GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GreA_GreB - Transcription elongation factor GreAGreB C-term
Pfam: PF01272 (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: CL0487
Length: 77
Sequences: 2830
Seq/Len: 36.75
HH_delta: -0.023 (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
60_E67_E1.245952.808
13_T74_E1.142762.576
13_T22_E1.036692.337
62_E67_E0.962752.170
55_V74_E0.958062.159
13_T76_E0.937492.113
15_K20_G0.933612.104
60_E69_K0.929392.095
49_A61_V0.913462.059
34_D37_N0.906822.044
53_K59_V0.882631.989
30_P43_D0.872841.967
15_K73_L0.854321.926
53_K57_D0.839831.893
13_T24_T0.798861.801
11_T26_T0.793691.789
15_K22_E0.770031.736
58_E69_K0.755821.704
14_L25_Y0.719171.621
14_L70_Y0.691281.558
15_K71_E0.677181.526
26_T39_K0.673151.517
5_V54_K0.671661.514
58_E71_E0.663031.494
63_L68_R0.647241.459
8_I29_G0.64661.457
28_V39_K0.646561.457
24_T76_E0.626461.412
14_L23_E0.620451.398
16_D19_D0.607861.370
11_T24_T0.567721.280
11_T76_E0.564091.271
13_T73_L0.560071.262
6_V72_I0.54861.236
56_G71_E0.486351.096
27_L47_G0.484261.091
6_V12_V0.469431.058
16_D68_R0.463461.045
7_T10_S0.456921.030
55_V75_I0.448981.012
44_S47_G0.44641.006
22_E73_L0.420430.948
53_K72_I0.410720.926
4_D54_K0.392240.884
7_T52_G0.387520.873
10_S75_I0.378670.853
28_V32_E0.378370.853
30_P47_G0.371940.838
27_L42_I0.365670.824
25_Y40_I0.365660.824
41_S44_S0.361580.815
9_G32_E0.355440.801
9_G29_G0.348540.786
14_L50_L0.347140.782
40_I46_L0.344110.776
8_I32_E0.339660.766
48_K53_K0.337470.761
40_I45_P0.332670.750
16_D70_Y0.318780.719
18_D68_R0.314080.708
29_G32_E0.307730.694
6_V27_L0.30470.687
33_A39_K0.299890.676
26_T35_P0.283170.638
55_V73_L0.283030.638
61_V70_Y0.281910.635
30_P41_S0.280010.631
25_Y53_K0.278520.628
5_V52_G0.277650.626
42_I51_L0.272020.613
30_P42_I0.266220.600
54_K57_D0.265960.599
43_D52_G0.25660.578
50_L59_V0.25660.578
34_D38_G0.255210.575
15_K58_E0.250930.566
4_D75_I0.247550.558
23_E68_R0.246470.556
3_D10_S0.244380.551
3_D7_T0.24410.550
65_G68_R0.2440.550
7_T31_D0.242210.546
25_Y28_V0.236180.532
24_T74_E0.236170.532
63_L66_G0.235110.530
47_G50_L0.234270.528
16_D46_L0.233920.527
15_K18_D0.233840.527
35_P39_K0.231190.521
43_D48_K0.22930.517
14_L46_L0.228370.515
8_I31_D0.227140.512
46_L70_Y0.224980.507
53_K61_V0.224370.506
35_P38_G0.224290.506
8_I42_I0.22210.501
8_I51_L0.216320.488
23_E70_Y0.216110.487
16_D23_E0.213970.482
61_V64_P0.211180.476
31_D42_I0.210690.475
49_A63_L0.210080.474
49_A70_Y0.208630.470
10_S56_G0.20550.463
14_L53_K0.204140.460
7_T51_L0.202220.456
25_Y70_Y0.201590.454
35_P40_I0.201420.454
60_E65_G0.200520.452
46_L61_V0.198980.448
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
2p4vA0.98799.7-0.023
1grjA199.7-0.022
3bmbA199.7-0.012
2pn0A199.7-0.012
2f23A199.7-0.006
3gtyX0.96178.10.789
1t11A0.97474.60.794
1w26A0.948172.70.797
1hxvA0.96165.20.807
1cz4A0.98746.40.827

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