GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OrfB_IS605 - Probable transposase
Pfam: PF01385 (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: 227
Sequences: 2663
Seq/Len: 11.73
HH_delta: 0.933 (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
197_D201_K1.099366.413
219_V222_D0.962685.615
204_K208_K0.585853.417
200_H203_S0.428882.502
67_L108_L0.384352.242
157_I194_R0.381562.226
136_L198_F0.378762.209
164_L180_L0.365432.132
180_L184_L0.364572.127
178_R181_R0.334441.951
105_K189_R0.333291.944
127_V139_V0.324831.895
157_I191_I0.31231.822
101_E189_R0.311771.819
168_L181_R0.309041.803
135_N138_T0.297261.734
171_K180_L0.290851.697
127_V210_A0.288391.682
168_L184_L0.283541.654
139_V143_D0.281841.644
164_L167_R0.280751.638
19_D23_K0.279861.632
22_F40_P0.279311.629
9_Q56_K0.277231.617
29_K38_P0.276651.614
3_Y11_L0.276021.610
15_I19_D0.257851.504
17_R54_N0.257461.502
199_L203_S0.257351.501
164_L187_L0.257181.500
66_K80_W0.254121.482
165_R188_H0.253711.480
164_L184_L0.251651.468
189_R193_N0.251361.466
129_V137_A0.251031.464
167_R171_K0.24431.425
192_R196_K0.243341.419
13_Q16_R0.240021.400
138_T147_F0.239231.395
20_K24_S0.237431.385
153_E194_R0.237271.384
9_Q57_N0.236621.380
15_I18_A0.235691.375
7_P10_V0.233771.364
83_G86_H0.233431.362
24_S29_K0.227821.329
63_D66_K0.226641.322
161_L188_H0.225971.318
93_G97_I0.224391.309
28_K38_P0.22321.302
96_V108_L0.2211.289
122_D125_K0.219051.278
93_G96_V0.217211.267
160_R164_L0.214391.251
28_K39_G0.213671.246
123_T211_D0.21241.239
45_K48_R0.211871.236
161_L184_L0.210661.229
154_L158_K0.209131.220
25_F40_P0.208821.218
129_V139_V0.208461.216
6_L9_Q0.208221.215
163_K167_R0.206011.202
168_L180_L0.205631.199
13_Q17_R0.20431.192
51_F54_N0.200781.171
25_F41_P0.198761.159
165_R184_L0.196031.143
61_K68_K0.195051.138
9_Q13_Q0.19491.137
94_R113_E0.193661.130
143_D205_K0.192851.125
24_S27_K0.192521.123
53_V56_K0.192161.121
24_S38_P0.191281.116
137_A148_I0.191041.114
153_E157_I0.189561.106
202_V205_K0.189011.103
9_Q58_D0.188461.099
79_G82_K0.187221.092
162_R166_R0.186361.087
127_V140_S0.185641.083
181_R185_A0.185591.083
191_I195_R0.18381.072
12_Q16_R0.183591.071
143_D148_I0.183021.068
18_A22_F0.181381.058
188_H192_R0.179661.048
135_N147_F0.178841.043
133_I155_K0.177091.033
167_R170_R0.175731.025
193_N197_D0.175691.025
161_L191_I0.174761.019
9_Q12_Q0.17441.017
205_K209_E0.174391.017
101_E105_K0.17391.014
68_K80_W0.173421.012
222_D225_K0.172581.007
22_F25_F0.172521.006
6_L11_L0.170820.996
198_F202_V0.169060.986
165_R169_Q0.168840.985
86_H89_L0.168690.984
190_K194_R0.168630.984
23_K27_K0.168130.981
168_L171_K0.167610.978
12_Q15_I0.166880.973
11_L14_A0.166610.972
188_H195_R0.166520.971
132_G137_A0.166410.971
171_K175_S0.165420.965
55_Y69_L0.165410.965
19_D22_F0.165080.963
14_A18_A0.16240.947
206_I210_A0.160060.934
21_A41_P0.159980.933
83_G89_L0.159590.931
9_Q15_I0.157720.920
203_S206_I0.157430.918
24_S28_K0.157360.918
48_R51_F0.156730.914
135_N149_I0.156730.914
56_K59_G0.155430.907
125_K141_S0.154810.903
139_V142_G0.154190.899
9_Q59_G0.153940.898
127_V218_L0.153940.898
14_A17_R0.15260.890
206_I213_I0.152060.887
11_L15_I0.151530.884
164_L183_K0.151480.884
22_F26_F0.151010.881
210_A215_V0.150840.880
85_L88_R0.150560.878
183_K186_R0.150060.875
210_A218_L0.149850.874
207_V210_A0.149820.874
150_N153_E0.149290.871
136_L199_L0.148130.864
155_K158_K0.147130.858
107_Y189_R0.146910.857
167_R180_L0.146170.853
169_Q180_L0.146140.852
95_A98_I0.145980.852
126_V214_G0.145920.851
196_K200_H0.145590.849
7_P55_Y0.145330.848
10_V53_V0.145310.848
132_G138_T0.145020.846
138_T148_I0.144740.844
218_L223_L0.144510.843
172_K175_S0.144140.841
