GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Helicase_RecD - Helicase
Pfam: PF05127 (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: CL0023
Length: 177
Sequences: 5134
Seq/Len: 29.01
HH_delta: 0.253 (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
28_R92_D0.913983.986
122_T125_G0.675622.946
157_P160_Y0.624922.725
14_L120_S0.561412.448
18_A31_V0.543282.369
41_T45_F0.494472.156
21_L93_L0.488792.132
5_D8_R0.459152.002
4_A8_R0.434541.895
3_T123_I0.428111.867
12_A45_F0.410191.789
31_V42_L0.38651.686
16_L19_A0.377011.644
6_R124_H0.376171.640
33_A38_N0.360921.574
99_A119_F0.356731.556
33_A39_V0.356461.555
126_Y130_G0.355721.551
20_A24_K0.355441.550
17_A118_V0.349141.523
36_P39_V0.348191.518
35_S38_N0.338941.478
30_L91_A0.33691.469
6_R160_Y0.316391.380
78_F81_P0.315081.374
54_G57_E0.314991.374
14_L95_I0.31181.360
91_A94_L0.309821.351
139_K142_K0.303791.325
55_Y58_E0.303011.321
154_L159_R0.297881.299
127_E130_G0.294481.284
107_L110_L0.293381.279
34_P101_A0.293281.279
128_G131_R0.293221.279
12_A16_L0.285071.243
44_E48_K0.284581.241
2_L120_S0.284231.240
37_E41_T0.280041.221
125_G159_R0.278691.215
93_L118_V0.276441.206
7_G10_K0.276411.205
12_A158_I0.273431.192
54_G58_E0.273341.192
68_K72_N0.2731.191
17_A21_L0.270781.181
82_D85_L0.268621.171
121_T125_G0.26821.170
67_I71_F0.267041.165
32_T39_V0.261751.141
14_L31_V0.259841.133
130_G133_F0.25961.132
96_V102_I0.259081.130
17_A95_I0.258811.129
96_V107_L0.258191.126
6_R122_T0.256911.120
96_V119_F0.25511.112
80_A83_E0.250071.091
126_Y129_T0.249411.088
75_R79_V0.249121.086
2_L118_V0.249111.086
1_V119_F0.248411.083
6_R125_G0.247761.080
17_A93_L0.246981.077
30_L94_L0.246391.074
77_E81_P0.243921.064
127_E133_F0.243021.060
94_L110_L0.241931.055
48_K51_K0.241271.052
81_P85_L0.238161.039
16_L20_A0.235421.027
67_I72_N0.234891.024
17_A20_A0.234111.021
52_A56_K0.233361.018
18_A29_I0.232231.013
73_K77_E0.231931.011
139_K143_K0.231371.009
99_A102_I0.231241.008
12_A15_G0.230811.007
31_V34_P0.230141.004
142_K151_E0.224350.978
154_L158_I0.22240.970
93_L116_R0.221610.966
153_E156_E0.220690.962
18_A95_I0.220580.962
152_L155_S0.219510.957
140_Q144_H0.218860.954
73_K76_I0.218590.953
136_K139_K0.216730.945
51_K54_G0.215860.941
16_L49_G0.213660.932
74_Q77_E0.213190.930
98_E159_R0.21310.929
128_G132_G0.213060.929
76_I80_A0.212670.927
26_K92_D0.211760.923
7_G11_S0.210240.917
6_R11_S0.20950.914
69_L72_N0.208710.910
4_A41_T0.207860.906
70_R73_K0.207160.903
106_L110_L0.206810.902
11_S148_N0.206050.899
19_A46_A0.205010.894
127_E131_R0.204270.891
4_A9_G0.204050.890
82_D86_A0.202080.881
133_F138_L0.201970.881
39_V43_F0.200540.875
35_S100_A0.199970.872
38_N41_T0.199680.871
5_D124_H0.199640.871
