GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_IS66 - Transposase IS66 family
Pfam: PF03050 (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: CL0219
Length: 271
Sequences: 2510
Seq/Len: 9.26
HH_delta: 0.886 (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
125_S139_H0.45953.522
141_L229_E0.340242.608
200_K227_W0.313782.405
74_E89_Y0.290122.224
254_V257_R0.284862.184
172_Y242_D0.283672.174
243_N246_A0.283242.171
148_R152_D0.269232.064
248_R251_R0.267222.048
122_I140_Q0.248431.904
227_W231_F0.244491.874
141_L226_H0.239691.837
75_T254_V0.237951.824
71_H246_A0.235811.808
124_V240_P0.234111.795
146_L230_L0.233781.792
13_A49_V0.233421.789
107_R131_Y0.225341.727
144_A148_R0.223671.715
256_G260_S0.217621.668
244_N247_E0.217591.668
233_F241_L0.213061.633
177_R191_Y0.210281.612
138_T235_E0.210031.610
164_A202_W0.207331.589
106_S111_V0.204341.566
146_L223_L0.202861.555
54_K58_E0.201681.546
123_L137_I0.200171.534
251_R261_L0.198741.523
250_I253_V0.198741.523
109_S133_K0.194961.494
69_V124_V0.192411.475
74_E107_R0.187881.440
85_G89_Y0.187761.439
72_A116_L0.186811.432
93_F115_F0.186571.430
72_A123_L0.183131.404
251_R254_V0.182341.398
122_I239_V0.180911.387
17_Y23_L0.180581.384
163_Q167_R0.180191.381
113_K117_G0.180071.380
15_L29_M0.177771.363
13_A46_I0.176821.355
196_M200_K0.174551.338
250_I254_V0.174521.338
248_R252_P0.174421.337
59_A62_E0.171251.313
221_K225_K0.170891.310
132_N229_E0.170031.303
193_K197_E0.169841.302
245_A248_R0.168841.294
143_W168_I0.168381.291
68_P121_G0.168081.288
89_Y95_S0.167821.286
72_A125_S0.166381.275
140_Q239_V0.165741.270
87_K91_W0.165581.269
104_A111_V0.163621.254
233_F239_V0.162711.247
12_I42_I0.162191.243
109_S130_A0.159821.225
76_G87_K0.158651.216
23_L46_I0.157591.208
91_W95_S0.157211.205
21_L29_M0.157081.204
252_P255_L0.156021.196
94_V246_A0.154751.186
85_G91_W0.154211.182
150_F219_A0.153271.175
142_C244_N0.15321.174
127_G141_L0.153031.173
203_L220_I0.152951.172
24_Y39_R0.152731.171
243_N247_E0.152341.168
226_H229_E0.151831.164
22_P25_R0.151111.158
69_V97_E0.150491.154
149_D152_D0.150451.153
27_Q39_R0.14931.144
40_G44_N0.148111.135
255_L264_R0.147821.133
191_Y195_L0.147741.132
161_A165_L0.147541.131
107_R128_Y0.147391.130
144_A242_D0.147231.129
51_E54_K0.146451.123
251_R255_L0.146141.120
69_V240_P0.146021.119
217_R221_K0.145961.119
138_T232_T0.145441.115
259_N262_F0.144171.105
30_L35_I0.144111.105
214_S217_R0.143141.097
102_F118_D0.143091.097
197_E200_K0.142391.091
26_I42_I0.141661.086
17_Y20_H0.140931.080
74_E131_Y0.140871.080
196_M234_L0.140591.078
258_K261_L0.140291.075
194_P197_E0.139681.071
37_I45_W0.139041.066
200_K224_L0.138421.061
196_M227_W0.138061.058
167_R211_S0.13761.055
89_Y93_F0.137291.052
94_V245_A0.137181.052
15_L19_Y0.137151.051
125_S131_Y0.137111.051
