GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RVT_1 - Reverse transcriptase (RNA-dependent DNA polymerase)
Pfam: PF00078 (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: CL0027
Length: 214
Sequences: 5877
Seq/Len: 27.46
HH_delta: 0.328 (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
72_S192_K0.849023.149
5_N8_K0.757752.811
73_K77_S0.751832.789
73_K76_D0.730732.710
74_A137_F0.683832.536
145_D160_R0.664142.463
69_L165_I0.609042.259
45_F162_A0.583832.166
76_D128_Q0.582282.160
84_L101_Q0.575412.134
27_N31_Q0.552872.051
171_S174_E0.519041.925
69_L193_L0.509681.890
24_R27_N0.509251.889
71_I186_L0.50531.874
172_K176_Q0.499031.851
183_S195_P0.491241.822
89_R143_D0.475541.764
166_L209_F0.474441.760
67_L175_L0.455951.691
169_S175_L0.439911.632
83_L136_L0.438871.628
187_E192_K0.431751.601
86_K143_D0.430551.597
183_S187_E0.430061.595
179_L183_S0.428081.588
72_S194_N0.423411.570
194_N197_K0.415011.539
77_S124_R0.410171.521
46_R49_R0.40511.503
39_S142_D0.403841.498
88_K101_Q0.39541.467
144_L182_I0.395021.465
27_N135_L0.39181.453
184_Q188_E0.388981.443
127_P130_S0.38821.440
25_V29_R0.381831.416
176_Q180_E0.381531.415
145_D158_Y0.373461.385
88_K94_K0.369791.372
70_D75_F0.367561.363
79_P82_R0.360521.337
164_D197_K0.357471.326
19_D23_Q0.357241.325
68_K166_L0.353851.312
177_K181_K0.352781.309
83_L140_Y0.352141.306
159_L168_I0.349481.296
142_D146_R0.345581.282
38_F46_R0.344061.276
130_S133_S0.339021.257
169_S178_I0.3381.254
62_G170_K0.334591.241
193_L198_T0.331321.229
185_W188_E0.330371.225
79_P190_G0.329351.222
141_L160_R0.323131.199
82_R190_G0.320761.190
66_F166_L0.318811.183
144_L185_W0.318271.181
5_N196_E0.31251.159
67_L179_L0.31231.158
8_K196_E0.311841.157
185_W189_L0.308061.143
23_Q130_S0.304271.129
208_K212_Y0.301631.119
82_R85_R0.300221.114
71_I137_F0.298491.107
174_E177_K0.296611.100
65_Y172_K0.296041.098
194_N198_T0.295581.096
160_R165_I0.295571.096
38_F42_Q0.290231.077
42_Q45_F0.289111.072
125_G128_Q0.287851.068
78_I140_Y0.287561.067
4_K8_K0.285761.060
21_I25_V0.285741.060
180_E184_Q0.284841.057
31_Q47_P0.284351.055
83_L86_K0.280711.041
128_Q133_S0.280681.041
66_F207_V0.28051.040
43_F49_R0.27961.037
183_S193_L0.27721.028
186_L193_L0.276931.027
72_S77_S0.271841.008
148_L158_Y0.269621.000
17_V20_R0.26820.995
119_P122_Q0.267610.993
159_L209_F0.267470.992
27_N131_P0.267080.991
68_K207_V0.266620.989
20_R23_Q0.265310.984
87_L139_I0.264390.981
128_Q134_P0.262440.973
178_I181_K0.262170.972
82_R86_K0.261590.970
80_H126_L0.259520.963
24_R28_K0.259440.962
24_R131_P0.258570.959
63_Y170_K0.2580.957
147_E188_E0.255270.947
75_F133_S0.2540.942
167_I178_I0.252970.938
68_K199_K0.252240.936
75_F134_P0.25170.934
147_E185_W0.250420.929
147_E150_Q0.250380.929
84_L87_L0.249650.926
63_Y157_S0.249010.924
82_R189_L0.248270.921
209_F212_Y0.24750.918
71_I77_S0.247080.916
145_D148_L0.245920.912
78_I83_L0.245380.910
33_I90_F0.244170.906
206_S212_Y0.244150.906
181_K184_Q0.24230.899
38_F139_I0.241870.897
148_L182_I0.240390.892
26_L99_L0.23980.889
134_P137_F0.239710.889
90_F142_D0.236990.879
132_L136_L0.236070.876
66_F168_I0.235340.873
177_K180_E0.232860.864
86_K189_L0.232340.862
67_L169_S0.231240.858
57_L60_F0.231040.857
