GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
P22_Cro - DNA-binding transcriptional regulator Cro
Pfam: PF14549 (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: 60
Sequences: 24434
Seq/Len: 407.23
HH_delta: 0.105 (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
18_A44_L3.194022.480
13_S23_P2.952142.292
14_K18_A2.562591.989
23_P27_S2.553971.983
25_A29_W2.502051.942
5_A8_Y2.440841.895
5_A9_F2.436411.891
12_Q27_S2.102021.632
13_S17_K2.061251.600
21_V37_R1.914171.486
24_Q27_S1.900381.475
29_W37_R1.891391.468
4_D8_Y1.862561.446
11_G14_K1.79251.392
15_L26_V1.720861.336
19_L44_L1.712831.330
50_K53_P1.605561.246
25_A28_Q1.581051.227
37_R40_Q1.57041.219
21_V25_A1.48121.150
39_Y43_K1.376361.068
6_I12_Q1.361751.057
15_L45_T1.344131.043
29_W33_I1.340081.040
16_A23_P1.333221.035
28_Q31_E1.280090.994
3_K12_Q1.258240.977
12_Q23_P1.222020.949
49_L53_P1.20630.936
4_D7_K1.199770.931
5_A49_L1.195050.928
24_Q28_Q1.194320.927
3_K7_K1.176830.914
14_K17_K1.159050.900
16_A26_V1.153720.896
22_S25_A1.142060.887
32_R36_E1.141260.886
21_V26_V1.13970.885
42_E51_C1.080590.839
5_A53_P1.077490.836
38_A42_E1.073070.833
35_A38_A1.050730.816
19_L41_I1.031670.801
9_F46_N1.023510.795
6_I26_V1.017630.790
5_A45_T1.016470.789
40_Q44_L1.007070.782
35_A51_C0.996010.773
39_Y51_C0.990690.769
22_S28_Q0.947130.735
38_A51_C0.936160.727
34_P37_R0.935360.726
3_K6_I0.915450.711
25_A37_R0.905830.703
36_E40_Q0.888740.690
21_V40_Q0.884880.687
35_A39_Y0.874990.679
41_I45_T0.867970.674
16_A19_L0.86690.673
15_L44_L0.863710.671
33_I37_R0.816070.634
32_R35_A0.809410.628
42_E54_E0.795140.617
42_E50_K0.786160.610
15_L41_I0.76350.593
25_A31_E0.756620.587
29_W34_P0.755830.587
19_L37_R0.747910.581
9_F45_T0.745050.578
6_I15_L0.744970.578
42_E49_L0.731080.568
12_Q16_A0.72040.559
21_V29_W0.710180.551
20_G40_Q0.708310.550
15_L19_L0.70630.548
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
4ichA0.966798.10.105
3mlfA0.9667980.133
2kpjA0.9667980.138
3op9A0.966797.90.144
1y9qA0.966797.90.149
2fjrA0.9597.90.155
1b0nA0.966797.90.156
1adrA0.966797.90.158
3bd1A197.90.158
2bnmA0.966797.90.158

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