GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Wzz - Chain length determinant protein
Pfam: PF02706 (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: 152
Sequences: 3711
Seq/Len: 24.41
HH_delta: 0.731 (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
136_A142_A1.194273.900
13_W16_K1.066053.482
33_Y37_A0.945923.089
143_A147_N0.908312.966
42_E135_T0.870312.842
136_A141_R0.854042.789
95_E148_A0.790492.582
45_A150_A0.779562.546
42_E133_S0.771722.520
134_Y145_V0.664472.170
134_Y146_A0.640972.093
19_I23_T0.620062.025
140_E144_D0.566361.850
90_E94_K0.558721.825
44_S131_T0.554351.810
40_Q135_T0.538331.758
46_Q129_I0.524761.714
118_N134_Y0.508421.660
26_F30_A0.504161.647
22_V26_F0.502931.643
97_N100_E0.502731.642
89_L116_R0.500891.636
75_P79_Y0.467191.526
118_N136_A0.452371.477
43_S142_A0.446651.459
89_L115_L0.44621.457
146_A150_A0.437131.428
38_P137_T0.437061.427
31_F35_F0.436621.426
148_A151_E0.43621.425
45_A146_A0.43461.419
46_Q131_T0.433221.415
93_V98_L0.432181.411
89_L149_I0.428781.400
138_D141_R0.428081.398
43_S143_A0.419281.369
91_E95_E0.410361.340
141_R144_D0.410081.339
78_T128_N0.406541.328
119_L134_Y0.395881.293
34_A37_A0.392421.282
124_N127_S0.39041.275
132_I146_A0.387061.264
23_T27_A0.385031.257
92_V149_I0.381751.247
32_I36_F0.381681.247
30_A34_A0.378541.236
37_A40_Q0.375551.227
13_W17_W0.371851.214
144_D148_A0.365561.194
80_V84_K0.358551.171
132_I150_A0.357861.169
80_V130_I0.357531.168
16_K20_I0.35521.160
92_V148_A0.343121.121
87_D90_E0.342781.119
92_V145_V0.338191.104
93_V115_L0.335851.097
23_T26_F0.335051.094
18_L21_I0.327171.068
120_S133_S0.325921.064
33_Y36_F0.325281.062
113_E117_K0.318671.041
147_N151_E0.318191.039
12_L19_I0.317911.038
119_L149_I0.313831.025
86_R116_R0.309851.012
122_S131_T0.309661.011
48_L78_T0.309441.011
40_Q137_T0.304630.995
27_A34_A0.303340.991
79_Y134_Y0.301590.985
81_E84_K0.301440.984
11_I15_R0.301290.984
92_V96_L0.300430.981
91_E94_K0.296480.968
83_L149_I0.292940.957
81_E124_N0.292820.956
83_L132_I0.290790.950
134_Y149_I0.289670.946
79_Y82_I0.289440.945
44_S133_S0.287860.940
18_L22_V0.285060.931
88_V149_I0.279120.912
80_V121_V0.276830.904
28_I31_F0.275780.901
139_P143_A0.27320.892
76_I128_N0.267030.872
15_R18_L0.265640.868
45_A132_I0.26560.867
8_L11_I0.265220.866
124_N131_T0.263820.862
29_L33_Y0.263380.860
48_L129_I0.256960.839
6_R10_R0.252290.824
21_I28_I0.24770.809
27_A31_F0.24750.808
144_D147_N0.245030.800
47_L132_I0.243360.795
48_L79_Y0.24160.789
50_E128_N0.239950.784
114_E118_N0.239260.781
86_R90_E0.239240.781
80_V123_P0.237690.776
115_L134_Y0.235490.769
115_L149_I0.228550.746
96_L145_V0.228220.745
120_S135_T0.227810.744
19_I26_F0.22390.731
82_I85_S0.223660.730
9_L13_W0.223130.729
98_L145_V0.223090.729
10_R13_W0.222420.726
17_W28_I0.222260.726
49_V79_Y0.222140.725
51_S72_N0.221670.724
96_L148_A0.220110.719
48_L51_S0.216850.708
137_T141_R0.21680.708
122_S133_S0.21560.704
123_P131_T0.215060.702
47_L150_A0.214140.699
28_I32_I0.210070.686
101_S141_R0.208780.682
77_N81_E0.208390.681
123_P128_N0.206540.675
25_L29_L0.205840.672
46_Q81_E0.202250.661
82_I129_I0.202120.660
48_L82_I0.201830.659
142_A146_A0.20150.658
44_S86_R0.20120.657
25_L32_I0.20120.657
141_R145_V0.199680.652
88_V92_V0.1990.650
27_A30_A0.197410.645
10_R17_W0.196750.643
10_R14_R0.19480.636
84_K116_R0.194280.634
47_L71_D0.193980.634
75_P78_T0.192420.628
16_K28_I0.191810.626
76_I79_Y0.18770.613
77_N123_P0.18760.613
82_I90_E0.186270.608
47_L83_L0.185760.607
43_S139_P0.183630.600
15_R19_I0.183430.599
139_P142_A0.182750.597
42_E120_S0.18220.595
43_S146_A0.181870.594
70_Q74_Q0.181760.594
119_L146_A0.180820.591
68_D71_D0.179680.587
17_W21_I0.178210.582
79_Y88_V0.176830.578
115_L145_V0.176760.577
81_E127_S0.174340.569
74_Q128_N0.174210.569
75_P128_N0.171430.560
18_L29_L0.170950.558
126_D129_I0.169350.553
93_V119_L0.169110.552
113_E116_R0.169010.552
118_N135_T0.16760.547
90_E102_P0.167150.546
75_P121_V0.166940.545
84_K121_V0.166730.545
31_F34_A0.165640.541
9_L14_R0.165160.539
78_T127_S0.164890.539
138_D142_A0.164660.538
140_E143_A0.164580.537
7_D11_I0.164490.537
134_Y142_A0.164250.536
33_Y40_Q0.164210.536
56_S59_S0.163970.536
86_R89_L0.163060.533
83_L88_V0.162730.531
6_R15_R0.162530.531
15_R22_V0.162270.530
115_L119_L0.16220.530
19_I87_D0.161040.526
17_W20_I0.16030.524
49_V128_N0.159870.522
96_L144_D0.159280.520
78_T88_V0.157680.515
40_Q118_N0.157620.515
95_E151_E0.15620.510
6_R13_W0.15590.509
101_S114_E0.155490.508
94_K147_N0.155320.507
83_L119_L0.154230.504
138_D143_A0.153930.503
48_L128_N0.153850.502
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
3b8oA0.743497.30.731
3b8mA0.822496.30.77
4e29A0.703992.80.813
3ne5A0.953987.50.833
2v50A0.921174.80.854
3w9iA0.947470.10.859
4dx5A0.9211690.86
3gsdA0.289516.70.901
2qn6B0.48689.60.91
3aqpA0.70399.30.911
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