GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sigma70_r2 - Sigma-70 region 2
Pfam: PF04542 (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: CL0123
Length: 71
Sequences: 17478
Seq/Len: 246.17
HH_delta: -0.032 (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
33_K60_R3.506812.817
8_L50_R2.756882.214
58_R62_L2.672662.147
13_A57_A2.329391.871
30_A57_A2.321541.865
42_D45_R2.027361.628
48_S51_A1.874981.506
37_A40_S1.847511.484
60_R63_D1.78621.435
63_D66_R1.781941.431
16_Y61_I1.749621.405
12_Y54_F1.735621.394
55_R58_R1.732951.392
8_L54_F1.721851.383
34_L53_L1.690011.357
14_R20_P1.65071.326
29_E60_R1.611521.294
21_E24_E1.591341.278
5_Y50_R1.591261.278
22_D64_Y1.5861.274
19_D22_D1.583811.272
55_R59_N1.576911.267
2_Y6_Y1.534921.233
32_I36_R1.512541.215
50_R54_F1.496831.202
33_K63_D1.47181.182
59_N62_L1.455871.169
34_L52_W1.425871.145
33_K37_A1.422791.143
9_L57_A1.421141.141
13_A61_I1.372421.102
20_P24_E1.337721.074
10_Y20_P1.335941.073
10_Y14_R1.329761.068
63_D67_K1.327981.067
10_Y24_E1.302781.046
9_L27_V1.297041.042
60_R64_Y1.265821.017
26_L64_Y1.260861.013
11_R15_R1.236690.993
6_Y10_Y1.234520.992
17_T26_L1.229240.987
61_I65_L1.228440.987
30_A56_I1.217160.978
12_Y58_R1.191130.957
28_Q32_I1.19050.956
17_T61_I1.18690.953
13_A26_L1.1770.945
14_R23_A1.175550.944
27_V31_F1.171820.941
52_W56_I1.164830.936
9_L30_A1.150820.924
30_A60_R1.149670.923
64_Y68_R1.128350.906
13_A27_V1.117090.897
5_Y8_L1.095850.880
41_Y46_G1.084440.871
2_Y31_F1.081550.869
29_E32_I1.039130.835
7_P11_R1.036070.832
35_W38_I1.031780.829
10_Y27_V1.026910.825
62_L65_L1.022790.822
8_L12_Y1.005940.808
5_Y31_F0.982610.789
26_L60_R0.982490.789
5_Y53_L0.978190.786
10_Y23_A0.966020.776
65_L69_R0.958480.770
23_A27_V0.956780.768
13_A23_A0.951040.764
46_G51_A0.950350.763
9_L53_L0.947940.761
29_E64_Y0.946370.760
22_D68_R0.94130.756
31_F35_W0.903580.726
6_Y27_V0.888070.713
3_E6_Y0.885750.711
26_L61_I0.88530.711
54_F58_R0.860770.691
33_K36_R0.858770.690
41_Y44_D0.857690.689
38_I49_F0.837440.673
34_L49_F0.827360.665
17_T23_A0.820330.659
25_D28_Q0.814230.654
55_R62_L0.812140.652
13_A16_Y0.784680.630
41_Y45_R0.771430.620
6_Y31_F0.770210.619
16_Y58_R0.758950.610
18_G23_A0.753850.606
38_I41_Y0.738990.594
62_L66_R0.737860.593
5_Y49_F0.736340.591
26_L57_A0.715090.574
12_Y16_Y0.710870.571
12_Y15_R0.709150.570
14_R18_G0.693390.557
16_Y62_L0.68940.554
51_A54_F0.689070.553
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
3n0rA0.971899.2-0.032
1sigA0.985999.2-0.027
3vdoA0.985999.2-0.012
1h3lA0.971899.2-0.001
2o7gA0.957799.20.007
2q1zA0.985999.20.014
3iydF199.20.016
4kn7X199.10.021
2lfwA0.971899.10.032
1or7A0.957799.10.039

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