A131_L0.098081.011
85_P175_V0.09791.009
157_L182_A0.097531.005
23_L169_Y0.097491.005
68_L182_A0.097171.001
83_A167_T0.096530.995
85_P125_V0.096510.995
102_V105_G0.09610.990
43_Q181_G0.096090.990
24_A28_W0.095990.989
82_P126_A0.095890.988
87_R172_Q0.095690.986
165_F169_Y0.095160.981
133_V182_A0.094760.977
69_L76_V0.094340.972
40_F43_Q0.09420.971
40_F174_Y0.093710.966
124_G172_Q0.093490.963
78_Y86_P0.093470.963
101_P158_A0.093210.961
156_F160_N0.092880.957
46_F49_L0.092870.957
55_R67_L0.092720.956
71_L135_W0.09270.955
85_P123_N0.09260.954
35_F181_G0.092540.954
41_F125_V0.092340.952
58_D186_L0.091790.946
28_W58_D0.091670.945
143_L147_G0.091570.944
141_L148_R0.091550.944
46_F166_S0.090820.936
80_L158_A0.090310.931
67_L88_F0.090140.929
112_A155_L0.090120.929
127_A172_Q0.090120.929
176_I188_A0.08990.926
37_Y167_T0.089730.925
125_V172_Q0.089660.924
131_L172_Q0.089490.922
161_V179_I0.089270.920
18_S22_W0.089160.919
86_P128_F0.089020.917
28_W158_A0.088940.917
65_R182_A0.088680.914
27_P161_V0.088540.912
66_A188_A0.088090.908
22_W141_L0.08750.902
136_A160_N0.087430.901
69_L81_F0.087330.900
20_Q172_Q0.087230.899
22_W157_L0.08680.895
72_L182_A0.086560.892
38_A48_V0.086530.892
37_Y141_L0.086390.890
48_V105_G0.086340.890
18_S32_I0.086330.890
179_I188_A0.085710.883
19_L22_W0.085630.882
46_F136_A0.085610.882
37_Y131_L0.085130.877
157_L160_N0.085020.876
85_P128_F0.084960.876
76_V79_I0.084740.873
74_G167_T0.084360.869
149_P183_A0.084340.869
23_L27_P0.084140.867
52_A160_N0.084110.867
19_L36_A0.08410.867
20_Q23_L0.084010.866
25_S32_I0.083980.865
28_W46_F0.083970.865
23_L32_I0.083920.865
127_A167_T0.083860.864
50_L135_W0.083790.864
37_Y129_P0.083740.863
59_R62_R0.083730.863
107_F111_H0.083590.861
158_A161_V0.083230.858
68_L80_L0.083220.858
83_A127_A0.083030.856
72_L143_L0.082870.854
50_L151_W0.082740.853
24_A187_L0.082710.852
74_G127_A0.082650.852
132_H173_H0.082650.852
137_V186_L0.082510.850
78_Y83_A0.081930.844
32_I50_L0.081890.844
57_P183_A0.081850.844
84_A90_P0.081560.841
66_A138_L0.08150.840
135_W163_I0.081380.839
86_P169_Y0.081310.838
37_Y82_P0.081260.837
20_Q85_P0.081250.837
184_L188_A0.081220.837
26_H76_V0.081130.836
76_V104_G0.081130.836
89_L123_N0.081030.835
139_C143_L0.081020.835
31_W34_A0.080920.834
48_V151_W0.08090.834
43_Q183_A0.080850.833
127_A133_V0.080810.833
73_I183_A0.080760.832
127_A131_L0.080640.831
101_P143_L0.080550.830
112_A179_I0.080550.830
45_A182_A0.080290.827
45_A57_P0.080270.827
158_A187_L0.080240.827
154_A161_V0.080180.826
127_A134_A0.079980.824
128_F131_L0.079910.824
163_I185_A0.079740.822
49_L143_L0.079730.822
78_Y131_L0.079460.819
126_A170_T0.07940.818
41_F79_I0.079380.818
43_Q139_C0.079370.818
53_L69_L0.079310.817
176_I180_A0.07930.817
70_A142_A0.079020.814
63_F139_C0.079010.814
125_V185_A0.079010.814
28_W161_V0.0790.814
69_L72_L0.078780.812
78_Y178_V0.078650.811
36_A73_I0.078630.810
64_F87_R0.078420.808
32_I45_A0.078410.808
55_R80_L0.078330.807
164_L168_V0.078210.806
133_V137_V0.078070.805
43_Q47_V0.077950.803
138_L174_Y0.077950.803
102_V107_F0.077790.802
53_L57_P0.077560.799
60_F136_A0.077530.799
74_G170_T0.077520.799
85_P170_T0.07740.798
54_R187_L0.077250.796
43_Q171_G0.077190.796
73_I79_I0.076720.791
76_V149_P0.076620.790
54_R77_I0.076490.788
56_R59_R0.076330.787
169_Y172_Q0.075990.783
55_R165_F0.075910.782
161_V183_A0.075860.782
47_V188_A0.075840.782
54_R57_P0.075790.781
147_G159_F0.075720.780
179_I186_L0.075590.779
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
1d2tA0.863999.10.67
2ipbA0.8639990.694
1qi9A0.890198.30.767
1up8A0.921597.90.794
3bb0A0.853496.80.838
4b19A0.12574.50.948
2c52B0.1784.20.949
1kbhA0.13613.50.951
1iijA0.18322.70.953
2l2tA0.22512.50.954
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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