GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pirin_C - Pirin C-terminal cupin domain
Pfam: PF05726 (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: CL0029
Length: 104
Sequences: 3113
Seq/Len: 29.93
HH_delta: 0.156 (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
31_V63_A0.926533.308
3_D64_R0.810062.892
32_E57_T0.7382.635
13_T55_E0.702192.507
11_S57_T0.681562.433
28_E64_R0.647532.312
40_L46_V0.614992.196
41_E44_Q0.588282.100
93_Q97_D0.578242.064
11_S55_E0.576942.060
88_R92_E0.569892.035
24_I48_L0.562582.008
7_E62_G0.549691.962
32_E59_G0.53641.915
30_S41_E0.509931.820
6_L10_A0.462991.653
4_I65_F0.460941.646
32_E37_E0.45971.641
17_P20_H0.45651.630
23_F68_L0.424121.514
92_E95_F0.408961.460
30_S61_E0.403271.440
92_E96_E0.388061.385
20_H69_G0.381841.363
86_N90_E0.373781.334
85_M90_E0.371381.326
7_E10_A0.369831.320
13_T53_E0.355341.269
89_E93_Q0.354421.265
5_K64_R0.344831.231
16_L22_A0.328541.173
8_P61_E0.327721.170
90_E93_Q0.325631.163
28_E61_E0.325231.161
94_A97_D0.322581.152
87_T90_E0.320081.143
17_P54_I0.319211.140
58_A62_G0.30711.096
6_L58_A0.301411.076
23_F45_L0.30021.072
95_F99_Q0.29651.059
17_P22_A0.294741.052
28_E42_A0.292151.043
85_M91_I0.291131.039
56_L65_F0.288461.030
80_Y95_F0.287541.027
30_S59_G0.286691.023
80_Y91_I0.286241.022
96_E99_Q0.276980.989
22_A54_I0.275150.982
15_P53_E0.273480.976
27_L64_R0.264670.945
59_G62_G0.262320.936
75_E85_M0.261530.934
26_V29_G0.257570.920
79_Q83_F0.256770.917
79_Q98_Y0.254450.908
93_Q96_E0.254160.907
22_A69_G0.250170.893
12_F65_F0.240730.859
81_G98_Y0.238550.852
42_A61_E0.235870.842
12_F15_P0.23160.827
41_E59_G0.230570.823
92_E99_Q0.230150.822
83_F89_E0.229690.820
78_V87_T0.226840.810
21_N47_V0.226660.809
40_L44_Q0.224750.802
89_E92_E0.219490.784
78_V81_G0.21940.783
88_R95_F0.216050.771
78_V91_I0.215370.769
82_P98_Y0.215270.769
81_G85_M0.213950.764
91_I95_F0.212370.758
6_L63_A0.212190.758
26_V63_A0.212030.757
26_V40_L0.2110.753
21_N82_P0.210830.753
80_Y99_Q0.210690.752
24_I65_F0.210150.750
70_G73_L0.209110.747
20_H71_E0.209050.746
14_L69_G0.204840.731
67_L70_G0.203310.726
33_V48_L0.200020.714
22_A68_L0.199580.713
4_I67_L0.197750.706
18_P35_G0.196780.703
48_L54_I0.195720.699
85_M97_D0.193130.689
70_G81_G0.190760.681
73_L76_P0.190030.678
31_V56_L0.18960.677
33_V56_L0.185860.664
27_L43_G0.185850.663
21_N98_Y0.185270.661
4_I12_F0.185250.661
81_G84_V0.184740.660
21_N81_G0.18030.644
28_E62_G0.179130.639
9_G61_E0.178950.639
77_I86_N0.17860.638
25_Y43_G0.178410.637
90_E97_D0.177660.634
34_G49_E0.17740.633
68_L80_Y0.175510.627
62_G79_Q0.174710.624
23_F81_G0.174270.622
84_V94_A0.174140.622
16_L23_F0.173440.619
23_F47_V0.173340.619
94_A98_Y0.172510.616
15_P22_A0.17210.614
34_G48_L0.171270.611
56_L84_V0.171220.611
18_P50_D0.170980.610
22_A50_D0.170540.609
25_Y42_A0.169060.604
19_G71_E0.168990.603
58_A74_N0.168420.601
4_I24_I0.167760.599
88_R99_Q0.166840.596
33_V46_V0.166640.595
72_P75_E0.166240.593
75_E86_N0.165480.591
83_F86_N0.165360.590
78_V90_E0.163750.585
78_V88_R0.16340.583
8_P62_G0.161290.576
50_D55_E0.160570.573
80_Y88_R0.160380.573
8_P58_A0.158890.567
15_P20_H0.158460.566
88_R93_Q0.158220.565
12_F24_I0.157270.561
11_S32_E0.157220.561
26_V42_A0.156980.560
90_E94_A0.156060.557
15_P49_E0.155810.556
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
2p17A0.990499.50.156
4eweA199.50.165
1j1lA199.50.207
1j58A198.90.406
2d5fA198.90.411
3c3vA198.90.411
1fxzA198.80.415
2vqaA198.80.418
2o8qA0.836598.80.427
3fjsA0.721298.80.431

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