203_L224_L0.137021.050
140_Q233_F0.135971.042
112_I115_F0.135961.042
124_V140_Q0.135761.041
257_R261_L0.135511.039
127_G226_H0.134411.030
76_G89_Y0.133691.025
150_F223_L0.133611.024
255_L259_N0.133261.021
252_P256_G0.133051.020
219_A222_Y0.132941.019
143_W242_D0.13281.018
198_E201_E0.13161.009
140_Q232_T0.131481.008
78_R85_G0.131421.007
151_Q155_E0.13121.006
70_V93_F0.130240.998
171_L233_F0.129070.989
232_T239_V0.128770.987
107_R112_I0.128220.983
110_K113_K0.126490.970
154_A157_D0.124650.955
247_E250_I0.124390.953
258_K265_S0.124190.952
88_G93_F0.123630.948
218_K221_K0.123510.947
72_A93_F0.122320.938
144_A244_N0.121510.931
102_F115_F0.121190.929
52_A55_P0.120960.927
21_L25_R0.120870.927
16_K26_I0.120840.926
27_Q42_I0.120510.924
58_E62_E0.120060.920
197_E201_E0.119890.919
257_R262_F0.119720.918
43_A47_K0.119650.917
163_Q166_K0.119380.915
212_P217_R0.119290.914
260_S263_F0.118840.911
196_M199_L0.118670.910
147_R150_F0.118380.907
232_T235_E0.11830.907
171_L192_A0.118090.905
70_V123_L0.118010.905
252_P261_L0.117970.904
143_W230_L0.117640.902
244_N248_R0.117340.899
254_V263_F0.117250.899
162_A166_K0.117060.897
249_A258_K0.116980.897
143_W241_L0.116560.893
125_S135_A0.116510.893
22_P259_N0.116480.893
230_L233_F0.116280.891
57_Y61_K0.116270.891
260_S264_R0.116080.890
83_G93_F0.115610.886
169_R176_R0.115410.885
123_L134_L0.115090.882
108_S111_V0.114640.879
193_K234_L0.114640.879
90_L253_V0.114240.876
248_R261_L0.114220.876
173_R176_R0.113860.873
44_N48_R0.113530.870
245_A249_A0.1130.866
85_G95_S0.112620.863
248_R255_L0.112340.861
86_K89_Y0.112330.861
54_K57_Y0.111960.858
139_H229_E0.111690.856
41_T44_N0.11160.855
83_G95_S0.111090.852
16_K29_M0.110820.849
57_Y100_L0.110630.848
88_G91_W0.11060.848
19_Y29_M0.110290.845
46_I50_A0.109890.842
173_R238_G0.109670.841
22_P26_I0.109370.838
193_K235_E0.109170.837
89_Y108_S0.108650.833
23_L43_A0.10850.832
37_I41_T0.108420.831
128_Y131_Y0.108370.831
247_E251_R0.108330.830
42_I203_L0.108090.829
257_R263_F0.108070.828
61_K100_L0.1080.828
191_Y198_E0.107910.827
113_K133_K0.10790.827
48_R52_A0.107840.827
242_D248_R0.107840.827
77_W88_G0.107790.826
110_K133_K0.107680.825
220_I223_L0.107450.824
69_V122_I0.107450.824
93_F102_F0.107130.821
90_L101_F0.107010.820
192_A233_F0.106620.817
138_T228_D0.106420.816
114_E197_E0.105620.810
174_I177_R0.104790.803
166_K170_E0.104620.802
255_L258_K0.104390.800
98_V142_C0.104380.800
14_Y19_Y0.104270.799
15_L18_V0.104140.798
192_A196_M0.10390.796
103_Y266_E0.103810.796
84_K238_G0.103490.793
93_F111_V0.103220.791
195_L198_E0.103050.790
170_E173_R0.102580.786
62_E228_D0.10250.786
167_R198_E0.102440.785
47_K105_P0.102350.785
215_P218_K0.102320.784
131_Y139_H0.102270.784
150_F153_A0.102140.783
256_G259_N0.102140.783
87_K93_F0.102060.782
