GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SRF-TF - SRF-type transcription factor (DNA-binding and dimerisation domain)
Pfam: PF00319 (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: 51
Sequences: 1129
Seq/Len: 22.14
HH_delta: -0.029 (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
24_A35_V0.650662.519
22_K26_E0.531552.058
18_K25_S0.500961.940
13_F47_Y0.461971.789
23_K26_E0.439791.703
40_F46_L0.426891.653
25_S29_T0.395861.533
23_K31_C0.367621.423
21_F25_S0.351641.362
36_A50_P0.348431.349
19_G30_L0.324651.257
11_V14_S0.323931.254
10_K14_S0.298171.155
34_D50_P0.29491.142
18_K44_G0.293041.135
12_T19_G0.292641.133
39_V47_Y0.288971.119
19_G23_K0.287791.114
26_E30_L0.275551.067
24_A37_L0.269591.044
6_K27_L0.264811.025
11_V29_T0.263381.020
25_S49_F0.262581.017
25_S43_D0.261171.011
28_S36_A0.253030.980
4_E7_S0.250950.972
17_K47_Y0.250260.969
9_R15_K0.247040.957
21_F33_V0.244440.947
2_R9_R0.242170.938
18_K42_P0.23960.928
25_S48_T0.23950.927
37_L44_G0.238640.924
25_S50_P0.235140.910
28_S35_V0.234940.910
2_R32_G0.234640.909
25_S46_L0.233640.905
14_S44_G0.232580.901
21_F37_L0.231850.898
8_R11_V0.231840.898
20_L38_I0.229160.887
4_E41_S0.224950.871
11_V15_K0.224760.870
3_I8_R0.221010.856
14_S41_S0.220040.852
19_G22_K0.219650.851
3_I9_R0.216390.838
32_G50_P0.215480.834
8_R18_K0.214380.830
41_S47_Y0.211860.820
5_N8_R0.211340.818
15_K22_K0.21030.814
23_K30_L0.209780.812
41_S46_L0.208630.808
2_R5_N0.205740.797
13_F36_A0.203370.787
13_F41_S0.20050.776
43_D50_P0.200060.775
6_K18_K0.197090.763
37_L50_P0.195270.756
9_R28_S0.193430.749
25_S42_P0.193080.748
12_T30_L0.190220.737
9_R42_P0.189440.734
15_K45_K0.188650.730
40_F47_Y0.187550.726
47_Y50_P0.186990.724
16_R19_G0.178690.692
4_E14_S0.176140.682
14_S49_F0.175910.681
27_L41_S0.175530.680
2_R10_K0.174120.674
3_I7_S0.173930.673
8_R12_T0.170680.661
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
3p57A199.8-0.029
1k6oB199.7-0.023
1mnmA199.7-0.023
1hbxA199.7-0.021
1egwA199.7-0.019
2phnA135.60.842
3nrfA0.90220.10.858
4dq9A0.9216180.861
2wk0A0.686315.80.865
4dy4A0.372515.60.865

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