GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sushi - Sushi domain (SCR repeat)
Pfam: PF00084 (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: 56
Sequences: 4167
Seq/Len: 74.41
HH_delta: -0.077 (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
14_C25_V1.595823.796
7_I10_G1.344683.199
41_I51_P1.292253.074
11_S30_N0.815851.941
11_S28_S0.77991.855
35_L54_P0.74711.777
27_F53_P0.73021.737
9_N33_Y0.717871.708
24_T40_T0.71341.697
41_I50_S0.713141.696
24_T42_T0.692211.647
19_Y23_S0.639881.522
9_N30_N0.621981.480
13_S28_S0.611641.455
4_P27_F0.602661.434
26_T40_T0.58671.396
27_F54_P0.541711.289
44_Q50_S0.519411.236
14_C19_Y0.514071.223
20_S23_S0.513251.221
14_C18_P0.483161.149
36_S55_T0.460711.096
44_Q48_Q0.436571.039
19_Y25_V0.435971.037
43_C56_C0.415910.989
27_F41_I0.402540.958
43_C49_W0.401210.954
1_C4_P0.400750.953
26_T39_S0.388320.924
21_Y45_S0.378710.901
12_I19_Y0.374160.890
3_P12_I0.368440.876
6_P10_G0.365460.869
10_G30_N0.357320.850
44_Q47_G0.352070.838
7_I27_F0.349380.831
38_S51_P0.339530.808
12_I25_V0.329790.785
4_P25_V0.323750.770
29_C32_G0.320670.763
18_P23_S0.320550.763
45_S48_Q0.318210.757
41_I53_P0.308560.734
15_T25_V0.308470.734
13_S26_T0.30630.729
41_I54_P0.304340.724
2_P44_Q0.303940.723
8_P55_T0.303430.722
3_P17_N0.303120.721
27_F35_L0.302740.720
1_C43_C0.302630.720
22_G42_T0.296780.706
11_S15_T0.296590.706
19_Y49_W0.29610.704
41_I52_P0.295920.704
4_P12_I0.295110.702
20_S45_S0.293760.699
42_T45_S0.293550.698
35_L39_S0.290480.691
3_P6_P0.289220.688
5_P53_P0.285480.679
6_P26_T0.281170.669
10_G54_P0.276610.658
7_I12_I0.273820.651
2_P19_Y0.269080.640
5_P12_I0.268810.639
13_S18_P0.268290.638
18_P21_Y0.264340.629
49_W56_C0.259670.618
8_P11_S0.259130.616
25_V41_I0.258910.616
14_C23_S0.253430.603
29_C43_C0.253260.602
15_T26_T0.250160.595
21_Y47_G0.246640.587
22_G47_G0.244560.582
1_C29_C0.242540.577
34_E51_P0.242450.577
21_Y35_L0.241940.576
32_G41_I0.241160.574
2_P5_P0.234460.558
31_P34_E0.23410.557
28_S39_S0.232360.553
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
3hrzD199-0.077
3t5oA199-0.073
2atyA199-0.073
2yraA198.9-0.057
4igdA198.9-0.053
1zjkA198.9-0.04
4j1yA0.982198.9-0.034
3iypF198.9-0.032
1ly2A198.8-0.026
3govA198.8-0.026

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