GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GSH-S_N - Prokaryotic glutathione synthetase N-terminal domain
Pfam: PF02951 (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: 119
Sequences: 1108
Seq/Len: 9.31
HH_delta: 0.545 (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
2_K33_E0.838014.163
84_M97_A0.528812.627
105_E114_D0.506982.519
61_D64_D0.495472.461
4_A79_F0.473232.351
4_A37_Y0.459712.284
26_E29_R0.439542.184
5_F24_M0.418182.077
64_D67_K0.410882.041
35_F79_F0.374381.860
101_L111_V0.358441.781
15_P21_F0.346711.722
39_P90_F0.345611.717
24_M36_Y0.343771.708
27_A34_V0.339361.686
104_A108_G0.339011.684
59_K64_D0.323561.607
113_N118_L0.311391.547
19_T23_L0.295091.466
5_F83_L0.294341.462
5_F20_T0.292331.452
39_P97_A0.289481.438
105_E115_P0.283921.410
2_K80_D0.279231.387
35_F74_I0.274121.362
39_P86_K0.267971.331
114_D117_S0.258661.285
6_V37_Y0.239251.189
91_D99_Y0.231761.151
2_K35_F0.230141.143
26_E92_M0.229051.138
19_T22_A0.22891.137
13_I38_E0.227591.131
59_K67_K0.225781.122
105_E108_G0.222671.106
44_L100_L0.222631.106
38_E41_D0.217411.080
77_D109_V0.21421.064
78_D109_V0.212871.057
16_Y62_P0.212841.057
13_I20_T0.209811.042
96_Y99_Y0.207781.032
3_I92_M0.206991.028
25_L29_R0.206591.026
75_P78_D0.206151.024
86_K118_L0.200860.998
102_E116_Q0.200040.994
17_K104_A0.196370.976
4_A82_V0.193110.959
111_V114_D0.189680.942
3_I32_H0.189330.941
12_S36_Y0.186540.927
3_I27_A0.184760.918
106_R109_V0.18440.916
86_K96_Y0.179370.891
102_E105_E0.179240.890
20_T89_P0.176380.876
21_F25_L0.174770.868
82_V109_V0.171980.854
32_H80_D0.169140.840
44_L103_L0.168750.838
43_S68_L0.168590.838
47_G101_L0.168390.837
20_T36_Y0.167330.831
18_D87_D0.16710.830
77_D108_G0.166860.829
74_I78_D0.166060.825
14_K17_K0.164970.820
23_L97_A0.164890.819
15_P25_L0.163010.810
23_L83_L0.162640.808
29_R35_F0.160890.799
12_S40_G0.158310.786
24_M28_Q0.157510.782
63_K78_D0.156260.776
101_L115_P0.156130.776
21_F26_E0.155110.771
44_L47_G0.155020.770
24_M81_V0.154790.769
15_P61_D0.154470.767
26_E30_R0.153040.760
13_I21_F0.152630.758
18_D89_P0.152160.756
47_G113_N0.15210.756
43_S82_V0.151280.752
101_L118_L0.151190.751
2_K79_F0.150830.749
29_R75_P0.149580.743
31_G34_V0.148990.740
89_P101_L0.147570.733
99_Y103_L0.145140.721
12_S62_P0.141720.704
17_K86_K0.141720.704
15_P26_E0.141250.702
85_R113_N0.141190.701
96_Y103_L0.140880.700
21_F28_Q0.139890.695
12_S20_T0.139180.691
19_T86_K0.138950.690
111_V116_Q0.138490.688
82_V101_L0.138210.687
101_L116_Q0.137830.685
16_Y109_V0.137770.684
59_K62_P0.136930.680
19_T46_D0.134890.670
59_K63_K0.134770.670
92_M96_Y0.134740.669
31_G85_R0.134680.669
99_Y102_E0.133590.664
22_A25_L0.133350.662
60_D64_D0.133260.662
87_D90_F0.133110.661
16_Y60_D0.132590.659
28_Q65_W0.132580.659
18_D90_F0.131540.653
62_P68_L0.130340.648
99_Y118_L0.129450.643
23_L67_K0.129390.643
6_V118_L0.128710.639
21_F91_D0.128570.639
76_L112_V0.128380.638
65_W118_L0.127610.634
41_D60_D0.126540.629
75_P107_Q0.125110.622
3_I67_K0.124850.620
59_K106_R0.124670.619
2_K78_D0.124410.618
44_L96_Y0.123780.615
12_S46_D0.122720.610
102_E115_P0.122150.607
3_I34_V0.1220.606
27_A87_D0.120690.600
18_D84_M0.120010.596
84_M101_L0.119190.592
103_L106_R0.119020.591
60_D111_V0.118890.591
12_S64_D0.118580.589
15_P109_V0.11850.589
4_A32_H0.118430.588
6_V86_K0.118210.587
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
1gsaA199.40.545
4iwxA0.798399.20.59
3vpbA0.689198.90.632
2p0aA0.815198.60.68
1pk8A0.840398.50.694
1i7nA0.840398.30.714
3vpdA0.705998.10.73
1z2nX0.663997.90.742
1uc8A0.705997.90.743
3r5xA0.739597.90.746
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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