220_I225_K0.102020.782
23_L39_R0.101310.777
251_R258_K0.10130.776
194_P198_E0.100940.774
220_I224_L0.100820.773
143_W196_M0.100550.771
78_R87_K0.100450.770
169_R175_E0.100210.768
92_V250_I0.099950.766
71_H124_V0.099890.766
61_K102_F0.099760.765
99_V244_N0.099610.764
39_R43_A0.09960.763
169_R172_Y0.099530.763
74_E125_S0.099330.761
13_A45_W0.09930.761
155_E215_P0.099170.760
72_A131_Y0.098950.758
164_A168_I0.098860.758
199_L223_L0.098450.755
13_A110_K0.098310.754
190_R193_K0.098140.752
27_Q30_L0.097960.751
70_V137_I0.097780.750
15_L21_L0.097690.749
177_R193_K0.097560.748
214_S221_K0.097380.746
21_L30_L0.097380.746
99_V142_C0.097310.746
127_G222_Y0.097280.746
151_Q154_A0.097020.744
247_E253_V0.096770.742
69_V241_L0.096560.740
20_H25_R0.096230.738
153_A219_A0.096160.737
166_K201_E0.095990.736
171_L195_L0.095960.736
14_Y18_V0.095780.734
242_D245_A0.095440.732
133_K225_K0.095160.729
17_Y46_I0.094960.728
126_D145_H0.094680.726
13_A134_L0.094010.721
71_H245_A0.093910.720
37_I200_K0.093870.720
20_H23_L0.093680.718
17_Y26_I0.093590.717
161_A164_A0.093490.717
25_R147_R0.093440.716
127_G139_H0.093310.715
75_T257_R0.09330.715
167_R170_E0.093210.714
62_E197_E0.09320.714
230_L234_L0.093180.714
222_Y226_H0.093030.713
100_L112_I0.092990.713
89_Y107_R0.092830.712
50_A54_K0.092620.710
16_K24_Y0.092580.710
61_K118_D0.09250.709
85_G88_G0.092420.708
248_R256_G0.092410.708
41_T165_L0.092360.708
201_E214_S0.092270.707
143_W233_F0.092190.707
23_L26_I0.092190.707
229_E232_T0.091930.705
15_L30_L0.091840.704
259_N264_R0.091710.703
48_R51_E0.091380.700
223_L230_L0.091260.700
77_W260_S0.091250.699
125_S132_N0.091140.699
160_R215_P0.091140.699
102_F116_L0.090970.697
95_S125_S0.090940.697
199_L202_W0.090850.696
72_A248_R0.09070.695
170_E195_L0.090410.693
249_A252_P0.090310.692
130_A242_D0.090.690
84_K88_G0.089850.689
14_Y29_M0.089660.687
91_W107_R0.089660.687
87_K95_S0.089580.687
54_K138_T0.089410.685
171_L174_I0.089330.685
218_K222_Y0.089330.685
234_L242_D0.089270.684
122_I236_D0.089210.684
50_A57_Y0.089160.683
95_S98_V0.08910.683
68_P148_R0.088930.682
78_R112_I0.088880.681
108_S130_A0.088770.680
155_E158_P0.088730.680
91_W94_V0.088650.680
243_N251_R0.088580.679
127_G149_D0.088350.677
129_S132_N0.088310.677
17_Y43_A0.088130.676
135_A139_H0.088110.675
12_I29_M0.087950.674
101_F151_Q0.087820.673
77_W254_V0.08780.673
16_K37_I0.087750.673
57_Y60_L0.087740.673
195_L199_L0.087720.672
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
3hotA0.789796.50.886
2lvsA0.177194.40.904
2gloA0.195693.80.907
2elhA0.250992.20.912
1tc3C0.1808920.912
2jn6A0.3469880.919
3vfzA0.21487.80.92
1jkoC0.184587.50.92
3hugA0.21487.50.92
1pdnC0.184587.30.92
If you are interested in a protein containing this domain,
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