GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_integrase - Phage integrase family
Pfam: PF00589 (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: CL0382
Length: 173
Sequences: 21123
Seq/Len: 122.1
HH_delta: 0.046 (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
138_A155_M3.466784.236
34_G137_F2.166672.648
45_W84_I1.994972.438
30_L130_P1.960282.395
68_R156_G1.951232.384
37_P131_H1.843822.253
137_F154_L1.798772.198
129_T132_S1.771852.165
4_T7_E1.627981.989
44_R105_P1.59531.949
30_L40_L1.562821.910
147_P150_V1.523331.862
53_G77_A1.519471.857
44_R96_Y1.510661.846
32_Y73_S1.46361.789
56_Y69_T1.388841.697
135_H168_K1.386961.695
149_E152_A1.363221.666
44_R95_D1.354091.655
25_L83_Y1.350071.650
142_A151_I1.343711.642
77_A81_R1.343651.642
157_H163_T1.3341.630
49_D52_N1.281311.566
44_R47_D1.24771.525
155_M163_T1.239431.515
31_L140_N1.207391.475
141_L146_V1.17991.442
7_E10_Q1.17731.439
54_E69_T1.169161.429
35_L40_L1.168561.428
141_L151_I1.161851.420
108_R112_N1.15311.409
37_P41_L1.145211.399
137_F141_L1.143431.397
5_E140_N1.131091.382
66_K158_S1.130311.381
39_E68_R1.12121.370
24_R28_L1.117251.365
45_W97_L1.116861.365
152_A160_I1.115651.363
162_M165_H1.111871.359
23_N114_I1.109481.356
71_P154_L1.107591.353
142_A167_L1.10141.346
26_I111_I1.094761.338
72_I77_A1.08181.322
26_I40_L1.076271.315
161_E164_R1.057731.293
36_R131_H1.0341.264
31_L136_T1.033811.263
37_P108_R1.030571.259
28_L79_L1.025721.253
38_S42_R1.015531.241
149_E153_K1.003681.227
49_D54_E0.994161.215
50_L81_R0.981561.199
8_I31_L0.979221.197
16_E24_R0.95891.172
119_I128_F0.956451.169
25_L82_E0.940571.149
138_A151_I0.939721.148
37_P112_N0.939541.148
107_S110_T0.910621.113
3_L128_F0.907551.109
32_Y76_L0.902151.102
139_T168_K0.886261.083
12_L28_L0.882191.078
110_T113_K0.881631.077
31_L133_L0.880351.076
3_L7_E0.879261.074
8_I140_N0.861951.053
159_S162_M0.860091.051
25_L79_L0.858191.049
109_Q112_N0.856791.047
5_E144_S0.853181.043
152_A163_T0.852171.041
26_I98_F0.850261.039
136_T140_N0.846771.035
5_E9_K0.843791.031
146_V150_V0.842231.029
10_Q14_A0.841011.028
73_S76_L0.840791.027
41_L108_R0.835251.021
14_A121_K0.831681.016
15_L118_I0.827941.012
96_Y105_P0.826061.009
137_F155_M0.823061.006
140_N143_R0.820991.003
96_Y99_P0.816070.997
46_D95_D0.814960.996
148_I164_R0.804120.983
9_K13_D0.803330.982
39_E62_T0.802260.980
46_D94_D0.797190.974
29_L98_F0.796630.973
24_R79_L0.79440.971
32_Y75_E0.791020.967
72_I76_L0.786270.961
131_H135_H0.782350.956
159_S164_R0.776120.948
114_I117_R0.773910.946
53_G74_P0.762820.932
61_R67_S0.762540.932
28_L75_E0.760660.930
143_R170_S0.759530.928
14_A122_A0.755160.923
112_N116_R0.75410.922
112_N130_P0.742240.907
135_H165_H0.726210.887
74_P78_E0.726210.887
3_L11_L0.72070.881
132_S135_H0.718710.878
115_F119_I0.717120.876
83_Y87_R0.706140.863
15_L27_I0.703690.860
138_A167_L0.69940.855
61_R65_G0.698830.854
35_L57_I0.694820.849
30_L133_L0.694280.848
