GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNase_H - RNase H
Pfam: PF00075 (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: CL0219
Length: 132
Sequences: 5613
Seq/Len: 42.52
HH_delta: 0.101 (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
61_T108_R1.552983.975
67_Q71_N1.242713.181
6_I51_A1.204773.084
50_E53_K1.200263.072
48_I69_V1.067532.733
59_K104_K1.029492.635
71_N75_K1.019862.611
13_R128_K1.007422.579
53_K98_L0.968842.480
30_N122_R0.918962.352
7_Y63_Y0.84562.165
64_T70_L0.810152.074
8_T64_T0.802342.054
5_I63_Y0.778881.994
63_Y108_R0.773111.979
61_T106_R0.760161.946
48_I62_I0.731491.872
5_I61_T0.667871.710
21_A33_F0.662331.695
67_Q109_W0.616891.579
7_Y119_G0.616771.579
23_Y31_F0.615881.577
122_R125_R0.610181.562
32_S129_E0.599841.535
9_D65_D0.561421.437
46_Q50_E0.557821.428
70_L107_F0.552641.415
41_N72_A0.550771.410
125_R129_E0.532141.362
67_Q70_L0.531151.360
33_F50_E0.528161.352
11_S127_A0.504291.291
19_G43_A0.501641.284
21_A50_E0.496291.270
23_Y51_A0.495561.269
70_L74_N0.484681.241
41_N68_Y0.482751.236
123_A127_A0.474031.213
21_A35_L0.471051.206
124_D128_K0.468261.199
49_I53_K0.458911.175
53_K94_E0.452831.159
11_S128_K0.451721.156
6_I25_V0.438851.123
21_A47_A0.436841.118
58_R103_I0.433891.111
48_I64_T0.433431.109
59_K106_R0.43141.104
8_T48_I0.427831.095
113_H121_E0.4111.052
66_S69_V0.402611.031
64_T69_V0.393231.007
33_F36_G0.392951.006
30_N35_L0.38580.988
113_H119_G0.384960.985
124_D127_A0.37720.966
42_R94_E0.370850.949
22_G126_L0.36950.946
49_I95_I0.365840.936
30_N126_L0.364210.932
9_D124_D0.357730.916
38_Q42_R0.354350.907
7_Y110_V0.353470.905
94_E97_E0.352660.903
45_L68_Y0.347040.888
92_K96_W0.344950.883
60_V105_V0.344320.881
49_I94_E0.344030.881
54_A60_V0.343930.880
73_L107_F0.331330.848
20_G127_A0.323240.827
52_L62_I0.323120.827
65_D124_D0.323030.827
46_Q49_I0.322380.825
120_N124_D0.321330.823
39_S42_R0.319260.817
125_R128_K0.316340.810
32_S128_K0.315720.808
93_N96_W0.313780.803
52_L60_V0.312360.800
24_V122_R0.310260.794
24_V123_A0.306470.784
9_D44_E0.305450.782
98_L101_R0.305360.782
12_C40_N0.304860.780
31_F35_L0.300150.768
32_S126_L0.300130.768
71_N81_G0.299040.765
8_T51_A0.298710.765
11_S14_P0.29760.762
4_I26_W0.296980.760
14_P20_G0.29620.758
45_L69_V0.295520.756
120_N123_A0.290890.745
8_T47_A0.289280.740
49_I98_L0.282770.724
45_L49_I0.282610.723
93_N97_E0.281270.720
84_K87_N0.279350.715
113_H127_A0.278060.712
41_N66_S0.277420.710
6_I60_V0.277270.710
65_D120_N0.271620.695
35_L43_A0.271330.695
48_I107_F0.271320.695
40_N66_S0.269450.690
10_G43_A0.268310.687
4_I60_V0.266980.683
26_W29_R0.266720.683
81_G85_T0.266590.682
24_V27_G0.266490.682
39_S68_Y0.265890.681
69_V72_A0.265840.680
75_K81_G0.26210.671
82_W93_N0.259050.663
84_K88_G0.258860.663
23_Y50_E0.258790.662
87_N90_P0.256990.658
81_G84_K0.254860.652
5_I26_W0.254040.650
121_E125_R0.252810.647
57_H102_G0.251650.644
85_T90_P0.250120.640
13_R16_P0.249910.640
90_P93_N0.249640.639
119_G123_A0.248930.637
82_W86_S0.248880.637
113_H120_N0.24880.637
7_Y23_Y0.248530.636
74_N107_F0.248440.636
109_W112_G0.247420.633
25_V57_H0.246990.632
100_S107_F0.246360.631
12_C39_S0.245380.628
59_K103_I0.244680.626
6_I62_I0.243870.624
22_G123_A0.242550.621
101_R104_K0.242340.620
95_I99_L0.242290.620
72_A75_K0.237830.609
46_Q91_I0.236220.605
41_N45_L0.235660.603
50_E54_A0.233370.597
123_A128_K0.232580.595
31_F50_E0.231860.594
39_S66_S0.231710.593
68_Y72_A0.229390.587
63_Y119_G0.228370.585
6_I23_Y0.22580.578
14_P17_G0.225760.578
37_G46_Q0.225620.578
110_V119_G0.224170.574
19_G38_Q0.223250.571
83_K87_N0.22260.570
90_P94_E0.221740.568
57_H103_I0.221570.567
85_T88_G0.221170.566
12_C16_P0.21980.563
63_Y110_V0.21950.562
113_H124_D0.218490.559
30_N34_R0.216990.555
91_I98_L0.216110.553
92_K95_I0.214730.550
23_Y33_F0.214230.548
32_S35_L0.213950.548
70_L73_L0.213750.547
44_E65_D0.211710.542
9_D120_N0.211360.541
126_L129_E0.210930.540
87_N93_N0.210480.539
45_L72_A0.210430.539
54_A57_H0.208840.535
112_G124_D0.208640.534
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
3qioA0.984899.90.101
1mu2A0.924299.90.118
2zd1A0.916799.80.126
1rilA0.984899.80.165
3h08A0.984899.80.166
2qkbA0.984899.80.168
2e4lA0.984899.80.169
4e19A0.924299.80.17
4g1qA0.916799.80.177
1jl1A0.984899.80.177

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