GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RVT_3 - Reverse transcriptase-like
Pfam: PF13456 (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: CL0219
Length: 87
Sequences: 5034
Seq/Len: 57.86
HH_delta: 0.049 (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
25_I67_S1.636623.592
31_Q35_D1.476243.240
11_E14_Q1.253832.752
9_L33_V1.228822.697
48_R52_Q1.1272.474
35_D39_G1.110612.438
23_K63_N1.095352.404
14_Q53_D1.020572.240
9_L26_V0.955952.098
28_S34_V0.92972.041
27_E67_S0.842381.849
14_Q57_L0.788681.731
7_L11_E0.771421.693
25_I65_S0.764041.677
57_L60_R0.749451.645
10_L53_D0.745551.636
34_V66_V0.729921.602
79_A83_F0.715471.570
76_V79_A0.664941.459
10_L14_Q0.65951.447
17_W60_R0.648071.422
58_L66_V0.621391.364
16_A24_I0.598771.314
31_Q68_H0.592871.301
72_E76_V0.566881.244
80_L84_A0.54661.200
34_V38_N0.54011.185
31_Q34_V0.534191.172
7_L10_L0.53181.167
2_L32_L0.517891.137
81_A84_A0.510651.121
77_A84_A0.502531.103
74_N78_D0.496861.091
28_S33_V0.496341.089
77_A81_A0.494111.084
10_L54_I0.485871.066
22_R62_W0.481441.057
56_S59_D0.471081.034
2_L36_A0.456221.001
3_E49_P0.455731.000
71_R75_K0.444090.975
36_A51_I0.443520.973
30_S33_V0.441250.968
78_D82_K0.438680.963
13_L26_V0.433840.952
55_R59_D0.430620.945
11_E15_L0.425450.934
9_L28_S0.41850.919
15_L19_L0.41730.916
23_K62_W0.416470.914
47_L51_I0.409060.898
51_I55_R0.405390.890
10_L50_L0.403010.885
74_N77_A0.396540.870
2_L6_A0.389520.855
70_P73_Q0.38570.847
53_D56_S0.379770.834
54_I58_L0.37360.820
70_P75_K0.364030.799
15_L18_E0.363330.797
72_E75_K0.355440.780
13_L24_I0.35440.778
47_L50_L0.351590.772
41_S44_R0.350940.770
7_L50_L0.346680.761
17_W22_R0.341970.751
5_E78_D0.332170.729
5_E29_D0.332030.729
17_W20_G0.330780.726
2_L30_S0.328880.722
37_I54_I0.327690.719
32_L36_A0.325910.715
79_A82_K0.323640.710
9_L66_V0.320540.704
77_A82_K0.317270.696
37_I58_L0.310880.682
6_A33_V0.308790.678
23_K65_S0.30760.675
73_Q84_A0.305440.670
43_S47_L0.303950.667
53_D57_L0.302810.665
2_L78_D0.298940.656
69_I74_N0.298470.655
8_A28_S0.296740.651
21_I62_W0.29510.648
37_I66_V0.294770.647
8_A12_A0.293470.644
34_V37_I0.292270.641
27_E69_I0.286870.630
10_L57_L0.285280.626
29_D74_N0.283980.623
6_A36_A0.283430.622
4_A7_L0.282520.620
39_G55_R0.280910.617
54_I66_V0.279720.614
35_D40_R0.276180.606
36_A40_R0.275960.606
12_A16_A0.274140.602
46_E49_P0.27330.600
6_A32_L0.272920.599
17_W62_W0.270380.593
21_I24_I0.270250.593
3_E50_L0.269920.592
76_V84_A0.269770.592
24_I64_V0.268540.589
40_R43_S0.260840.573
29_D78_D0.260250.571
60_R63_N0.256660.563
3_E46_E0.253090.555
68_H78_D0.248520.545
27_E73_Q0.246890.542
49_P52_Q0.243280.534
26_V64_V0.241480.530
49_P53_D0.241110.529
50_L54_I0.240280.527
48_R51_I0.239450.526
78_D81_A0.238960.524
30_S36_A0.238620.524
46_E52_Q0.237760.522
12_A26_V0.23730.521
35_D38_N0.236370.519
80_L83_F0.236040.518
75_K79_A0.235310.516
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
4e19A199.50.049
3hstB199.40.078
2ehgA0.988599.40.082
3u3gD199.40.091
2qkbA0.988599.20.192
1mu2A0.90899.10.211
2zd1A0.896699.10.218
3h08A0.965599.10.224
4ibnA0.988599.10.232
2kq2A0.95499.10.233

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