GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RVT_2 - Reverse transcriptase (RNA-dependent DNA polymerase)
Pfam: PF07727 (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: 246
Sequences: 1231
Seq/Len: 5
HH_delta: 0.868 (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
5_E118_K0.422453.751
136_D154_F0.352183.127
88_F128_P0.327312.906
101_Q105_F0.308052.735
8_P113_K0.307142.727
135_L167_V0.302172.683
135_L139_L0.301232.674
96_E116_R0.299652.660
17_G42_R0.284012.522
134_T192_K0.281082.495
9_R15_P0.265832.360
18_S99_M0.262662.332
163_I185_F0.258532.295
64_S153_L0.253392.250
207_I218_L0.249922.219
92_D134_T0.237272.107
27_D31_E0.220651.959
107_D111_P0.213411.895
174_I182_I0.209451.860
132_Y154_F0.205011.820
52_Y125_K0.204611.817
76_G211_R0.199711.773
222_A226_K0.19811.759
24_I35_Y0.195761.738
16_I45_T0.190651.693
185_F189_L0.188681.675
77_L175_A0.187481.664
82_M174_I0.184681.640
173_L201_L0.180561.603
73_A216_I0.178421.584
6_L101_Q0.173841.543
13_A96_E0.170611.515
2_G118_K0.169941.509
228_L236_A0.168091.492
233_M236_A0.167361.486
26_R32_I0.164621.462
186_K197_D0.164531.461
135_L172_I0.160281.423
80_H186_K0.160271.423
203_Y208_E0.159721.418
228_L233_M0.15921.413
189_L196_K0.158541.408
120_A130_L0.157851.401
79_L175_A0.156681.391
82_M195_I0.156411.389
72_A79_L0.152511.354
130_L134_T0.151961.349
2_G5_E0.150361.335
88_F91_G0.149091.324
4_W115_C0.148231.316
18_S39_L0.147831.312
122_Y126_Q0.146861.304
220_Q227_I0.145861.295
200_E211_R0.143861.277
226_K231_F0.143861.277
84_V195_I0.143821.277
59_V168_Y0.143681.276
208_E222_A0.143551.274
221_K225_E0.142411.264
211_R216_I0.142331.264
78_E179_E0.140991.252
27_D33_E0.140821.250
161_G178_S0.140671.249
17_G100_R0.140391.246
67_I71_I0.139371.237
10_P13_A0.139081.235
43_G46_Q0.138881.233
132_Y146_Q0.138881.233
153_L204_F0.136591.213
157_K160_D0.136111.208
121_L128_P0.135841.206
201_L209_I0.135431.202
167_V172_I0.135361.202
229_E234_Q0.135121.200
135_L165_I0.134321.193
199_G205_L0.133561.186
9_R100_R0.132971.181
138_F192_K0.132811.179
68_L175_A0.132221.174
208_E219_S0.131081.164
212_T215_G0.130811.161
37_A41_A0.129571.150
86_T173_L0.127841.135
225_E234_Q0.126591.124
138_F142_L0.126231.121
38_R43_G0.126021.119
172_I205_L0.125461.114
19_K40_V0.124731.107
183_E187_K0.12381.099
83_D87_A0.123541.097
7_V15_P0.123241.094
82_M197_D0.121561.079
138_F193_F0.12131.077
158_S161_G0.120061.066
65_I69_L0.119461.061
198_L205_L0.118861.055
114_V117_L0.118241.050
57_A60_A0.118211.049
85_K195_I0.118051.048
201_L204_F0.117931.047
83_D88_F0.117821.046
127_A130_L0.117361.042
49_G126_Q0.117081.039
146_Q151_P0.11661.035
34_R61_R0.116331.033
141_K192_K0.116011.030
49_G58_P0.115721.027
99_M115_C0.115421.025
16_I41_A0.11521.023
69_L79_L0.114961.021
9_R12_G0.114781.019
25_K36_K0.114131.013
117_L122_Y0.113681.009
196_K204_F0.112560.999
41_A46_Q0.112510.999
82_M172_I0.112490.999
149_A155_I0.111850.993
