GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
5_nucleotid_C - 5-nucleotidase C-terminal domain
Pfam: PF02872 (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. )
Length: 156
Sequences: 2594
Seq/Len: 16.63
HH_delta: 0.042 (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_K132_D1.055063.989
107_T120_D0.86453.269
77_A81_E0.85443.231
75_T78_Q0.839863.176
131_D134_K0.823233.113
73_E135_T0.813113.075
73_E137_T0.686422.596
121_L130_I0.686122.594
109_D112_R0.609242.304
32_R102_S0.586032.216
4_T53_D0.543332.054
80_K121_L0.533662.018
71_V137_T0.524531.983
74_I138_V0.522751.977
39_V79_L0.519311.964
84_E117_R0.50211.899
29_D102_S0.47821.808
77_A132_D0.473141.789
112_R116_Q0.472191.785
105_R124_T0.467581.768
75_T135_T0.438891.660
5_T54_I0.424331.605
113_P116_Q0.406641.538
84_E115_G0.404631.530
76_G136_Y0.401741.519
20_E25_N0.397871.504
82_L153_A0.395381.495
58_D61_E0.394031.490
72_V145_A0.388431.469
77_A133_D0.387981.467
83_L121_L0.384131.452
112_R119_T0.373141.411
74_I78_Q0.369581.397
26_L30_A0.367061.388
75_T133_D0.362761.372
85_Y153_A0.362541.371
124_T129_P0.359271.358
27_I47_I0.353171.335
8_D51_A0.34511.305
68_K142_D0.344351.302
78_Q81_E0.340741.288
74_I79_L0.340251.287
23_L62_L0.338781.281
128_K134_K0.337611.277
80_K130_I0.33491.266
2_I59_L0.330581.250
31_L40_A0.322611.220
109_D117_R0.305471.155
72_V140_T0.304741.152
39_V138_V0.302451.144
31_L69_L0.301731.141
101_V104_I0.301541.140
5_T8_D0.300761.137
48_R65_F0.300361.136
41_F79_L0.296851.122
79_L130_I0.295481.117
27_I63_L0.293871.111
24_G100_Q0.293831.111
40_A139_A0.291011.100
7_V22_P0.290911.100
41_F82_L0.290861.100
38_D134_K0.289871.096
78_Q153_A0.285151.078
77_A80_K0.284451.076
99_L151_Y0.282941.070
49_G62_L0.281911.066
37_A137_T0.28091.062
46_G67_N0.280031.059
69_L139_A0.279571.057
65_F143_Y0.278421.053
107_T119_T0.271591.027
109_D119_T0.270211.022
35_T71_V0.267631.012
42_I46_G0.266861.009
44_G96_G0.263850.998
11_S23_L0.261310.988
142_D146_T0.259810.982
39_V136_Y0.259660.982
84_E118_I0.256770.971
31_L63_L0.255240.965
83_L106_Y0.254570.963
46_G65_F0.254250.961
46_G141_N0.251180.950
70_A145_A0.250450.947
45_G48_R0.249840.945
103_G125_I0.247930.937
140_T145_A0.246030.930
32_R40_A0.244760.926
108_Y120_D0.243470.921
5_T9_L0.240970.911
28_A42_I0.240130.908
105_R127_G0.239150.904
39_V103_G0.237410.898
42_I63_L0.233810.884
125_I136_Y0.231890.877
131_D136_Y0.231840.877
25_N29_D0.224690.850
32_R137_T0.223720.846
130_I136_Y0.222370.841
28_A40_A0.222150.840
24_G47_I0.22090.835
85_Y97_G0.220710.835
141_N144_L0.220280.833
43_N46_G0.219870.831
55_T58_D0.219040.828
120_D124_T0.216920.820
83_L104_I0.216660.819
128_K131_D0.216520.819
143_Y149_D0.216280.818
43_N144_L0.21610.817
9_L22_P0.215450.815
143_Y148_G0.211310.799
82_L138_V0.211190.799
47_I100_Q0.211160.798
67_N141_N0.210940.798
104_I125_I0.210550.796
3_G6_D0.207610.785
12_E50_S0.207380.784
56_R63_L0.206080.779
108_Y118_I0.203640.770
49_G61_E0.201720.763
54_I59_L0.201410.762
24_G29_D0.201260.761
38_D125_I0.191510.724
109_D116_Q0.191320.723
128_K133_D0.190670.721
28_A102_S0.188590.713
129_P132_D0.188030.711
45_G65_F0.186910.707
27_I62_L0.186820.706
39_V104_I0.186070.704
70_A142_D0.18490.699
7_V51_A0.183970.696
43_N67_N0.183660.694
43_N141_N0.182640.691
20_E29_D0.182470.690
18_F94_Q0.181590.687
45_G64_P0.181220.685
11_S62_L0.180480.682
95_D98_F0.180410.682
30_A66_P0.179920.680
72_V138_V0.179280.678
42_I141_N0.178350.674
24_G44_G0.178050.673
73_E134_K0.17780.672
81_E153_A0.176660.668
44_G151_Y0.175380.663
8_D33_E0.175120.662
97_G151_Y0.172810.653
80_K84_E0.171420.648
76_G133_D0.171230.647
48_R149_D0.170860.646
29_D33_E0.170770.646
106_Y120_D0.170620.645
42_I67_N0.168780.638
3_G28_A0.16790.635
29_D32_R0.16780.634
11_S21_S0.167780.634
112_R115_G0.167760.634
32_R38_D0.167720.634
84_E109_D0.167190.632
56_R60_Y0.167080.632
79_L104_I0.166110.628
5_T10_S0.165790.627
32_R36_G0.165170.625
31_L42_I0.163970.620
105_R125_I0.163340.618
24_G28_A0.16310.617
32_R35_T0.16280.616
37_A139_A0.161570.611
88_Q91_Y0.161510.611
39_V125_I0.16140.610
31_L141_N0.160170.606
28_A31_L0.160.605
96_G99_L0.159540.603
11_S50_S0.158840.601
20_E98_F0.158130.598
7_V10_S0.157210.594
41_F72_V0.15660.592
41_F138_V0.155930.590
20_E102_S0.154650.585
35_T139_A0.15430.583
57_G61_E0.154030.582
32_R103_G0.153460.580
38_D137_T0.152490.577
24_G45_G0.151810.574
45_G149_D0.151790.574
88_Q106_Y0.151620.573
43_N48_R0.150970.571
85_Y95_D0.150910.571
56_R95_D0.149690.566
116_Q119_T0.149210.564
69_L106_Y0.148940.563
96_G150_G0.148860.563
67_N142_D0.148370.561
83_L118_I0.148330.561
111_D128_K0.147620.558
43_N63_L0.146250.553
91_Y97_G0.145890.552
93_G97_G0.145550.550
11_S98_F0.144430.546
28_A101_V0.143910.544
120_D130_I0.143860.544
97_G100_Q0.143850.544
56_R68_K0.1430.541
8_D12_E0.142950.541
44_G100_Q0.14220.538
32_R126_N0.141880.536
27_I42_I0.141730.536
147_G150_G0.141640.536
11_S22_P0.141550.535
132_D136_Y0.141060.533
60_Y64_P0.13970.528
101_V106_Y0.139640.528
33_E132_D0.139640.528
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
4h2gA0.99361000.042
2z1aA0.98081000.066
4h1sA0.99361000.067
3ztvA11000.08
3iveA0.92951000.082
3qfkA0.98721000.089
1hp1A0.94231000.097
2wdcA0.91671000.233
3c9fA0.935999.70.55
2jtdA0.5769220.931

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