122_T159_R0.199580.870
43_F46_A0.199530.870
21_L95_I0.199080.868
69_L73_K0.198230.864
4_A100_A0.197450.861
134_S137_F0.196980.859
136_K140_Q0.196770.858
74_Q79_V0.196030.855
101_A125_G0.193740.845
13_A154_L0.192890.841
138_L141_L0.189190.825
77_E80_A0.188590.822
4_A120_S0.188580.822
126_Y137_F0.186860.815
8_R157_P0.186510.813
38_N45_F0.18560.809
4_A126_Y0.185420.809
3_T153_E0.185220.808
46_A49_G0.185210.808
103_P106_L0.184790.806
15_G18_A0.184460.804
53_L57_E0.184150.803
67_I73_K0.183750.801
67_I70_R0.183440.800
150_R153_E0.183310.799
40_Q44_E0.182770.797
101_A106_L0.182270.795
68_K71_F0.179610.783
39_V42_L0.179050.781
14_L97_D0.1780.776
79_V83_E0.177690.775
86_A89_P0.176930.772
7_G125_G0.176630.770
53_L56_K0.176560.770
28_R90_Q0.175880.767
2_L13_A0.175770.767
12_A49_G0.175660.766
15_G19_A0.175050.763
83_E86_A0.174430.761
41_T120_S0.174340.760
3_T151_E0.173530.757
28_R91_A0.173460.756
8_R160_Y0.173330.756
34_P106_L0.172630.753
13_A17_A0.172120.751
122_T126_Y0.172110.751
144_H150_R0.172020.750
13_A118_V0.170850.745
11_S114_F0.170690.744
15_G45_F0.170610.744
4_A128_G0.170590.744
135_L139_K0.170340.743
77_E83_E0.169750.740
4_A7_G0.169650.740
75_R80_A0.169280.738
133_F137_F0.167990.733
96_V117_V0.167680.731
34_P157_P0.167370.730
128_G133_F0.16690.728
36_P41_T0.166420.726
129_T132_G0.165710.723
74_Q78_F0.165240.721
6_R101_A0.164550.718
37_E40_Q0.164280.716
35_S121_T0.164080.716
141_L149_W0.163890.715
139_K144_H0.163350.712
6_R15_G0.163310.712
74_Q80_A0.1630.711
106_L109_Q0.162390.708
19_A49_G0.161830.706
8_R17_A0.161550.705
79_V82_D0.16050.700
36_P40_Q0.16020.699
105_P109_Q0.159560.696
123_I153_E0.159540.696
94_L115_P0.158040.689
130_G138_L0.157980.689
92_D115_P0.157040.685
72_N77_E0.157010.685
100_A121_T0.156930.684
31_V38_N0.156760.684
101_A121_T0.15620.681
120_S123_I0.156190.681
6_R100_A0.156040.680
4_A101_A0.155970.680
58_E67_I0.155840.680
23_Q26_K0.154810.675
4_A38_N0.15480.675
94_L117_V0.154530.674
135_L140_Q0.15420.672
12_A103_P0.153360.669
26_K48_K0.153280.668
16_L95_I0.153230.668
3_T124_H0.153070.668
152_L158_I0.152650.666
1_V141_L0.152630.666
102_I107_L0.151970.663
129_T135_L0.151710.662
4_A160_Y0.151620.661
39_V160_Y0.15120.659
70_R78_F0.151080.659
108_K112_R0.151070.659
50_L53_L0.150950.658
11_S50_L0.150230.655
130_G135_L0.150180.655
95_I118_V0.150130.655
152_L156_E0.149880.654
6_R108_K0.149850.653
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
4b3fX0.977499.90.253
2xzlA0.971899.90.284
2wjyA0.971899.90.289
2gk6A0.971899.90.292
3e1sA0.858899.80.318
1w36D0.983199.80.323
3upuA0.920999.80.325
3lfuA0.983199.80.327
1uaaA0.983199.80.368
1pjrA0.983199.80.369

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