GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
tRNA_NucTran2_2 - tRNA nucleotidyltransferase domain 2 putative
Pfam: PF13735 (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: CL0237
Length: 149
Sequences: 1959
Seq/Len: 13.15
HH_delta: 0.245 (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
34_S37_E0.666943.293
106_N109_D0.660293.260
110_L122_I0.596672.946
121_W124_E0.416232.055
24_A45_V0.413662.043
48_H79_L0.40992.024
120_P124_E0.389231.922
62_Y134_L0.383661.894
28_L41_V0.38271.890
40_R71_D0.382071.887
28_L38_I0.376111.857
132_A138_I0.368251.818
116_I121_W0.362331.789
25_R42_L0.36231.789
132_A137_P0.355641.756
20_D79_L0.333431.646
29_K38_I0.331541.637
133_V140_N0.318161.571
90_E94_Q0.317411.567
59_R135_E0.310851.535
57_S60_D0.30991.530
62_Y130_L0.309051.526
140_N143_E0.308571.524
111_I122_I0.302161.492
125_I129_L0.30081.485
69_F73_L0.297661.470
44_L72_A0.289141.428
20_D48_H0.287371.419
109_D142_K0.287121.418
27_I30_R0.285251.409
110_L126_L0.282941.397
38_I42_L0.282741.396
44_L75_L0.278631.376
125_I128_R0.271051.338
20_D23_E0.265941.313
116_I125_I0.264751.307
141_E144_A0.264161.304
138_I144_A0.259871.283
35_N38_I0.259271.280
77_Q81_K0.258081.274
23_E48_H0.2581.274
123_G127_E0.255091.260
25_R29_K0.251311.241
28_L33_F0.247761.223
108_N111_I0.243781.204
48_H82_A0.233381.152
88_L92_Y0.230681.139
60_D63_R0.226421.118
70_E93_D0.223271.102
100_L130_L0.2231.101
72_A75_L0.219021.081
109_D112_E0.216421.069
27_I31_L0.215521.064
114_L125_I0.213981.057
28_L37_E0.213381.054
124_E128_R0.211671.045
37_E41_V0.211231.043
108_N112_E0.210911.041
139_P144_A0.210061.037
117_K121_W0.209911.037
120_P123_G0.209191.033
128_R132_A0.204871.012
89_K93_D0.20421.008
116_I123_G0.203281.004
129_L132_A0.202851.002
101_K133_V0.202330.999
23_E79_L0.202260.999
102_D133_V0.201190.993
54_Q94_Q0.199230.984
95_L137_P0.198390.980
36_K40_R0.197840.977
136_G139_P0.194980.963
32_K35_N0.194090.958
102_D140_N0.193560.956
109_D126_L0.19340.955
25_R38_I0.192220.949
118_P122_I0.190450.940
79_L82_A0.189880.938
119_G123_G0.188870.933
110_L125_I0.18430.910
83_E87_R0.182920.903
21_P42_L0.182560.901
20_D49_M0.181990.899
109_D129_L0.181650.897
133_V144_A0.180010.889
50_R67_E0.179910.888
107_G110_L0.179310.885
22_E26_E0.177940.879
109_D141_E0.177080.874
86_E90_E0.176430.871
20_D24_A0.172280.851
124_E127_E0.169120.835
115_G119_G0.169070.835
62_Y131_E0.167590.828
31_L107_G0.16720.826
71_D74_R0.165890.819
24_A28_L0.164580.813
107_G118_P0.164480.812
42_L46_E0.164060.810
100_L133_V0.163690.808
130_L138_I0.159850.789
111_I126_L0.15830.782
133_V138_I0.158160.781
132_A136_G0.156940.775
33_F37_E0.156240.771
24_A91_I0.155470.768
28_L45_V0.15540.767
25_R39_K0.154820.764
21_P46_E0.154720.764
112_E115_G0.152240.752
80_G88_L0.152030.751
20_D45_V0.151170.746
26_E128_R0.150660.744
33_F41_V0.148810.735
43_S68_L0.148560.734
127_E131_E0.148530.733
47_L64_Y0.148160.732
107_G122_I0.147390.728
115_G127_E0.146880.725
49_M52_Q0.146350.723
106_N111_I0.146120.722
51_L72_A0.145790.720
116_I122_I0.144950.716
26_E46_E0.144370.713
61_L88_L0.144370.713
62_Y69_F0.144340.713
87_R135_E0.143550.709
133_V141_E0.141680.700
54_Q57_S0.141550.699
130_L134_L0.141150.697
114_L129_L0.140480.694
39_K43_S0.139630.689
39_K112_E0.138630.685
107_G129_L0.137270.678
97_I130_L0.136230.673
60_D64_Y0.136060.672
62_Y97_I0.136030.672
57_S91_I0.135570.669
118_P121_W0.134170.663
92_Y98_H0.132490.654
25_R46_E0.131880.651
86_E94_Q0.131710.650
45_V79_L0.131590.650
66_E130_L0.131370.649
20_D81_K0.131250.648
31_L102_D0.131070.647
92_Y95_L0.130740.646
36_K128_R0.130110.642
66_E70_E0.128740.636
45_V77_Q0.128630.635
47_L50_R0.12810.633
93_D136_G0.127840.631
44_L67_E0.12770.631
58_R64_Y0.127480.629
49_M79_L0.126720.626
49_M82_A0.12590.622
98_H102_D0.125860.621
124_E143_E0.125680.621
116_I119_G0.12520.618
110_L119_G0.124830.616
69_F72_A0.124750.616
115_G121_W0.124680.616
48_H88_L0.124260.614
43_S47_L0.124210.613
53_S56_W0.124130.613
29_K42_L0.123960.612
21_P93_D0.123410.609
107_G114_L0.12340.609
30_R82_A0.123320.609
33_F38_I0.123250.609
32_K37_E0.123180.608
41_V45_V0.122950.607
65_G140_N0.121920.602
45_V48_H0.121560.600
86_E89_K0.121150.598
75_L80_G0.120710.596
49_M75_L0.120460.595
73_L98_H0.119820.592
52_Q76_A0.119660.591
60_D69_F0.119640.591
137_P144_A0.119380.589
131_E135_E0.119210.589
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
1miwA0.986699.80.245
1ou5A0.919599.70.327
3h38A0.932999.50.412
1vfgA0.845699.30.476
3aqlA0.711481.50.851
3gw7A0.919539.60.886
2zkzA0.530229.80.893
3jthA0.550326.70.896
3cuoA0.5503210.9
2qgsA0.852320.20.901

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