22_V99_L0.230090.853
126_L132_L0.229810.852
146_R149_Q0.229370.851
170_K174_E0.228960.849
144_L148_L0.228430.847
125_G129_G0.227290.843
158_Y165_I0.2250.835
192_K196_E0.224380.832
141_L165_I0.222540.825
126_L133_S0.221180.820
3_K10_R0.220750.819
207_V210_L0.219910.816
39_S149_Q0.218330.810
178_I182_I0.217210.806
177_K184_Q0.216570.803
81_H85_R0.21570.800
201_L207_V0.215620.800
76_D80_H0.215560.800
141_L144_L0.215440.799
129_G164_D0.213970.794
198_T201_L0.213880.793
30_L92_V0.213690.793
69_L198_T0.213670.793
65_Y171_S0.212730.789
81_H101_Q0.211990.786
70_D74_A0.211660.785
74_A78_I0.211390.784
82_R140_Y0.210850.782
180_E183_S0.207460.769
178_I185_W0.206590.766
44_G134_P0.206110.764
67_L200_I0.205820.763
11_P76_D0.203240.754
74_A77_S0.202680.752
10_R163_D0.201840.749
138_N160_R0.201180.746
3_K128_Q0.20080.745
71_I191_L0.199980.742
77_S191_L0.199960.742
201_L206_S0.199810.741
60_F63_Y0.198710.737
78_I126_L0.198250.735
40_P43_F0.198120.735
8_K12_I0.197670.733
22_V26_L0.196840.730
86_K89_R0.196270.728
194_N199_K0.195650.726
193_L197_K0.195410.725
150_Q184_Q0.195110.724
137_F145_D0.195050.723
144_L186_L0.19480.723
129_G133_S0.19320.717
134_P162_A0.192210.713
86_K140_Y0.192060.712
75_F162_A0.191970.712
87_L136_L0.190690.707
137_F141_L0.190450.706
129_G163_D0.19030.706
45_F48_G0.190130.705
182_I186_L0.189480.703
139_I150_Q0.189460.703
31_Q135_L0.184920.686
21_I24_R0.184860.686
41_S149_Q0.184820.686
79_P124_R0.183760.682
64_L170_K0.183610.681
75_F126_L0.183330.680
87_L100_I0.183190.679
200_I207_V0.183190.679
68_K201_L0.183010.679
58_N61_K0.182590.677
77_S192_K0.182590.677
69_L179_L0.181890.675
28_K131_P0.181360.673
199_K207_V0.180510.670
184_Q187_E0.180480.669
42_Q160_R0.17950.666
63_Y168_I0.179290.665
43_F46_R0.179270.665
12_I128_Q0.178850.663
8_K194_N0.178840.663
46_R138_N0.178630.663
126_L136_L0.178360.662
201_L212_Y0.177840.660
43_F50_S0.177830.660
201_L205_D0.177470.658
45_F51_C0.176980.656
86_K142_D0.17650.655
80_H84_L0.176270.654
12_I20_R0.175830.652
30_L33_I0.175260.650
205_D210_L0.17510.649
126_L137_F0.174920.649
39_S146_R0.174870.649
205_D208_K0.174120.646
136_L140_Y0.173890.645
171_S178_I0.173670.644
29_R32_P0.173440.643
145_D149_Q0.173220.642
156_I178_I0.172920.641
208_K211_G0.172380.639
4_K7_G0.171930.638
45_F134_P0.171860.637
118_S123_K0.171440.636
75_F131_P0.17140.636
31_Q46_R0.171380.636
3_K7_G0.171320.635
22_V33_I0.171230.635
195_P198_T0.17120.635
29_R33_I0.171190.635
26_L132_L0.171170.635
147_E181_K0.17050.632
138_N141_L0.170290.632
174_E178_I0.170110.631
12_I75_F0.17010.631
18_D22_V0.169590.629
12_I17_V0.169560.629
205_D209_F0.169110.627
28_K31_Q0.169010.627
161_Y164_D0.168820.626
167_I182_I0.168630.625
60_F168_I0.168490.625
169_S174_E0.168150.624
175_L200_I0.167870.623
173_E176_Q0.167560.622
146_R150_Q0.167350.621
43_F47_P0.167180.620
80_H83_L0.167150.620
139_I142_D0.166260.617
63_Y171_S0.165390.613
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
3kylA0.925299.90.328
3fsiA0.803799.70.518
4hkqA0.808499.60.527
2zd1A0.794499.60.537
1rw3A0.803799.60.537
2zd1B0.799199.60.537
1mu2A0.799199.60.544
4g1qA0.799199.60.553
4g1qB0.799199.50.569
1xr5A0.929999.20.645

Page generated in 0.026 seconds.