GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GidB - rRNA small subunit methyltransferase G
Pfam: PF02527 (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: CL0063
Length: 184
Sequences: 5632
Seq/Len: 30.61
HH_delta: 0.231 (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
117_D139_K1.012873.426
76_T116_F0.947383.204
74_Q101_E0.929773.144
51_K74_Q0.866152.929
79_E85_V0.845622.860
63_G77_L0.796182.693
138_L142_G0.793032.682
53_L116_F0.747992.530
81_V84_K0.694672.349
53_L119_V0.664282.247
57_S77_L0.664242.246
105_G109_E0.654752.214
76_T103_I0.653222.209
85_V102_V0.622482.105
67_A99_N0.613572.075
92_V100_V0.607422.054
92_V102_V0.546291.848
82_G104_N0.54181.832
82_G86_A0.530621.795
53_L78_V0.52511.776
80_S106_R0.52131.763
85_V104_N0.517651.751
128_D132_E0.476711.612
59_A84_K0.461351.560
89_K93_R0.45951.554
119_V138_L0.45221.529
78_V105_G0.441811.494
79_E102_V0.439751.487
90_E94_E0.434841.471
52_V120_T0.430511.456
52_V75_V0.422321.428
51_K76_T0.421571.426
134_A144_L0.419631.419
51_K116_F0.418611.416
133_L136_P0.415381.405
55_I134_A0.413731.399
70_R73_L0.412691.396
57_S88_L0.410631.389
153_E157_E0.399811.352
126_P129_K0.397931.346
67_A75_V0.397271.344
86_A89_K0.388721.315
51_K117_D0.386811.308
86_A90_E0.378831.281
88_L102_V0.378471.280
76_T101_E0.378261.279
119_V134_A0.377391.276
66_L120_T0.371611.257
148_K155_E0.359071.214
52_V118_V0.358481.212
89_K102_V0.348881.180
90_E93_R0.342971.160
115_S139_K0.342881.160
53_L137_L0.338921.146
132_E136_P0.338211.144
121_A134_A0.336971.140
85_V89_K0.336291.137
89_K92_V0.335941.136
115_S137_L0.326971.106
113_R136_P0.321881.089
129_K133_L0.320361.083
138_L144_L0.319861.082
52_V73_L0.319791.082
77_L88_L0.309951.048
77_L100_V0.309721.047
39_L69_A0.305541.033
66_L75_V0.304451.030
26_D29_E0.303711.027
106_R109_E0.302561.023
67_A100_V0.292640.990
51_K115_S0.284730.963
64_I100_V0.283380.958
87_F91_V0.283230.958
130_L133_L0.283080.957
124_V130_L0.27730.938
78_V103_I0.274670.929
112_Y115_S0.271430.918
125_A129_K0.268120.907
139_K142_G0.267330.904
154_E157_E0.265830.899
27_P30_I0.263870.892
129_K132_E0.261780.885
112_Y116_F0.261060.883
64_I92_V0.252080.853
62_P122_R0.251180.849
19_I90_E0.247990.839
57_S79_E0.247910.838
63_G100_V0.246680.834
35_I61_F0.246130.832
41_L147_Y0.245410.830
54_D58_G0.244040.825
77_L102_V0.242590.820
74_Q99_N0.240690.814
23_S26_D0.23710.802
33_R37_D0.236350.799
63_G75_V0.236020.798
113_R140_P0.234460.793
152_A155_E0.234320.792
51_K139_K0.232790.787
20_N83_K0.232580.787
151_D154_E0.23050.780
55_I107_A0.228130.772
32_E35_I0.228020.771
89_K101_E0.227370.769
128_D131_L0.226930.767
49_G72_D0.22610.765
27_P31_W0.226090.765
34_H38_S0.225940.764
91_V95_L0.225290.762
121_A130_L0.225110.761
59_A87_F0.223430.756
65_P68_I0.222820.754
19_I22_T0.221480.749
69_A72_D0.219650.743
34_H37_D0.219140.741
29_E32_E0.218330.738
75_V99_N0.218280.738
61_F65_P0.217330.735
71_P99_N0.216710.733
57_S63_G0.21620.731
103_I112_Y0.215630.729
54_D57_S0.215510.729
57_S60_G0.2140.724
113_R116_F0.21380.723
31_W36_L0.213030.720
58_G77_L0.210730.713
22_T26_D0.208770.706
83_K87_F0.207160.701
127_L146_A0.204210.691
148_K156_L0.20250.685
54_D63_G0.200360.678
87_F90_E0.199590.675
84_K88_L0.199570.675
54_D62_P0.196930.666
32_E36_L0.195730.662
51_K73_L0.195650.662
131_L135_R0.194540.658
38_S145_L0.192480.651
62_P68_I0.19150.648
33_R83_K0.190290.644
60_G77_L0.190240.643
29_E33_R0.190230.643
149_G155_E0.189780.642
121_A156_L0.188210.637
64_I68_I0.186850.632
60_G88_L0.186760.632
111_E116_F0.18660.631
127_L130_L0.185790.628
127_L131_L0.185750.628
55_I123_A0.184820.625
122_R148_K0.184230.623
101_E114_E0.184210.623
43_P69_A0.183330.620
38_S61_F0.183220.620
42_L70_R0.182950.619
20_N26_D0.182440.617
55_I78_V0.182070.616
75_V100_V0.181690.614
61_F123_A0.181580.614
149_G152_A0.181440.614
54_D123_A0.180770.611
134_A142_G0.180440.610
41_L45_L0.180370.610
131_L146_A0.179070.606
45_L52_V0.178870.605
24_I33_R0.178760.605
118_V145_L0.178730.604
118_V143_R0.178640.604
55_I130_L0.178460.604
51_K114_E0.17810.602
110_P133_L0.177310.600
57_S84_K0.177250.599
150_P153_E0.176920.598
148_K152_A0.176810.598
113_R132_E0.175940.595
93_R96_G0.175840.595
56_G61_F0.175290.593
61_F122_R0.174830.591
68_I95_L0.1740.588
80_S108_E0.173590.587
125_A133_L0.173540.587
44_F47_D0.173360.586
22_T27_P0.172730.584
110_P113_R0.17270.584
134_A138_L0.171670.581
111_E114_E0.171180.579
93_R140_P0.170910.578
107_A137_L0.170080.575
113_R137_L0.169880.575
121_A124_V0.16960.574
64_I91_V0.168050.568
80_S84_K0.16740.566
56_G107_A0.167340.566
62_P123_A0.167130.565
116_F137_L0.16570.560
135_R140_P0.165370.559
88_L91_V0.165310.559
20_N25_R0.16490.558
86_A93_R0.164870.558
41_L145_L0.164630.557
56_G62_P0.164150.555
36_L121_A0.164110.555
89_K104_N0.163030.551
115_S136_P0.162530.550
48_F73_L0.162210.549
79_E88_L0.162180.548
111_E136_P0.162010.548
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
3g89A199.90.231
1xdzA199.90.262
1jsxA0.96299.80.352
3g2mA0.989199.70.44
2frnA0.967499.70.444
3dh0A0.934899.70.447
2b3tA0.967499.70.449
3dtnA0.96299.70.451
3mggA0.940299.70.461
4gekA0.983799.70.462

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