GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GTP_cyclohydro2 - GTP cyclohydrolase II
Pfam: PF00925 (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: 169
Sequences: 2049
Seq/Len: 12.12
HH_delta: -0.054 (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
21_Y137_D1.124.480
6_E17_R0.87733.509
142_K162_E0.847993.392
8_P15_E0.770513.082
51_E88_R0.769553.078
3_R19_H0.71982.879
144_R165_E0.707542.830
35_K77_A0.699262.797
76_I84_L0.679672.718
3_R137_D0.593882.375
73_M84_L0.581692.327
23_D26_D0.550132.200
98_N121_F0.533622.134
8_P17_R0.503172.012
20_A97_L0.498091.992
2_E24_T0.49181.967
83_V140_V0.490861.963
71_K74_R0.481191.925
6_E19_H0.479321.917
140_V143_M0.468321.873
74_R78_E0.463061.852
43_P164_V0.445531.782
43_P142_K0.442471.770
19_H34_V0.438461.754
7_C18_L0.42631.705
2_E22_R0.41191.647
144_R167_V0.40561.622
143_M161_L0.398571.594
34_V83_V0.398411.593
79_E144_R0.396791.587
11_T16_F0.385011.540
122_P125_L0.379881.519
104_N108_E0.377261.509
41_D81_R0.375751.503
75_R146_L0.3691.476
121_F125_L0.368071.472
12_R67_W0.363731.455
75_R79_E0.360851.443
12_R70_D0.359821.439
151_R155_A0.358061.432
154_V158_G0.357461.430
142_K164_V0.355961.424
147_T153_Y0.355531.422
157_E162_E0.354031.416
3_R6_E0.352771.411
5_A100_L0.33961.358
45_L167_V0.332061.328
45_L75_R0.33141.325
45_L79_E0.321441.286
40_P81_R0.318661.275
129_G158_G0.317191.269
4_V22_R0.314731.259
154_V157_E0.31441.257
85_V134_I0.310981.244
53_L58_F0.308861.235
42_E81_R0.306731.227
11_T14_G0.304711.219
131_G161_L0.302081.208
129_G133_Q0.300411.202
38_I81_R0.297421.190
133_Q159_F0.291911.168
32_A83_V0.291021.164
44_V81_R0.2881.152
75_R78_E0.286441.146
43_P165_E0.279821.119
5_A104_N0.276431.106
83_V138_L0.272421.090
75_R167_V0.271731.087
3_R21_Y0.266111.064
30_H88_R0.26131.045
16_F73_M0.261291.045
39_D42_E0.258431.034
45_L144_R0.257681.031
31_L58_F0.256291.025
132_A155_A0.256171.025
57_V107_D0.25471.019
32_A138_L0.253281.013
155_A158_G0.250971.004
22_R29_E0.248720.995
18_L31_L0.244660.979
52_C65_C0.244240.977
7_C100_L0.243480.974
33_L84_L0.243190.973
132_A159_F0.242720.971
153_Y166_R0.241880.967
38_I44_V0.239430.958
52_C63_C0.238810.955
14_G35_K0.238140.952
67_W70_D0.237210.949
12_R59_G0.236240.945
69_L84_L0.235050.940
8_P107_D0.231620.926
12_R61_L0.231530.926
48_V87_L0.229380.917
46_V143_M0.229270.917
37_D40_P0.22690.908
52_C55_G0.22680.907
25_I133_Q0.226410.906
13_F70_D0.225680.903
71_K75_R0.224730.899
144_R164_V0.224270.897
30_H134_I0.22370.895
20_A31_L0.223010.892
46_V135_L0.22170.887
98_N101_R0.218140.872
62_R107_D0.217990.872
104_N107_D0.217940.872
125_L153_Y0.217830.871
53_L57_V0.217630.870
58_F69_L0.2140.856
129_G159_F0.213640.854
128_Y153_Y0.208480.834
50_S55_G0.207320.829
60_S63_C0.207120.828
40_P44_V0.207090.828
31_L53_L0.204550.818
19_H32_A0.203850.815
92_R95_G0.201540.806
48_V85_V0.201030.804
94_I105_L0.200050.800
97_L101_R0.197380.789
100_L104_N0.197170.789
16_F35_K0.195450.782
43_P144_R0.195270.781
