GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RNase_T - Exonuclease
Pfam: PF00929 (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: 164
Sequences: 7852
Seq/Len: 47.88
HH_delta: 0.045 (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
19_E152_D1.257762.780
89_H119_T1.213112.681
88_G91_A1.202782.659
35_S158_R1.068372.361
5_T17_I0.981062.168
38_S75_E0.936742.070
134_S137_D0.935682.068
60_Q64_E0.921892.038
22_A76_F0.900531.990
59_T62_D0.872081.928
139_A159_A0.86711.917
53_T59_T0.864081.910
132_K137_D0.862631.907
43_E68_S0.862411.906
38_S67_P0.855471.891
50_P54_K0.84261.862
52_A56_H0.810241.791
7_T93_F0.786321.738
68_S71_E0.77091.704
40_I72_A0.769821.702
67_P72_A0.758131.676
23_V154_L0.748871.655
37_N152_D0.729521.612
45_P60_Q0.718981.589
19_E37_N0.718541.588
151_H156_D0.717721.586
16_E41_R0.716461.584
2_V160_T0.697961.543
41_R65_D0.687251.519
127_F142_F0.685841.516
90_N93_F0.653451.444
152_D155_D0.649291.435
21_G153_A0.644731.425
23_V157_A0.636461.407
25_V161_A0.632071.397
52_A55_V0.624731.381
36_F75_E0.611931.353
20_I76_F0.610211.349
1_V22_A0.609941.348
26_D29_E0.605471.338
11_D14_Q0.599281.325
21_G157_A0.594231.313
157_A161_A0.592231.309
139_A144_I0.589361.303
69_F73_L0.583741.290
6_E151_H0.575591.272
95_I116_F0.574541.270
6_E156_D0.570091.260
4_D156_D0.569761.259
2_V25_V0.568091.256
51_W54_K0.56161.241
2_V161_A0.560641.239
62_D66_A0.558991.236
16_E101_E0.550621.217
76_F80_L0.549571.215
9_G15_D0.547841.211
74_D78_E0.531341.174
4_D151_H0.527031.165
8_T18_I0.525591.162
39_L152_D0.517661.144
48_I63_L0.516211.141
158_R162_E0.514511.137
32_E35_S0.513431.135
24_K34_E0.513031.134
154_L158_R0.510631.129
16_E44_E0.50561.118
155_D158_R0.492331.088
91_A116_F0.491631.087
37_N154_L0.486841.076
36_F79_F0.486611.076
21_G154_L0.485541.073
39_L62_D0.482291.066
2_V157_A0.480571.062
140_E146_F0.479151.059
94_D98_L0.478481.058
101_E104_R0.469911.039
16_E43_E0.469131.037
48_I53_T0.466671.031
18_I56_H0.466641.031
5_T98_L0.465761.029
77_E102_D0.46461.027
22_A79_F0.464141.026
15_D97_F0.456811.010
38_S72_A0.455821.008
138_L142_F0.455261.006
100_R104_R0.454181.004
23_V161_A0.450740.996
39_L66_A0.44470.983
85_I117_I0.440840.974
15_D44_E0.43710.966
67_P71_E0.432690.956
51_W55_V0.431390.954
129_N133_Y0.430980.953
38_S66_A0.430790.952
117_I122_L0.428680.948
99_R110_I0.422220.933
1_V84_D0.421790.932
4_D94_D0.421240.931
138_L163_L0.418550.925
34_E79_F0.413690.914
42_P63_L0.412660.912
100_R103_K0.412250.911
26_D33_V0.410250.907
53_T60_Q0.409060.904
58_I62_D0.408280.902
120_L124_R0.408090.902
95_I99_R0.404740.895
94_D151_H0.402960.891
75_E78_E0.401330.887
144_I162_E0.399730.884
36_F76_F0.39910.882
39_L58_I0.398040.880
24_K79_F0.395140.873
101_E105_F0.39250.868
157_A160_T0.388560.859
67_P75_E0.388250.858
78_E81_K0.387630.857
21_G37_N0.386820.855