35_L39_E0.69190.846
27_I133_L0.690930.844
50_L77_A0.690650.844
138_A142_A0.68970.843
62_T68_R0.685970.838
138_A163_T0.68540.838
139_T167_L0.684790.837
41_L111_I0.684340.836
43_L55_I0.681610.833
128_F132_S0.680870.832
160_I164_R0.679990.831
114_I118_I0.674720.825
34_G155_M0.673790.823
3_L136_T0.669940.819
43_L48_V0.668040.816
115_F133_L0.667360.816
76_L79_L0.657290.803
64_T67_S0.655440.801
25_L29_L0.653950.799
152_A164_R0.653410.798
45_W87_R0.652670.798
117_R121_K0.650260.795
37_P130_P0.646010.789
25_L98_F0.644570.788
21_L25_L0.642180.785
148_I160_I0.639030.781
2_Y136_T0.638920.781
81_R84_I0.638880.781
29_L76_L0.638790.781
110_T114_I0.636980.778
100_S104_K0.636070.777
82_E86_R0.626090.765
113_K117_R0.618950.756
78_E82_E0.617430.755
28_L32_Y0.616150.753
75_E78_E0.608650.744
33_T70_V0.608150.743
6_E10_Q0.607980.743
12_L24_R0.597660.730
116_R127_K0.595260.727
28_L76_L0.5930.725
2_Y168_K0.592740.724
5_E143_R0.590960.722
79_L82_E0.590740.722
109_Q116_R0.58860.719
62_T67_S0.588510.719
150_V154_L0.586720.717
21_L86_R0.586080.716
106_L110_T0.583590.713
56_Y67_S0.583310.713
21_L82_E0.582330.712
37_P111_I0.581230.710
49_D56_Y0.580260.709
49_D55_I0.580240.709
14_A118_I0.580140.709
115_F130_P0.564910.690
11_L27_I0.564170.689
138_A157_H0.56360.689
25_L76_L0.563430.689
36_R61_R0.55860.683
142_A170_S0.555820.679
39_E156_G0.553060.676
140_N144_S0.551230.674
111_I130_P0.547220.669
21_L24_R0.542910.663
50_L53_G0.541520.662
51_E54_E0.539080.659
118_I121_K0.536670.656
109_Q113_K0.536550.656
78_E81_R0.536210.655
23_N26_I0.534710.653
22_R83_Y0.534130.653
81_R85_K0.533170.652
29_L40_L0.532740.651
32_Y140_N0.532730.651
11_L119_I0.531660.650
116_R120_K0.528960.646
80_L97_L0.528240.646
149_E164_R0.524980.642
6_E9_K0.523140.639
157_H166_Y0.521970.638
152_A155_M0.519850.635
36_R157_H0.516750.631
30_L37_P0.515910.630
47_D61_R0.515410.630
133_L137_F0.514310.628
8_I12_L0.51390.628
142_A149_E0.513140.627
139_T143_R0.509530.623
44_R94_D0.508570.621
49_D53_G0.508530.621
8_I136_T0.504120.616
29_L33_T0.503310.615
84_I87_R0.501780.613
50_L55_I0.499270.610
10_Q124_I0.498170.609
23_N118_I0.495690.606
3_L132_S0.494760.605
29_L43_L0.492670.602
22_R25_L0.492630.602
29_L35_L0.489920.599
131_H157_H0.488120.596
142_A169_S0.486130.594
148_I152_A0.484970.593
158_S162_M0.483180.590
160_I163_T0.480190.587
149_E160_I0.480030.587
141_L154_L0.479410.586
118_I122_A0.478270.584
16_E28_L0.47450.580
42_R105_P0.47370.579
139_T169_S0.47310.578
38_S62_T0.473020.578
22_R114_I0.471570.576
25_L80_L0.471560.576
82_E85_K0.470360.575
5_E136_T0.470170.575
112_N115_F0.46790.572
145_G151_I0.467190.571
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
2a3vA0.965399.90.046
3nkhA199.90.066
1a0pA0.982799.90.066
4a8eA0.942299.90.085
1xo0A199.90.091
1ae9A0.959599.90.123
1z19A0.959599.90.141
1z1bA0.959599.90.15
1aihA0.861399.90.182
3vcfA0.8208990.583

Page generated in 0.0198 seconds.