113_V123_E0.193870.775
13_F74_R0.193810.775
136_R141_K0.192620.770
128_Y132_A0.191050.764
131_G158_G0.190130.760
95_G99_K0.189960.760
132_A160_G0.188470.754
103_Y111_D0.187740.751
9_L33_L0.185980.744
19_H138_L0.185060.740
10_P60_S0.183430.734
91_G95_G0.182890.731
22_R28_Q0.182640.730
60_S103_Y0.181630.726
58_F96_L0.181590.726
67_W71_K0.18120.725
42_E142_K0.180850.723
153_Y157_E0.180630.722
72_A146_L0.18060.722
136_R158_G0.180280.721
28_Q85_V0.179670.719
149_N152_K0.179590.718
33_L73_M0.17850.714
10_P15_E0.177520.710
21_Y134_I0.173420.694
43_P81_R0.172880.691
46_V85_V0.172540.690
125_L151_R0.171330.685
20_A100_L0.171070.684
64_D103_Y0.168940.676
44_V83_V0.168930.676
3_R134_I0.168810.675
29_E97_L0.167890.671
151_R154_V0.167670.671
37_D44_V0.167220.669
47_R126_R0.166980.668
83_V135_L0.166830.667
132_A156_L0.166680.667
1_V133_Q0.166570.666
30_H48_V0.165520.662
7_C10_P0.165030.660
54_T68_Q0.163720.655
4_V97_L0.163630.654
55_G86_Y0.163010.652
94_I112_T0.161430.646
102_A106_Q0.16120.645
4_V20_A0.161070.644
91_G149_N0.160690.643
141_K158_G0.160250.641
4_V19_H0.159610.638
48_V156_L0.159560.638
70_D74_R0.157540.630
36_G44_V0.156830.627
13_F59_G0.15650.626
10_P107_D0.15610.624
132_A136_R0.155930.624
55_G65_C0.155770.623
46_V83_V0.155520.622
9_L16_F0.154830.619
87_L131_G0.154650.619
131_G143_M0.154210.617
30_H130_I0.153510.614
58_F67_W0.153340.613
40_P141_K0.152440.610
63_C92_R0.152430.610
86_Y99_K0.152170.609
124_D152_K0.151920.608
52_C91_G0.151370.605
106_Q111_D0.150930.604
37_D81_R0.15090.604
52_C86_Y0.15010.600
66_G70_D0.149820.599
127_D130_I0.149050.596
55_G66_G0.148910.596
36_G56_D0.148910.596
60_S109_G0.148440.594
59_G70_D0.148230.593
39_D78_E0.14690.588
90_E95_G0.146660.587
109_G112_T0.14610.584
13_F16_F0.145970.584
41_D140_V0.145320.581
4_V101_R0.144440.578
7_C61_L0.1440.576
45_L165_E0.143970.576
30_H51_E0.143310.573
135_L140_V0.143290.573
65_C124_D0.142720.571
58_F86_Y0.142140.568
89_Q98_N0.141980.568
143_M159_F0.141730.567
153_Y163_V0.141660.567
99_K103_Y0.141450.566
50_S89_Q0.141420.566
64_D112_T0.140590.562
99_K111_D0.140560.562
155_A159_F0.140410.562
35_K80_G0.139280.557
5_A97_L0.13920.557
41_D142_K0.138980.556
63_C95_G0.138680.555
129_G132_A0.138580.554
124_D128_Y0.138480.554
64_D85_V0.138180.553
62_R103_Y0.13790.552
106_Q112_T0.137640.551
60_S94_I0.13740.550
23_D30_H0.137150.549
67_W143_M0.137030.548
64_D111_D0.136920.548
102_A113_V0.136240.545
42_E157_E0.136160.545
129_G161_L0.136110.544
102_A112_T0.135850.543
16_F48_V0.135750.543
50_S65_C0.135280.541
141_K154_V0.135030.540
44_V140_V0.134870.539
55_G63_C0.134530.538
102_A111_D0.134490.538
113_V151_R0.134450.538
60_S91_G0.134410.538
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
2bz1A1100-0.054
3ur8A0.343255.20.933
3em5A0.337344.70.936
1un8A0.7337410.938
3e1sA0.3669160.948
3ct4A0.751513.90.95
1oi2A0.757413.60.95
2iu4A0.751512.50.951
2yi9A0.45568.70.954
3u02A0.53858.40.954

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