148_G155_D0.382080.845
12_P97_F0.38190.844
9_G97_F0.381760.844
49_S52_A0.378350.836
69_F101_E0.376320.832
62_D65_D0.376030.831
73_L102_D0.375470.830
70_E74_D0.372990.824
6_E94_D0.370810.820
88_G160_T0.369940.818
11_D15_D0.369450.817
98_L102_D0.368470.814
89_H138_L0.368190.814
7_T97_F0.367350.812
35_S154_L0.366750.811
136_D150_A0.366010.809
123_A133_Y0.365030.807
73_L101_E0.360380.797
16_E69_F0.357630.790
139_A146_F0.357350.790
3_F88_G0.354890.784
3_F86_L0.354790.784
118_D122_L0.352710.780
24_K33_V0.352690.780
5_T20_I0.352450.779
77_E81_K0.351390.777
110_I114_N0.347870.769
8_T16_E0.347560.768
128_P133_Y0.34460.762
53_T62_D0.342360.757
145_P162_E0.342170.756
16_E104_R0.342170.756
22_A36_F0.341620.755
153_A156_D0.340860.753
94_D156_D0.339280.750
18_I48_I0.339110.750
137_D140_E0.339080.749
81_K84_D0.339010.749
75_E79_F0.338440.748
73_L77_E0.338410.748
142_F163_L0.33680.744
43_E70_E0.33560.742
130_R141_Y0.331180.732
40_I69_F0.327940.725
155_D159_A0.327510.724
50_P53_T0.323940.716
16_E42_P0.32340.715
48_I60_Q0.322820.714
41_R64_E0.321530.711
92_S96_G0.32130.710
24_K84_D0.320510.708
102_D105_F0.320040.707
1_V79_F0.319510.706
60_Q63_L0.317620.702
9_G52_A0.316670.700
72_A75_E0.311080.688
139_A163_L0.309860.685
146_F155_D0.309390.684
3_F22_A0.308320.681
1_V24_K0.308050.681
135_L160_T0.307350.679
123_A127_F0.307070.679
3_F80_L0.306840.678
1_V80_L0.303220.670
159_A162_E0.302450.669
41_R68_S0.301580.667
5_T94_D0.300760.665
146_F159_A0.300520.664
143_G147_D0.300180.663
49_S53_T0.299010.661
150_A155_D0.298070.659
120_L123_A0.295560.653
99_R102_D0.293350.648
70_E105_F0.28890.639
74_D108_K0.288620.638
58_I63_L0.288110.637
17_I97_F0.286860.634
135_L138_L0.286320.633
90_N120_L0.285190.630
146_F150_A0.285120.630
61_E64_E0.283850.627
147_D155_D0.282360.624
122_L126_L0.281840.623
119_T123_A0.281380.622
20_I72_A0.281140.621
118_D121_E0.277070.612
3_F76_F0.275820.610
120_L133_Y0.275630.609
29_E33_V0.273990.606
12_P96_G0.271080.599
133_Y137_D0.269860.596
20_I40_I0.269360.595
17_I40_I0.268350.593
108_K111_P0.267220.591
94_D97_F0.26530.586
13_R100_R0.264430.584
23_V158_R0.264240.584
17_I101_E0.264170.584
48_I52_A0.264140.584
127_F141_Y0.263650.583
139_A143_G0.263620.583
18_I62_D0.263110.582
102_D110_I0.262930.581
88_G95_I0.261970.579
89_H94_D0.261870.579
38_S76_F0.261480.578
123_A138_L0.260810.576
53_T57_G0.259720.574
8_T48_I0.258190.571
127_F130_R0.254970.564
71_E75_E0.254830.563
124_R133_Y0.252940.559
144_I147_D0.252860.559
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
3mxmB0.969599.90.045
1zbhA0.993999.90.048
1w0hA0.993999.90.05
1zbuA0.993999.90.052
3u3yB0.975699.90.053
3cg7A0.987899.90.053
2p1jA0.945199.90.057
2xriA0.987899.90.068
2guiA0.963499.90.07
2qxfA0.993999.90.076

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