GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SpoU_methylase - SpoU rRNA Methylase family
Pfam: PF00588 (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: CL0098
Length: 142
Sequences: 6837
Seq/Len: 48.15
HH_delta: 0.013 (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
80_A116_C1.71783.251
101_F133_V1.642383.108
5_V98_A1.611383.049
81_T140_A1.510592.859
135_V138_A1.451172.746
101_F137_A1.382942.617
63_D66_E1.319842.498
29_G59_R1.317512.493
18_I137_A1.317432.493
110_E114_E1.257462.380
34_G62_D1.114792.110
3_I29_G1.031561.952
80_A108_L0.925461.751
29_G57_P0.921231.743
7_D109_S0.913141.728
65_E115_L0.905311.713
69_K115_L0.905231.713
27_V141_L0.895811.695
4_V141_L0.875111.656
19_I30_V0.872881.652
79_V120_V0.86341.634
25_F142_Y0.862711.633
4_V18_I0.857141.622
31_I61_V0.834661.579
77_T118_H0.821521.555
137_A141_L0.814221.541
99_L140_A0.807911.529
82_S113_L0.787371.490
71_L98_A0.779981.476
103_N106_R0.766991.451
22_A27_V0.756681.432
79_V118_H0.755851.430
23_A126_G0.750251.420
23_A56_L0.742081.404
49_S53_H0.721851.366
10_Q105_S0.71351.350
24_A124_M0.704271.333
4_V22_A0.685751.298
9_V133_V0.679731.286
76_Y96_K0.677731.282
85_A121_S0.672951.273
86_T118_H0.671371.270
25_F88_L0.662681.254
21_T138_A0.659281.248
120_V140_A0.651581.233
3_I31_I0.647011.224
19_I58_I0.639981.211
88_L140_A0.622761.178
32_L58_I0.614771.163
88_L93_F0.614071.162
79_V97_V0.613961.162
111_E114_E0.604431.144
72_K117_D0.585041.107
17_A48_A0.584681.106
77_T97_V0.583381.104
19_I56_L0.580121.098
8_N103_N0.57971.097
52_A128_V0.575871.090
62_D66_E0.571981.082
34_G60_R0.569361.077
7_D112_V0.568771.076
46_L53_H0.563031.065
65_E69_K0.553661.048
91_L120_V0.552641.046
17_A134_A0.547191.035
113_L119_R0.53891.020
78_I100_V0.536111.014
23_A55_H0.534671.012
109_S112_V0.530751.004
23_A52_A0.525980.995
7_D108_L0.524980.993
82_S119_R0.524270.992
21_T135_V0.520520.985
70_D74_N0.519420.983
122_I136_A0.517650.980
83_P121_S0.516050.977
131_L139_I0.508640.963
67_A71_L0.502390.951
78_I98_A0.502140.950
76_Y98_A0.498450.943
87_P121_S0.496990.940
6_L18_I0.495160.937
13_G17_A0.492360.932
18_I133_V0.490050.927
93_F97_V0.489620.927
77_T95_K0.489270.926
31_I67_A0.486010.920
66_E69_K0.483090.914
81_T101_F0.480940.910
87_P90_E0.476150.901
69_K73_E0.475240.899
64_L112_V0.472160.893
24_A128_V0.471710.893
23_A128_V0.47160.892
25_F141_L0.471190.892
80_A113_L0.471160.892
55_H127_G0.468530.887
17_A135_V0.467130.884
91_L118_H0.463350.877
68_L78_I0.460520.871
23_A127_G0.457020.865
67_A98_A0.455860.863
79_V91_L0.452880.857
8_N106_R0.452230.856
70_D73_E0.451610.855
13_G48_A0.4510.853
72_K115_L0.450620.853
86_T91_L0.444710.842
26_G125_Y0.443360.839
22_A30_V0.443170.839
69_K72_K0.437530.828
25_F139_I0.435410.824
94_P97_V0.434480.822
46_L54_E0.433170.820
61_V67_A0.42660.807
77_T117_D0.419270.793
101_F136_A0.411920.779
4_V101_F0.411360.778
3_I76_Y0.410340.776
21_T141_L0.408690.773
15_L45_V0.408180.772
33_V67_A0.407050.770
122_I139_I0.402910.762
68_L112_V0.400430.758
41_Y44_K0.398990.755
21_T24_A0.39810.753
13_G44_K0.396980.751
64_L68_L0.396470.750
8_N36_R0.383780.726
5_V67_A0.383260.725
5_V64_L0.383090.725
41_Y45_V0.382830.724
133_V137_A0.378170.716
19_I53_H0.376120.712
123_P142_Y0.37260.705
6_L9_V0.36820.697
86_T90_E0.366720.694
134_A138_A0.362940.687
2_L96_K0.362920.687
5_V33_V0.362660.686
15_L38_A0.361490.684
7_D103_N0.358180.678
100_V116_C0.354550.671
110_E113_L0.350820.664
6_L101_F0.350110.663
19_I45_V0.349290.661
25_F122_I0.348590.660
8_N109_S0.34670.656
13_G134_A0.344080.651
2_L97_V0.344010.651
80_A119_R0.342010.647
100_V112_V0.340820.645
89_Y93_F0.340360.644
3_I98_A0.339940.643
4_V27_V0.338770.641
5_V71_L0.338060.640
40_P60_R0.336950.638
81_T99_L0.336320.636
81_T120_V0.335060.634
2_L28_D0.333490.631
3_I71_L0.333360.631
5_V68_L0.331970.628
28_D76_Y0.331460.627
15_L32_L0.330090.625
68_L115_L0.329750.624
84_G119_R0.329720.624
101_F140_A0.328080.621
100_V108_L0.325610.616
32_L36_R0.323370.612
12_P42_N0.323180.612
21_T137_A0.322350.610
19_I52_A0.321890.609
6_L15_L0.321890.609
2_L27_V0.321470.608
71_L76_Y0.319970.605
41_Y46_L0.316520.599
111_E115_L0.316430.599
23_A54_E0.315780.598
66_E70_D0.314110.594
78_I116_C0.312150.591
32_L37_C0.31050.588
8_N34_G0.309840.586
107_G130_S0.307670.582
9_V15_L0.305980.579
10_Q103_N0.304840.577
77_T94_P0.303360.574
6_L133_V0.301830.571
18_I101_F0.301290.570
22_A141_L0.300640.569
139_I142_Y0.299460.567
116_C119_R0.298050.564
135_V139_I0.294980.558
61_V70_D0.292780.554
4_V137_A0.29270.554
49_S54_E0.287330.544
10_Q106_R0.286040.541
14_N104_E0.285940.541
108_L112_V0.284290.538
108_L116_C0.283920.537
25_F124_M0.283090.536
83_P129_D0.281760.533
2_L141_L0.281290.532
65_E111_E0.280460.531
25_F89_Y0.277840.526
5_V100_V0.272570.516
108_L113_L0.272090.515
47_R50_A0.270430.512
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
3nk6A0.98591000.013
1x7oA0.9931000.019
1gz0A0.9931000.022
1ipaA0.97891000.025
2i6dA0.9931000.033
4kgnA0.9931000.044
3e5yA0.9931000.044
3n4jA0.9931000.053
1v2xA0.97891000.061
1zjrA0.98591000.065

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