GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
mRNA_cap_enzyme - mRNA capping enzyme catalytic domain
Pfam: PF01331 (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: CL0078
Length: 192
Sequences: 2465
Seq/Len: 12.84
HH_delta: 0.09 (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
105_K109_E0.656983.343
31_L40_L0.553412.816
97_I113_Y0.49012.494
94_I113_Y0.489792.492
100_Q105_K0.47892.437
19_F22_E0.477152.428
72_L91_I0.441722.248
39_Y47_V0.439852.238
74_G89_F0.438612.232
18_Y21_C0.422512.150
28_R73_D0.407552.074
100_Q113_Y0.39382.004
108_D176_V0.37821.924
20_V173_F0.371631.891
34_T69_D0.367641.871
109_E112_A0.366951.867
31_L89_F0.362121.843
108_D177_N0.353651.800
21_C173_F0.336451.712
29_Y40_L0.323211.645
173_F191_W0.317861.617
106_P109_E0.308781.571
18_Y22_E0.306361.559
175_P187_N0.305691.555
23_K75_E0.300481.529
25_D75_E0.295471.503
157_F161_I0.283851.444
112_A116_E0.279691.423
32_L71_L0.279261.421
68_Q98_N0.266841.358
103_T182_P0.260571.326
69_D99_G0.251151.278
113_Y116_E0.250241.273
29_Y76_L0.247081.257
22_E168_T0.245661.250
21_C111_L0.2451.247
19_F107_L0.242491.234
75_E190_K0.24231.233
104_D179_P0.240251.222
32_L41_I0.239731.220
29_Y89_F0.238871.215
93_D110_R0.237211.207
112_A115_Q0.235131.196
49_K59_K0.232121.181
42_D48_F0.231521.178
33_I70_T0.231071.176
143_I146_F0.229591.168
174_T188_L0.229481.168
21_C174_T0.2291.165
77_V90_L0.22871.164
22_E163_K0.228071.161
30_L71_L0.227631.158
23_K190_K0.227191.156
158_E162_P0.226441.152
78_L85_K0.22551.147
181_V187_N0.225091.145
25_D43_R0.223931.139
102_V113_Y0.223311.136
23_K169_D0.223021.135
27_T48_F0.219811.118
40_L89_F0.215841.098
107_L111_L0.214881.093
57_S86_K0.213491.086
33_I38_V0.208191.059
173_F189_L0.207581.056
43_R75_E0.207311.055
161_I164_L0.206561.051
38_V59_K0.206171.049
19_F176_V0.206071.049
79_D83_G0.204281.039
43_R184_T0.204061.038
115_Q143_I0.203731.037
25_D190_K0.202741.032
107_L178_T0.20271.031
159_E163_K0.201741.027
94_I114_L0.199451.015
92_F190_K0.197711.006
162_P166_H0.195710.996
178_T187_N0.193650.985
23_K43_R0.191090.972
91_I114_L0.190790.971
160_F163_K0.190030.967
24_A42_D0.189060.962
78_L87_P0.188510.959
43_R169_D0.188040.957
75_E169_D0.187420.954
69_D98_N0.185670.945
105_K113_Y0.182270.927
88_R186_P0.182120.927
163_K168_T0.181110.922
148_P176_V0.181090.921
91_I94_I0.181030.921
58_K76_L0.179840.915
25_D192_K0.179690.914
108_D116_E0.179620.914
27_T42_D0.179340.913
169_D174_T0.178940.911
30_L46_N0.178740.910
40_L76_L0.176680.899
94_I117_E0.175260.892
24_A144_K0.174780.889
71_L96_A0.174640.889
95_L103_T0.17350.883
30_L173_F0.171610.873
101_N104_D0.16870.858
60_D64_G0.167810.854
70_T97_I0.166850.849
43_R190_K0.165470.842
73_D180_Y0.164330.836
75_E92_F0.163180.830
