GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Relaxase - RelaxaseMobilisation nuclease domain
Pfam: PF03432 (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: CL0169
Length: 242
Sequences: 1139
Seq/Len: 4.71
HH_delta: 0.822 (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
84_E136_E0.336963.824
70_T73_Q0.33533.805
91_Q110_N0.316373.590
80_E140_E0.298223.384
45_T91_Q0.292393.318
178_D230_F0.207862.359
111_R119_K0.206722.346
81_F130_L0.19112.169
83_E88_G0.185732.108
77_I141_Y0.184722.096
76_E80_E0.183742.085
89_N113_D0.183582.083
78_A105_V0.171951.951
62_I105_V0.168171.908
176_A199_I0.166011.884
12_I95_V0.165761.881
227_G230_F0.165681.880
6_K10_D0.16451.867
80_E141_Y0.162291.842
186_S189_D0.160171.818
12_I108_V0.150881.712
78_A94_V0.147161.670
77_I143_L0.146411.661
235_L239_L0.145631.653
34_D37_E0.138661.573
13_L95_V0.134651.528
131_R134_S0.133981.520
184_S193_R0.132871.508
222_K225_K0.129351.468
64_F74_A0.127641.448
194_L199_I0.127521.447
113_D118_K0.125561.425
74_A103_P0.12511.420
232_K236_E0.124071.408
8_A108_V0.123551.402
64_F77_I0.122081.385
62_I134_S0.121641.380
99_D102_H0.121391.377
177_I190_F0.120961.373
62_I81_F0.120331.365
46_R110_N0.120081.363
84_E133_A0.119811.360
75_H105_V0.118841.349
64_F143_L0.11841.344
65_P68_E0.117711.336
96_V105_V0.115491.311
64_F102_H0.114951.304
210_S220_R0.114891.304
9_L13_L0.113421.287
181_L239_L0.110531.254
173_I177_I0.10851.231
8_A12_I0.108331.229
139_K145_V0.108331.229
79_R83_E0.107541.220
158_E161_K0.107341.218
195_E200_E0.104491.186
60_I85_M0.104491.186
68_E144_S0.104061.181
5_F56_P0.103681.177
52_V119_K0.103631.176
180_A193_R0.103391.173
200_E212_K0.100981.146
62_I78_A0.100551.141
71_P96_V0.100491.140
79_R92_Y0.100431.140
231_T234_N0.100371.139
206_G210_S0.099611.130
89_N115_D0.098391.116
80_E84_E0.098311.116
76_E84_E0.098271.115
90_H120_L0.098161.114
174_R226_L0.098141.114
63_S102_H0.097771.109
192_E196_E0.097211.103
74_A105_V0.097191.103
46_R91_Q0.097121.102
127_Y131_R0.096691.097
193_R197_K0.096421.094
73_Q141_Y0.09621.092
185_S189_D0.095631.085
167_S175_Q0.095511.084
75_H96_V0.09521.080
156_R160_G0.094921.077
69_L143_L0.094641.074
58_Y126_D0.094591.073
60_I107_I0.092181.046
92_Y107_I0.091361.037
124_N127_Y0.091351.037
60_I81_F0.091221.035
96_V103_P0.091071.033
170_K173_I0.090441.026
64_F73_Q0.089961.021
82_A93_V0.089381.014
5_F57_V0.08931.013
155_N158_E0.089161.012
85_M133_A0.089111.011
67_D144_S0.089051.010
12_I15_K0.088251.001
173_I176_A0.087040.988
72_E188_E0.086860.986
193_R196_E0.086770.985
40_Q44_A0.086740.984
87_P120_L0.086640.983
60_I109_I0.086420.981
154_Q158_E0.086420.981
128_R132_E0.086230.978
126_D131_R0.086020.976
54_K195_E0.086020.976
23_R30_L0.085780.973
10_D39_A0.085240.967
191_I201_V0.084850.963
219_T222_K0.084740.962
187_F191_I0.084580.960
58_Y61_I0.084150.955
234_N237_K0.083630.949
60_I92_Y0.083610.949
75_H94_V0.083480.947
90_H110_N0.083290.945
183_K193_R0.083280.945
45_T110_N0.083280.945
58_Y109_I0.083230.944
204_K207_K0.082410.935
153_R157_K0.082250.933
88_G112_V0.082030.931
23_R29_G0.0820.930
62_I96_V0.081790.928
75_H78_A0.081640.926
86_G92_Y0.081520.925
72_E75_H0.081520.925
131_R135_D0.081480.925
45_T114_L0.081410.924
72_E76_E0.080860.918
39_A223_G0.080850.917
85_M130_L0.080270.911
4_S7_G0.080230.910
78_A96_V0.079620.903
94_V107_I0.079380.901
57_V111_R0.079130.898
64_F103_P0.078920.896
65_P144_S0.078890.895
54_K119_K0.078790.894
136_E139_K0.078670.893
224_S231_T0.078390.890
180_A196_E0.078360.889
179_K197_K0.078320.889
46_R56_P0.078290.888
105_V134_S0.078220.888
194_L211_Y0.078160.887
229_D236_E0.078130.887
57_V61_I0.078090.886
94_V105_V0.077950.885
5_F59_H0.077860.884
224_S228_K0.077750.882
5_F46_R0.077710.882
115_D198_G0.077670.881
98_T103_P0.077570.880
81_F85_M0.077550.880
118_K229_D0.07720.876
47_A50_K0.077130.875
156_R159_K0.076820.872
62_I75_H0.076730.871
221_I226_L0.07670.870
91_Q114_L0.076470.868
135_D146_V0.076310.866
92_Y109_I0.075730.859
67_D129_R0.075630.858
84_E140_E0.07560.858
137_L140_E0.075570.858
236_E239_L0.075510.857
