GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cro - Cro
Pfam: PF09048 (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: 59
Sequences: 26890
Seq/Len: 455.76
HH_delta: 0.107 (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
13_H21_A4.525623.397
9_Y21_A2.985822.241
25_T28_A2.697592.025
51_A55_R2.627351.972
17_K20_R2.297841.725
11_K51_A2.271421.705
13_H17_K2.192261.645
9_Y13_H2.129421.598
11_K41_V2.046751.536
24_V28_A1.992061.495
12_E55_R1.940531.456
15_Q33_L1.894651.422
35_A40_F1.838791.380
49_V53_E1.806141.356
9_Y12_E1.786961.341
30_S34_R1.62781.222
28_A32_A1.612041.210
18_A29_I1.583191.188
16_A26_Q1.537941.154
12_E21_A1.497051.124
48_S52_E1.493441.121
46_D49_V1.428321.072
50_E54_I1.40191.052
31_K34_R1.38181.037
35_A38_N1.338731.005
45_P48_S1.32210.992
9_Y22_L1.315540.987
41_V47_G1.234110.926
22_L29_I1.192890.895
52_E55_R1.188630.892
15_Q39_I1.179490.885
9_Y18_A1.154590.867
49_V52_E1.126280.845
24_V31_K1.125110.844
48_S51_A1.120680.841
12_E51_A1.105840.830
20_R23_G1.103190.828
45_P49_V1.080760.811
10_V33_L1.068470.802
24_V29_I1.06120.796
14_G40_F1.057380.794
13_H18_A1.044880.784
26_Q30_S1.044040.784
18_A22_L1.04080.781
17_K21_A1.023650.768
11_K14_G0.944010.709
16_A20_R0.918810.690
10_V18_A0.892950.670
27_S31_K0.881490.662
25_T31_K0.873760.656
28_A31_K0.847730.636
27_S30_S0.834210.626
24_V32_A0.829220.622
47_G52_E0.824010.618
14_G38_N0.804530.604
29_I32_A0.804410.604
10_V29_I0.790610.593
11_K47_G0.787980.591
46_D50_E0.775330.582
14_G48_S0.743670.558
42_T45_P0.733740.551
11_K48_S0.718440.539
15_Q26_Q0.713990.536
15_Q29_I0.709850.533
15_Q30_S0.688780.517
40_F48_S0.678760.509
10_V15_Q0.640020.480
11_K55_R0.63870.479
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
2ovgA198.90.107
2cw1A198.60.205
2h98A0.966198.50.225
1ixcA0.966198.40.253
1al3A0.966198.40.257
2h9bA0.966198.40.261
2esnA0.966198.30.268
1uthA0.966198.30.269
3szpA0.966198.30.272
3fzvA0.966198.30.281

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