76_G214_G0.111620.991
125_K131_W0.11150.990
46_Q52_Y0.111310.988
156_K181_E0.110880.984
5_E116_R0.110790.984
97_I102_P0.110630.982
55_T204_F0.110580.982
9_R14_K0.110460.981
82_M186_K0.109410.971
54_E105_F0.108920.967
52_Y56_F0.108670.965
46_Q126_Q0.108660.965
71_I75_N0.108470.963
85_K88_F0.108220.961
65_I168_Y0.108010.959
135_L195_I0.10730.953
46_Q49_G0.107210.952
49_G52_Y0.10710.951
72_A175_A0.107090.951
101_Q106_E0.106410.945
168_Y172_I0.105880.940
147_S150_D0.105210.934
123_G171_D0.105140.933
48_P239_V0.10490.931
165_I174_I0.104810.931
52_Y126_Q0.104720.930
179_E183_E0.104680.929
136_D140_K0.104660.929
122_Y125_K0.104520.928
15_P100_R0.104320.926
211_R214_G0.103940.923
175_A215_G0.103880.922
54_E57_A0.103460.919
60_A68_L0.103350.918
153_L166_L0.10330.917
67_I75_N0.102870.913
126_Q129_R0.102350.909
188_E191_K0.102310.908
20_W104_G0.102160.907
216_I223_Y0.102060.906
21_V40_V0.101910.905
17_G44_F0.101820.904
101_Q115_C0.101620.902
44_F91_G0.101450.901
77_L152_C0.101420.900
165_I172_I0.101170.898
117_L125_K0.099910.887
97_I103_P0.099590.884
85_K91_G0.099580.884
84_V88_F0.09930.882
41_A99_M0.098920.878
61_R70_A0.098620.876
201_L227_I0.098220.872
85_K194_E0.098180.872
37_A87_A0.097720.868
227_I231_F0.097710.867
153_L158_S0.09730.864
142_L188_E0.097270.864
147_S153_L0.097090.862
166_L172_I0.096950.861
203_Y222_A0.096650.858
40_V44_F0.09650.857
140_K146_Q0.096470.856
20_W23_K0.095990.852
29_D33_E0.095810.851
86_T204_F0.095560.848
65_I204_F0.095330.846
147_S155_I0.09470.841
25_K40_V0.094560.840
161_G181_E0.094390.838
81_Q88_F0.09420.836
236_A241_T0.094070.835
186_K195_I0.094040.835
232_G236_A0.093510.830
60_A166_L0.092950.825
55_T125_K0.092950.825
197_D205_L0.092570.822
101_Q114_V0.092160.818
85_K196_K0.09180.815
224_I236_A0.091760.815
122_Y131_W0.091730.814
144_F156_K0.091590.813
28_A31_E0.091480.812
115_C185_F0.091370.811
15_P21_V0.091230.810
168_Y205_L0.091180.810
183_E210_E0.091040.808
183_E191_K0.090980.808
109_G112_G0.090820.806
17_G39_L0.09020.801
130_L133_K0.09020.801
7_V11_P0.09020.801
34_R196_K0.090010.799
41_A55_T0.089940.799
173_L209_I0.089920.798
58_P65_I0.089830.798
38_R87_A0.089470.794
223_Y228_L0.089350.793
167_V173_L0.089050.791
152_C156_K0.088780.788
135_L138_F0.088510.786
22_F37_A0.088290.784
30_G34_R0.088070.782
101_Q107_D0.087870.780
177_P181_E0.087570.777
80_H179_E0.087570.777
129_R135_L0.087120.773
167_V231_F0.087080.773
39_L99_M0.086990.772
16_I23_K0.086910.772
73_A211_R0.086790.771
209_I216_I0.086710.770
60_A65_I0.086490.768
21_V25_K0.086360.767
119_K124_L0.086270.766
42_R46_Q0.086080.764
11_P188_E0.085640.760
75_N94_D0.085570.760
52_Y182_I0.085550.760
47_K50_V0.085480.759
56_F129_R0.085380.758
84_V90_N0.085340.758
56_F59_V0.085330.758
230_R234_Q0.085250.757
69_L216_I0.085230.757
2_G13_A0.085170.756
132_Y136_D0.084950.754
144_F163_I0.084740.752
139_L165_I0.084720.752
2_G162_F0.08460.751
28_A32_I0.08460.751
19_K22_F0.084560.751
