GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PSP1 - PSP1 C-terminal conserved region
Pfam: PF04468 (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: 88
Sequences: 766
Seq/Len: 8.7
HH_delta: 0.894 (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
38_L74_D0.650113.356
23_R53_G0.650023.356
11_E15_E0.448272.314
33_E37_E0.377141.947
35_V44_L0.366951.894
15_E18_E0.332031.714
17_L21_R0.309361.597
76_A84_E0.299751.547
76_A83_I0.294511.520
30_F34_L0.294431.520
60_Y72_V0.282711.459
60_Y85_M0.275781.424
31_C44_L0.274341.416
7_R13_D0.272751.408
47_V56_L0.270681.397
16_R19_R0.270621.397
30_F78_E0.250551.293
31_C58_F0.248631.284
42_M62_A0.241241.245
55_K58_F0.237651.227
65_R69_R0.236721.222
48_E55_K0.234221.209
48_E59_Y0.232791.202
3_K48_E0.231671.196
2_L51_F0.231371.194
34_L74_D0.231251.194
18_E22_E0.230831.192
28_L35_V0.228051.177
75_L82_R0.222781.150
62_A66_V0.220491.138
45_V88_I0.217591.123
12_E16_R0.212941.099
66_V77_R0.209991.084
31_C35_V0.201721.041
22_E33_E0.200571.035
19_R22_E0.199841.032
27_A58_F0.199461.030
44_L58_F0.198151.023
11_E39_G0.197011.017
8_V11_E0.196341.014
84_E87_Q0.192090.992
22_E26_E0.192050.991
42_M68_F0.190680.984
45_V61_T0.190110.981
38_L70_E0.189430.978
46_D85_M0.1880.971
29_K32_R0.187750.969
22_E32_R0.187710.969
34_L38_L0.186050.960
36_K80_K0.184540.953
76_A79_F0.184130.951
3_K52_D0.183140.945
19_R23_R0.182240.941
76_A87_Q0.180390.931
37_E74_D0.180260.931
51_F59_Y0.179810.928
29_K33_E0.179760.928
28_L36_K0.179390.926
14_I29_K0.178920.924
8_V41_P0.178630.922
40_L74_D0.17860.922
50_Q55_K0.177770.918
34_L72_V0.175960.908
24_E53_G0.17590.908
21_R24_E0.175330.905
50_Q76_A0.175220.905
28_L62_A0.174180.899
18_E39_G0.173080.894
53_G56_L0.172990.893
14_I18_E0.172520.891
74_D78_E0.171960.888
28_L32_R0.169560.875
4_R36_K0.168190.868
50_Q57_T0.166790.861
50_Q60_Y0.165940.857
43_K61_T0.165590.855
35_V71_L0.165020.852
49_Y58_F0.164880.851
10_T15_E0.162460.839
29_K83_I0.160010.826
24_E32_R0.159540.824
25_E28_L0.158930.820
70_E74_D0.154970.800
62_A65_R0.154320.797
50_Q85_M0.154280.796
11_E14_I0.153490.792
23_R30_F0.153310.791
49_Y79_F0.152160.786
13_D20_L0.150930.779
67_D73_R0.150660.778
63_E79_F0.150170.775
30_F79_F0.148590.767
43_K74_D0.147780.763
55_K73_R0.147570.762
31_C56_L0.147380.761
49_Y52_D0.14670.757
22_E41_P0.146120.754
20_L80_K0.145280.750
18_E21_R0.145190.750
6_L26_E0.145080.749
24_E50_Q0.144070.744
19_R53_G0.144040.744
17_L24_E0.143770.742
75_L83_I0.143650.742
13_D66_V0.143050.738
76_A86_R0.142980.738
59_Y72_V0.142640.736
42_M87_Q0.142020.733
20_L53_G0.141880.732
6_L16_R0.141750.732
9_A14_I0.13940.720
10_T14_I0.139150.718
41_P88_I0.138840.717
4_R18_E0.138610.716
15_E22_E0.138510.715
15_E19_R0.138060.713
44_L61_T0.138050.713
28_L44_L0.138030.713
35_V42_M0.137570.710
17_L57_T0.136330.704
40_L85_M0.135370.699
32_R35_V0.133910.691
55_K83_I0.133240.688
12_E15_E0.132880.686
27_A47_V0.132850.686
60_Y81_T0.132610.685
16_R20_L0.13260.685
25_E63_E0.132570.684
65_R73_R0.132560.684
3_K81_T0.132170.682
39_G78_E0.131960.681
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
3af5A0.795548.90.894
2ycbA0.727343.20.897
3o3uN0.443230.30.905
2xr1A0.772729.60.905
3tfgA0.897719.50.913
3txvA0.965916.80.915
3iotA0.443215.60.916
4febA0.443213.50.918
1p9oA0.965912.90.919
3ob4A0.443212.20.92
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