55_F88_R0.163050.830
25_D169_D0.161640.822
108_D111_L0.160660.818
161_I165_P0.160610.817
80_K83_G0.160350.816
28_R180_Y0.160210.815
178_T188_L0.159560.812
23_K92_F0.159420.811
106_P114_L0.159010.809
72_L94_I0.158110.805
107_L174_T0.157960.804
169_D188_L0.157360.801
37_G63_D0.157330.801
115_Q145_D0.157080.799
185_C189_L0.156090.794
19_F111_L0.155530.791
23_K26_G0.155320.790
34_T37_G0.154590.787
75_E192_K0.154390.786
77_V92_F0.153020.779
17_D120_E0.152310.775
146_F149_I0.152090.774
71_L95_L0.152060.774
175_P178_T0.151960.773
169_D184_T0.151930.773
94_I97_I0.151070.769
30_L95_L0.151030.769
29_Y42_D0.150420.765
112_A158_E0.149790.762
27_T46_N0.149640.761
32_L96_A0.148810.757
81_D86_K0.148360.755
70_T118_I0.148350.755
33_I36_N0.148120.754
25_D92_F0.147940.753
83_G151_Q0.147420.750
27_T55_F0.145220.739
28_R184_T0.145080.738
145_D151_Q0.14490.737
119_I145_D0.144160.734
40_L56_P0.144160.734
29_Y55_F0.143010.728
29_Y48_F0.142640.726
72_L89_F0.142320.724
112_A120_E0.141870.722
60_D82_P0.141710.721
96_A101_N0.140930.717
74_G91_I0.14070.716
79_D88_R0.140090.713
24_A90_L0.13870.706
65_R116_E0.138420.704
113_Y117_E0.136640.695
46_N85_K0.136640.695
77_V174_T0.136390.694
111_L146_F0.1360.692
162_P165_P0.135910.692
20_V149_I0.133810.681
42_D54_H0.133470.679
65_R104_D0.13340.679
21_C30_L0.133310.678
73_D91_I0.13320.678
159_E171_L0.133130.677
42_D173_F0.133090.677
111_L115_Q0.132060.672
38_V58_K0.13180.671
42_D169_D0.131430.669
169_D190_K0.131190.668
33_I67_H0.131190.668
60_D63_D0.131110.667
79_D90_L0.130840.666
28_R77_V0.13070.665
31_L91_I0.130180.662
73_D107_L0.13010.662
100_Q145_D0.130010.662
57_S84_E0.129640.660
41_I172_I0.129010.656
69_D97_I0.128810.655
17_D176_V0.128060.652
33_I63_D0.127760.650
60_D104_D0.127740.650
44_K185_C0.126810.645
32_L103_T0.126630.644
64_G120_E0.126310.643
169_D173_F0.125990.641
147_F150_Y0.124960.636
75_E174_T0.124420.633
176_V179_P0.124340.633
65_R158_E0.124240.632
119_I122_R0.123940.631
147_F159_E0.12390.630
103_T171_L0.12380.630
57_S87_P0.123390.628
66_H158_E0.123280.627
24_A191_W0.122880.625
17_D175_P0.122660.624
67_H98_N0.122380.623
18_Y175_P0.121720.619
164_L184_T0.121540.618
18_Y189_L0.121420.618
34_T39_Y0.121320.617
23_K192_K0.121120.616
116_E120_E0.120930.615
31_L38_V0.120240.612
147_F162_P0.119720.609
74_G186_P0.119660.609
174_T178_T0.119570.608
94_I105_K0.119510.608
110_R114_L0.119390.608
32_L164_L0.119010.606
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
3rtxA0.97921000.09
3kyhC0.98441000.114
1p16A0.98961000.149
1ckmA0.89061000.182
3w1bA0.89061000.237
2cfmA0.89061000.248
2hivA0.89061000.248
1x9nA0.89581000.253
3gdeA0.88541000.261
1vs0A0.85941000.28

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