3_T6_L0.084350.749
119_K140_K0.084190.747
57_A113_K0.083910.745
70_A73_A0.083890.745
116_R180_E0.08370.743
233_M241_T0.083640.743
90_N156_K0.083480.741
131_W135_L0.083310.740
145_K155_I0.083280.739
69_L72_A0.083140.738
117_L121_L0.083050.737
18_S41_A0.083010.737
134_T193_F0.082990.737
240_S244_D0.08290.736
14_K17_G0.082760.735
150_D154_F0.082740.735
214_G224_I0.082730.734
134_T139_L0.082630.734
101_Q111_P0.082490.732
153_L201_L0.082360.731
68_L164_I0.082250.730
2_G22_F0.082140.729
210_E219_S0.082020.728
2_G76_G0.081990.728
94_D191_K0.081840.727
83_D89_L0.08180.726
90_N152_C0.081770.726
56_F61_R0.081380.723
4_W17_G0.081020.719
238_P241_T0.080650.716
62_L207_I0.08060.716
193_F198_L0.080440.714
19_K44_F0.080440.714
147_S174_I0.080320.713
69_L209_I0.080110.711
36_K40_V0.079980.710
161_G177_P0.079960.710
19_K91_G0.079840.709
63_T74_S0.079810.709
17_G45_T0.079750.708
147_S177_P0.079680.707
44_F241_T0.079610.707
50_V56_F0.079540.706
212_T230_R0.079490.706
168_Y173_L0.079460.705
124_L127_A0.079450.705
210_E238_P0.079430.705
59_V65_I0.079390.705
184_E188_E0.079310.704
52_Y98_Y0.079150.703
176_G193_F0.079110.702
81_Q86_T0.078610.698
176_G182_I0.078590.698
71_I164_I0.07810.693
83_D86_T0.077750.690
210_E225_E0.077460.688
2_G191_K0.077380.687
50_V212_T0.077370.687
157_K181_E0.077360.687
232_G244_D0.077340.687
142_L157_K0.077330.687
235_D238_P0.077140.685
117_L126_Q0.077130.685
42_R228_L0.077110.685
24_I120_A0.076940.683
180_E187_K0.076850.682
156_K159_G0.076790.682
24_I32_I0.076780.682
5_E9_R0.076770.682
160_D180_E0.076670.681
76_G92_D0.076660.681
76_G142_L0.076620.680
9_R13_A0.076440.679
78_E175_A0.076370.678
208_E221_K0.076210.677
115_C120_A0.076190.676
195_I198_L0.076160.676
136_D152_C0.076020.675
113_K116_R0.075960.674
210_E217_F0.075780.673
126_Q130_L0.075610.671
137_K141_K0.075580.671
194_E208_E0.075540.671
22_F105_F0.075470.670
29_D69_L0.075450.670
27_D63_T0.075350.669
61_R128_P0.075290.668
26_R222_A0.075190.668
99_M120_A0.075170.667
25_K123_G0.075140.667
94_D133_K0.075090.667
40_V43_G0.075070.666
124_L128_P0.075060.666
222_A237_K0.074990.666
16_I193_F0.074980.666
46_Q50_V0.074710.663
79_L201_L0.074680.663
48_P52_Y0.074630.663
231_F235_D0.074590.662
88_F95_E0.074530.662
50_V54_E0.07440.661
118_K133_K0.074390.660
108_P182_I0.074380.660
67_I106_E0.074210.659
78_E98_Y0.07420.659
119_K122_Y0.074170.658
220_Q223_Y0.074130.658
86_T231_F0.074010.657
70_A74_S0.074010.657
187_K190_K0.0740.657
41_A45_T0.073970.657
64_S77_L0.073690.654
6_L115_C0.073660.654
216_I219_S0.073620.654
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
1rw3A0.796798.60.868
3fsiA0.739897.40.909
4g1qA0.849697.20.912
2zd1B0.841597.10.914
4hkqA0.8618970.916
2zd1A0.853796.90.917
4g1qB0.853796.70.92
1mu2A0.841596.70.92
3h6rA0.41879.70.97
2hdcA0.15457.70.971
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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