GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gate - Nucleoside recognition
Pfam: PF07670 (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. )
Length: 109
Sequences: 4259
Seq/Len: 39.07
HH_delta: 0.647 (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
26_R30_L0.786452.916
30_L33_P0.752252.789
78_S81_E0.579522.149
94_P102_I0.574782.131
26_R29_R0.56692.102
44_A85_L0.565462.097
79_K83_I0.546552.027
33_P37_P0.50471.871
51_G58_G0.460711.708
6_P10_P0.436341.618
35_F45_A0.434281.610
80_R84_A0.425571.578
19_E24_L0.421781.564
100_A103_V0.411161.525
12_S60_A0.410041.520
32_E36_R0.390751.449
77_L81_E0.383941.424
51_G89_S0.379481.407
29_R32_E0.368351.366
23_L26_R0.368171.365
100_A104_K0.364711.352
87_L90_S0.361591.341
8_I60_A0.357291.325
5_L9_I0.35351.311
27_I30_L0.352891.309
9_I13_I0.35231.306
36_R41_P0.349841.297
50_L61_T0.346561.285
55_N89_S0.346081.283
7_I10_P0.338111.254
55_N94_P0.333021.235
48_L89_S0.327151.213
86_I90_S0.32391.201
101_V104_K0.311331.154
29_R36_R0.302151.120
43_E66_Y0.299921.112
34_L38_L0.298291.106
41_P81_E0.295721.097
33_P38_L0.2951.094
47_A61_T0.29451.092
35_F40_L0.293551.088
6_P9_I0.28631.062
32_E42_G0.282451.047
32_E45_A0.26920.998
22_G26_R0.26360.977
10_P13_I0.259760.963
84_A88_F0.254350.943
31_L34_L0.254130.942
52_F55_N0.252280.935
22_G25_E0.251190.931
36_R79_K0.250730.930
35_F42_G0.249990.927
4_A56_E0.248910.923
55_N90_S0.247460.918
53_F57_A0.245380.910
57_A60_A0.244750.908
61_T65_L0.24050.892
20_E23_L0.239380.888
40_L44_A0.236490.877
80_R85_L0.234690.870
40_L45_A0.232280.861
51_G94_P0.22980.852
28_S42_G0.22940.851
11_F55_N0.226730.841
44_A77_L0.224860.834
25_E29_R0.223820.830
7_I12_S0.223190.828
25_E46_I0.221560.822
40_L48_L0.220970.819
15_I50_L0.220460.817
89_S94_P0.220410.817
16_W19_E0.219710.815
52_F89_S0.218170.809
83_I87_L0.217680.807
30_L34_L0.217480.806
4_A97_A0.216140.801
17_I21_S0.214270.795
5_L12_S0.214130.794
95_C98_T0.213560.792
31_L35_F0.213450.791
65_L77_L0.212690.789
96_I99_I0.212460.788
53_F102_I0.212270.787
11_F57_A0.211070.783
18_L23_L0.210210.779
52_F93_T0.209770.778
57_A89_S0.209650.777
18_L27_I0.208290.772
26_R36_R0.207550.770
11_F104_K0.206130.764
34_L37_P0.206070.764
40_L85_L0.20550.762
13_I16_W0.205290.761
51_G95_C0.205210.761
3_R6_P0.205030.760
50_L53_F0.204660.759
59_I88_F0.204360.758
15_I83_I0.202780.752
15_I66_Y0.202030.749
58_G82_A0.201620.748
36_R78_S0.20070.744
39_G83_I0.200450.743
3_R7_I0.199740.741
29_R42_G0.199270.739
57_A98_T0.198680.737
48_L93_T0.198440.736
41_P83_I0.197650.733
44_A91_F0.195920.726
55_N59_I0.193990.719
8_I97_A0.193520.718
15_I53_F0.193230.716
16_W48_L0.193050.716
47_A59_I0.191160.709
59_I86_I0.189620.703
28_S52_F0.187880.697
80_R83_I0.187660.696
82_A86_I0.187540.695
63_A82_A0.18730.695
55_N98_T0.187160.694
15_I19_E0.187080.694
14_L18_L0.186830.693
7_I103_V0.185550.688
49_I95_C0.184880.686
21_S41_P0.182910.678
93_T102_I0.18130.672
7_I100_A0.180260.668
11_F97_A0.179540.666
11_F51_G0.179380.665
24_L28_S0.177330.658
44_A104_K0.176360.654
58_G93_T0.17590.652
58_G88_F0.175410.650
12_S23_L0.175180.650
96_I100_A0.175180.650
13_I17_I0.174950.649
99_I103_V0.17490.649
58_G89_S0.174280.646
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
3tijA0.917497.40.647
4f35D0.981710.30.884
4ainA0.96336.90.892
2wswA0.95414.30.901
1y8qA0.50463.20.907
4huqT0.88992.80.91
2a65A0.97252.10.915
3v5uA0.90831.90.917
3pjzA0.82571.70.918
1pp9D0.33941.70.918
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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