150_P162_A0.075460.856
185_S196_E0.075450.856
104_H107_I0.075440.856
179_K196_E0.075380.855
175_Q189_D0.075070.852
5_F8_A0.074990.851
103_P109_I0.074620.847
155_N177_I0.074260.843
158_E162_A0.074170.842
159_K162_A0.074070.841
87_P138_E0.074010.840
55_R122_P0.073940.839
168_S179_K0.073530.834
180_A190_F0.07340.833
192_E220_R0.073080.829
233_E237_K0.072870.827
105_V140_E0.072850.827
212_K215_D0.072780.826
229_D233_E0.072490.823
121_N137_L0.072130.818
138_E146_V0.072030.817
138_E222_K0.071930.816
31_N34_D0.071810.815
175_Q194_L0.071750.814
36_D44_A0.071640.813
74_A96_V0.071610.813
231_T235_L0.071580.812
149_K153_R0.071550.812
6_K9_L0.071480.811
52_V108_V0.071450.811
82_A186_S0.071220.808
167_S172_E0.071180.808
41_E44_A0.071040.806
157_K160_G0.0710.806
120_L124_N0.070920.805
42_F92_Y0.070860.804
28_G94_V0.07080.803
41_E112_V0.070730.803
177_I230_F0.070670.802
34_D77_I0.07040.799
228_K233_E0.070360.798
78_A92_Y0.07010.795
59_H107_I0.070010.794
41_E215_D0.069820.792
199_I213_L0.069440.788
212_K220_R0.068790.781
61_I194_L0.068720.780
69_L74_A0.068510.777
43_I46_R0.068380.776
120_L135_D0.068370.776
57_V86_G0.068350.776
7_G34_D0.068330.775
63_S100_T0.068270.775
40_Q229_D0.067980.771
76_E79_R0.067970.771
184_S190_F0.067940.771
24_V27_S0.067910.771
134_S230_F0.067790.769
69_L138_E0.067620.767
183_K186_S0.067480.766
39_A42_F0.067350.764
224_S236_E0.067310.764
73_Q76_E0.06730.764
186_S192_E0.067280.763
165_K179_K0.067140.762
86_G90_H0.066990.760
45_T48_L0.066950.760
52_V111_R0.066920.759
82_A109_I0.06690.759
202_R220_R0.06690.759
60_I94_V0.066880.759
66_P143_L0.066840.758
209_I223_G0.066690.757
104_H226_L0.066690.757
123_S130_L0.066420.754
4_S10_D0.066260.752
51_K226_L0.066240.752
189_D193_R0.066140.751
196_E200_E0.066030.749
215_D221_I0.065880.748
109_I120_L0.065820.747
23_R72_E0.065780.746
27_S30_L0.065650.745
44_A115_D0.065480.743
33_C36_D0.065460.743
231_T238_R0.065420.742
68_E135_D0.065370.742
64_F96_V0.065230.740
31_N110_N0.06510.739
101_D234_N0.064950.737
212_K216_K0.064950.737
135_D138_E0.064790.735
42_F207_K0.064770.735
76_E136_E0.064680.734
4_S43_I0.064670.734
81_F134_S0.064520.732
46_R50_K0.064490.732
158_E169_W0.064420.731
140_E154_Q0.06440.731
41_E91_Q0.064310.730
66_P195_E0.064250.729
64_F137_L0.064190.728
138_E145_V0.06410.727
118_K183_K0.064050.727
190_F194_L0.064050.727
69_L103_P0.063980.726
222_K236_E0.063920.725
58_Y111_R0.063870.725
5_F39_A0.063790.724
31_N41_E0.063690.723
58_Y226_L0.063510.721
133_A141_Y0.063480.720
49_N52_V0.063360.719
8_A59_H0.063320.719
142_G162_A0.063220.717
59_H138_E0.063140.716
137_L147_E0.062930.714
42_F49_N0.062850.713
87_P111_R0.062840.713
94_V104_H0.062840.713
69_L73_Q0.062770.712
83_E198_G0.062750.712
7_G71_P0.06260.710
126_D134_S0.062590.710
54_K182_E0.062530.710
99_D103_P0.06250.709
61_I102_H0.062490.709
7_G12_I0.062470.709
154_Q180_A0.062460.709
127_Y135_D0.062390.708
187_F201_V0.062380.708
177_I194_L0.062320.707
4_S14_N0.062310.707
7_G10_D0.062270.707
138_E143_L0.062160.705
25_V43_I0.062080.704
5_F42_F0.062030.704
100_T201_V0.062020.704
208_Y211_Y0.061990.703
156_R162_A0.061840.702
81_F137_L0.06180.701
176_A194_L0.061770.701
84_E233_E0.061770.701
79_R179_K0.061680.700
76_E195_E0.061590.699
72_E156_R0.061490.698
154_Q157_K0.061450.697
60_I104_H0.061440.697
188_E192_E0.061360.696
122_P126_D0.061360.696
94_V122_P0.061330.696
192_E195_E0.061150.694
158_E170_K0.061150.694
94_V131_R0.061140.694
211_Y226_L0.061030.693
99_D211_Y0.061010.692
171_E175_Q0.060840.690
61_I86_G0.060820.690
69_L144_S0.06080.690
184_S187_F0.060690.689
65_P102_H0.060610.688
68_E74_A0.060540.687
168_S186_S0.060480.686
93_V175_Q0.06040.685
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
4ht4A0.673698.50.822
2ns6A0.681898.50.823
1whzA0.2521550.94
2eo4A0.516544.30.944
3lb5A0.516543.90.944
4eguA0.425639.80.945
1y23A0.524838.80.945
3l7xA0.578537.70.946
3sgiA0.636434.80.947
3nrdA0.479331.60.948
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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