200_H204_K0.144030.840
87_R90_K0.143840.839
162_R184_L0.143830.839
59_G70_P0.143490.837
84_R87_R0.143250.836
164_L171_K0.142140.829
94_R98_I0.141730.827
131_L220_V0.140910.822
27_K38_P0.140890.822
9_Q16_R0.140750.821
3_Y9_Q0.140640.820
85_L89_L0.140210.818
162_R165_R0.139880.816
193_N201_K0.139570.814
165_R191_I0.139550.814
97_I100_K0.139350.813
166_R169_Q0.13920.812
156_S159_K0.139060.811
219_V223_L0.138520.808
208_K212_E0.138130.806
89_L93_G0.13760.803
197_D200_H0.136950.799
137_A206_I0.136670.797
105_K193_N0.136580.797
124_E141_S0.135480.790
69_L98_I0.1350.787
148_I205_K0.134770.786
169_Q184_L0.134510.785
53_V57_N0.133910.781
99_Y109_S0.133610.779
7_P71_K0.132850.775
133_I152_K0.132660.774
10_V13_Q0.132660.774
116_V119_P0.132570.773
52_S97_I0.132180.771
13_Q56_K0.131890.769
165_R168_L0.131630.768
55_Y59_G0.131510.767
137_A202_V0.13120.765
60_F70_P0.13110.765
158_K194_R0.13080.763
67_L70_P0.130720.763
104_G189_R0.130590.762
8_S11_L0.130330.760
131_L137_A0.130240.760
160_R163_K0.129670.756
119_P122_D0.128960.752
213_I216_E0.128650.750
97_I109_S0.128430.749
166_R170_R0.128040.747
157_I190_K0.127870.746
128_G140_S0.12780.745
82_K85_L0.127510.744
137_A140_S0.127410.743
7_P78_I0.127310.743
187_L191_I0.126530.738
10_V55_Y0.126210.736
193_N196_K0.126150.736
51_F55_Y0.125850.734
148_I198_F0.125380.731
44_K184_L0.125370.731
139_V206_I0.125040.729
16_R19_D0.124590.727
12_Q18_A0.124510.726
182_R186_R0.12360.721
11_L18_A0.123450.720
161_L169_Q0.12320.719
91_G112_V0.122990.717
172_K178_R0.12270.716
7_P59_G0.122120.712
13_Q54_N0.122010.712
83_G87_R0.121680.710
118_P123_T0.12150.709
149_I198_F0.121380.708
156_S163_K0.121040.706
174_K178_R0.120830.705
62_I110_I0.120830.705
63_D68_K0.120640.704
21_A195_R0.120430.702
207_V213_I0.120240.701
125_K182_R0.119990.700
167_R183_K0.119930.700
210_A213_I0.119530.697
94_R97_I0.119180.695
166_R180_L0.119130.695
85_L93_G0.119120.695
218_L221_E0.118150.689
55_Y58_D0.118120.689
205_K210_A0.118110.689
195_R216_E0.118050.689
161_L165_R0.117670.686
178_R182_R0.117510.685
62_I65_G0.117260.684
14_A50_R0.117250.684
148_I202_V0.116790.681
20_K23_K0.116510.680
6_L17_R0.116270.678
178_R196_K0.116070.677
95_A99_Y0.115850.676
54_N95_A0.115750.675
78_I81_I0.115450.673
134_K138_T0.115430.673
214_G218_L0.115280.672
184_L188_H0.114550.668
21_A27_K0.11380.664
7_P56_K0.113770.664
169_Q181_R0.113760.664
157_I161_L0.113550.662
216_E222_D0.11340.661
171_K177_K0.113350.661
134_K147_F0.113210.660
62_I66_K0.113080.660
133_I136_L0.112240.655
151_G198_F0.112130.654
141_S210_A0.112120.654
8_S57_N0.11210.654
120_P124_E0.111820.652
154_L194_R0.111580.651
7_P11_L0.111460.650
8_S58_D0.111170.648
4_K7_P0.110950.647
13_Q20_K0.110770.646
57_N60_F0.11050.645
157_I187_L0.110380.644
81_I86_H0.109690.640
22_F112_V0.109670.640
162_R191_I0.109520.639
127_V141_S0.109050.636
60_F112_V0.108790.635
10_V93_G0.10860.633
7_P53_V0.108530.633
39_G42_K0.108090.631
22_F28_K0.107970.630
78_I83_G0.107860.629
214_G219_V0.107280.626
23_K115_E0.107060.624
105_K182_R0.106650.622
70_P81_I0.106470.621
181_R184_L0.106440.621
95_A110_I0.10640.621
3_Y6_L0.106290.620
52_S57_N0.106250.620
52_S56_K0.106010.618
154_L157_I0.105560.616
204_K207_V0.105290.614
7_P70_P0.104940.612
209_E213_I0.104850.612
136_L203_S0.104760.611
192_R195_R0.10470.611
26_F41_P0.104290.608
180_L188_H0.103950.606
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
4jneA0.458133.60.933
4dndA0.458127.30.936
4ichA0.409725.30.937
4b9qA0.458121.70.939
4gniA0.4934150.943
1vhxA0.299614.90.943
1yuwA0.462613.60.944
2khoA0.458113.40.944
2v7yA0.449310.30.947
1u6zA0.48029.10.948
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