GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Integrase_1 - Integrase
Pfam: PF12835 (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: 187
Sequences: 17459
Seq/Len: 93.36
HH_delta: 0.197 (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
147_A172_L3.477174.839
44_G146_Y2.075832.889
40_Q139_F2.004092.789
83_R173_G1.900492.645
138_G141_G1.812542.522
55_P101_A1.785872.485
146_Y171_E1.775272.470
47_R140_H1.757612.446
15_S18_E1.592342.216
160_S166_A1.513982.107
42_A88_L1.456162.026
40_Q50_A1.421791.978
54_R110_S1.334831.857
94_R98_E1.318471.835
160_S167_Q1.315291.830
166_A169_S1.286171.790
35_A100_A1.280061.781
45_L50_A1.196911.666
54_R109_G1.179581.641
87_I94_R1.152571.604
47_R51_L1.147711.597
54_R57_L1.113561.550
34_A38_E1.112811.548
86_P171_E1.099411.530
18_E21_Q1.094591.523
49_E83_R1.077641.500
81_R175_G1.055731.469
46_R140_H1.05121.463
41_R145_A1.05081.462
155_Q168_V1.019911.419
147_A168_V1.010341.406
88_L91_E1.002141.394
19_Y41_R0.998621.390
35_A99_R0.997531.388
14_I137_T0.980231.364
36_A50_A0.958751.334
166_A170_Q0.950981.323
14_I145_A0.949421.321
55_P111_L0.942071.311
48_E52_K0.931341.296
54_R116_S0.926761.290
121_L125_R0.909191.265
118_K121_L0.901231.254
128_L137_T0.881491.227
16_R157_Q0.875761.219
35_A96_A0.869681.210
23_L38_E0.862911.201
41_R142_L0.857911.194
33_V123_R0.851371.185
14_I18_E0.843431.174
26_A127_A0.840651.170
146_Y154_L0.837551.165
27_E34_A0.837521.165
13_A145_A0.831971.158
42_A93_Q0.829251.154
154_L159_F0.829011.154
119_Q122_R0.827511.151
16_R20_N0.825261.148
38_E96_A0.824761.148
160_S165_L0.821341.143
21_Q25_N0.819641.141
25_N130_K0.805761.121
20_N24_A0.783591.090
14_I22_V0.780111.086
25_N131_L0.768841.070
146_Y172_L0.767171.068
42_A92_K0.765711.065
87_I93_Q0.762921.062
110_S113_P0.758561.056
121_L124_Y0.748211.041
93_Q96_A0.729951.016
37_L142_L0.728931.014
159_F167_Q0.721621.004
12_R141_G0.721211.004
140_H144_H0.716090.996
56_S109_G0.706150.983
91_E95_E0.696440.969
18_E135_G0.695130.967
76_G82_P0.692390.963
38_E92_K0.692160.963
126_Y130_K0.688490.958
34_A96_A0.687220.956
154_L168_V0.683280.951
26_A37_L0.67860.944
88_L92_K0.674060.938
53_L58_A0.672040.935
12_R135_G0.669190.931
88_L93_Q0.66380.924
169_S174_H0.661150.920
44_G172_L0.653130.909
123_R126_Y0.636550.886
140_H174_H0.635660.885
167_Q171_E0.631420.879
39_L93_Q0.629180.876
141_G144_H0.621680.865
51_L120_A0.617990.860
101_A104_A0.615660.857
96_A99_R0.614360.855
95_E99_R0.612980.853
14_I141_G0.611220.851
45_L49_E0.610030.849
76_G80_G0.608990.847
16_R156_A0.607420.845
69_E94_R0.606060.843
72_R84_E0.604530.841
56_S108_N0.602390.838
31_P34_A0.601730.837
40_Q142_L0.599290.834
169_S172_L0.598120.832
35_A39_L0.597930.832
165_L169_S0.596780.830
43_F85_V0.594370.827
47_R139_F0.590930.822
92_K95_E0.589980.821
95_E98_E0.588920.819
31_P35_A0.587130.817
147_A169_S0.586610.816
11_D144_H0.585570.815
147_A174_H0.584860.814
72_R75_V0.574210.799
17_E21_Q0.574050.799
117_L121_L0.57270.797
36_A120_A0.572070.796
27_E38_E0.567280.789
16_R145_A0.566440.788
36_A112_I0.565720.787
100_A104_A0.560810.780
38_E42_A0.5530.770
47_R121_L0.550970.767
31_P99_R0.544950.758
77_T83_R0.54360.756
127_A130_K0.543040.756
125_R136_S0.541710.754
137_T141_G0.540790.753
23_L34_A0.539890.751
39_L45_L0.537390.748
123_R127_A0.536450.746
17_E20_N0.53470.744
11_D141_G0.532860.741
19_Y145_A0.532510.741
92_K96_A0.532490.741
124_Y139_F0.532320.741
40_Q47_R0.530590.738
124_Y128_L0.526540.733
13_A148_Q0.524190.729
46_R174_H0.523290.728
22_V37_L0.522890.728
19_Y23_L0.522040.726
33_V36_A0.517370.720
49_E77_T0.516620.719
118_K125_R0.514490.716
70_T84_E0.510690.711
77_T81_R0.508290.707
99_R103_V0.507940.707
39_L50_A0.505770.704
127_A131_L0.505160.703
55_P104_A0.504540.702
159_F168_V0.50370.701
38_E93_Q0.502420.699
55_P97_L0.50110.697
119_Q123_R0.497490.692
14_I19_Y0.496560.691
32_R35_A0.495260.689
21_Q133_L0.483980.673
147_A155_Q0.483780.673
46_R78_K0.481950.671
71_L75_V0.480410.668
25_N28_A0.475350.661
97_L111_L0.473470.659
22_V128_L0.468930.653
125_R129_R0.465670.648
46_R76_G0.462940.644
39_L97_L0.46280.644
13_A144_H0.461010.641
58_A87_I0.459420.639
13_A141_G0.457530.637
122_R126_Y0.456280.635
21_Q131_L0.453780.631
106_E109_G0.453740.631
125_R128_L0.453230.631
49_E173_G0.453220.631
91_E94_R0.447640.623
25_N127_A0.441930.615
77_T80_G0.441380.614
23_L41_R0.441110.614
98_E101_A0.44070.613
11_D138_G0.439220.611
126_Y129_R0.435450.606
39_L43_F0.433430.603
108_N113_P0.433420.603
155_Q160_S0.427840.595
73_V84_E0.424770.591
114_K117_L0.42360.589
124_Y142_L0.422440.588
39_L53_L0.420930.586
124_Y127_A0.419950.584
74_V82_P0.419150.583
116_S119_Q0.418260.582
168_V172_L0.417920.582
98_E102_A0.416850.580
43_F88_L0.413240.575
119_Q126_Y0.412410.574
32_R123_R0.411720.573
53_L111_L0.411330.572
109_G113_P0.411260.572
33_V127_A0.410050.571
97_L100_A0.408750.569
48_E140_H0.408120.568
45_L53_L0.40660.566
48_E77_T0.404760.563
39_L112_I0.403950.562
77_T173_G0.402510.560
23_L37_L0.400340.557
44_G144_H0.400330.557
35_A93_Q0.400030.557
85_V171_E0.398480.554
27_E30_D0.397670.553
12_R137_T0.39630.551
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
2a3vA0.87799.90.197
3nkhA0.935899.90.201
4a8eA0.871799.90.235
1a0pA0.887799.90.248
1xo0A0.909199.90.287
1ae9A0.812899.80.296
1z1bA0.87799.80.297
1aihA0.780799.80.298
1z19A0.866399.80.301
3vcfA0.748799.10.603

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