GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Plant_tran - Plant transposon protein
Pfam: PF04827 (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: 205
Sequences: 1017
Seq/Len: 4.96
HH_delta: 0.953 (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
65_A157_V0.518494.687
63_A161_F0.397693.595
62_E125_Y0.314552.843
52_G58_T0.304672.754
63_A71_I0.29552.671
34_M165_Q0.272562.464
69_L163_V0.26062.356
64_V93_L0.257942.332
62_E73_H0.239772.167
71_I160_A0.233632.112
121_A131_F0.222552.012
66_S70_W0.219731.986
35_H58_T0.211831.915
164_L190_C0.210451.902
171_I190_C0.209471.894
158_E162_G0.202561.831
154_R158_E0.198231.792
80_G84_D0.197851.789
37_E56_V0.194931.762
32_D84_D0.19481.761
32_D154_R0.193811.752
32_D158_E0.187551.695
41_C45_W0.180041.628
122_D125_Y0.168291.521
66_S72_W0.166891.509
69_L159_R0.166271.503
189_A192_I0.163061.474
121_A125_Y0.1631.474
74_A191_I0.162391.468
71_I161_F0.159391.441
140_G143_R0.155621.407
127_E132_V0.155551.406
147_A151_E0.15511.402
35_H52_G0.15351.388
155_K159_R0.153061.384
157_V161_F0.149881.355
156_D159_R0.147231.331
146_F150_Q0.146221.322
36_W171_I0.146041.320
167_R197_I0.142091.284
148_K152_S0.137341.242
59_I183_L0.137281.241
154_R162_G0.136611.235
62_E91_S0.136481.234
160_A164_L0.134481.216
18_I22_R0.134311.214
167_R194_H0.134291.214
166_A172_R0.131681.190
78_M87_V0.131071.185
128_W131_F0.13031.178
53_K83_N0.128931.166
31_I64_V0.128531.162
127_E133_K0.127311.151
84_D122_D0.126021.139
154_R157_V0.124691.127
35_H60_I0.123251.114
24_F153_A0.123171.113
79_P82_N0.122511.107
53_K84_D0.122011.103
122_D158_E0.121241.096
29_G64_V0.121211.096
33_C158_E0.12051.089
84_D154_R0.120381.088
64_V119_Y0.118621.072
83_N86_N0.118141.068
158_E161_F0.117681.064
17_Q68_D0.116511.053
83_N158_E0.11461.036
83_N125_Y0.113751.028
14_R19_G0.113261.024
85_I132_V0.111781.010
30_S120_L0.110941.003
117_G125_Y0.110340.997
30_S156_D0.110010.994
170_I190_C0.109560.990
88_L130_T0.108950.985
80_G154_R0.107480.972
97_L168_F0.10630.961
127_E135_I0.106190.960
180_R183_L0.105970.958
95_D99_Q0.104960.949
190_C193_L0.103780.938
21_A68_D0.103350.934
47_G63_A0.103090.932
134_T177_L0.102690.928
32_D80_G0.101020.913
73_H125_Y0.10090.912
33_C154_R0.100410.908
54_E158_E0.099880.903
121_A133_K0.099740.902
120_L150_Q0.099540.900
124_I162_G0.099450.899
145_L149_H0.099050.895
13_E16_L0.098210.888
121_A124_I0.097250.879
148_K155_K0.097170.878
16_L19_G0.097150.878
17_Q20_E0.096980.877
147_A194_H0.096690.874
123_G133_K0.096360.871
141_E144_K0.095970.868
33_C87_V0.095970.868
166_A173_G0.095760.866
78_M82_N0.095560.864
29_G146_F0.094580.855
84_D87_V0.094480.854
146_F194_H0.094210.852
188_R191_I0.094190.851
41_C46_K0.094070.850
27_M168_F0.09380.848
28_L98_L0.093720.847
164_L191_I0.093660.847
159_R163_V0.093640.846
119_Y131_F0.093610.846
117_G124_I0.09350.845
122_D154_R0.093250.843
17_Q67_H0.093230.843
54_E151_E0.092860.839
42_P181_E0.092660.838
125_Y150_Q0.092430.836
84_D158_E0.091730.829
32_D157_V0.091720.829
65_A163_V0.091540.828
32_D122_D0.091430.827
190_C195_N0.091410.826
66_S187_M0.091060.823
30_S154_R0.090980.822
168_F193_L0.090890.822
61_L77_G0.090870.821
69_L156_D0.090610.819
50_T57_P0.09050.818
49_Y164_L0.090290.816
168_F197_I0.090180.815
68_D89_D0.090110.815
73_H168_F0.090030.814
19_G22_R0.089830.812
57_P144_K0.089610.810
22_R153_A0.089560.810
23_G100_G0.089220.807
186_I190_C0.089080.805
27_M118_Y0.088970.804
170_I186_I0.088750.802
17_Q21_A0.088730.802
40_N44_A0.088710.802
139_Q142_K0.088290.798
98_L128_W0.088240.798
73_H94_F0.087540.791
54_E84_D0.087480.791
18_I30_S0.087470.791
64_V89_D0.087440.790
80_G168_F0.087130.788
154_R161_F0.087130.788
134_T147_A0.087040.787
41_C44_A0.086980.786
81_S84_D0.086890.785
49_Y54_E0.086620.783
37_E192_I0.086550.782
145_L148_K0.086490.782
189_A194_H0.086370.781
89_D94_F0.0860.777
63_A160_A0.085910.777
33_C162_G0.085590.774
13_E17_Q0.085290.771
187_M194_H0.085210.770
36_W187_M0.084950.768
92_P96_D0.084720.766
119_Y125_Y0.083960.759
171_I187_M0.083930.759
85_I126_P0.083780.757
30_S70_W0.083420.754
31_I121_A0.083050.751
49_Y173_G0.082770.748
33_C124_I0.082630.747
77_G81_S0.08260.747
78_M182_D0.082250.744
121_A127_E0.082240.743
100_G129_A0.082230.743
28_L96_D0.082230.743
165_Q174_P0.082150.743
191_I197_I0.082090.742
14_R17_Q0.081930.741
99_Q171_I0.081850.740
160_A167_R0.081670.738
94_F98_L0.081610.738
24_F118_Y0.081280.735
83_N123_G0.080970.732
124_I159_R0.080890.731
72_W100_G0.080430.727
29_G66_S0.080220.725
31_I68_D0.08010.724
30_S161_F0.080080.724
65_A72_W0.080040.724
175_A183_L0.07980.721
93_L97_L0.079750.721
20_E135_I0.079570.719
61_L76_F0.079490.719
27_M143_R0.079420.718
46_K50_T0.079410.718
35_H88_L0.079150.716
95_D176_R0.079040.715
124_I132_V0.078760.712
27_M197_I0.078730.712
32_D161_F0.078560.710
56_V168_F0.078560.710
151_E155_K0.078520.710
127_E130_T0.078260.707
96_D190_C0.078190.707
18_I21_A0.078150.706
22_R118_Y0.077980.705
119_Y124_I0.077780.703
99_Q139_Q0.077720.703
19_G24_F0.077540.701
89_D95_D0.077360.699
44_A49_Y0.07730.699
50_T55_G0.077260.698
169_A174_P0.077090.697
125_Y128_W0.077050.697
38_W92_P0.076760.694
46_K57_P0.076540.692
132_V146_F0.076520.692
61_L153_A0.076230.689
53_K157_V0.076150.688
73_H92_P0.076130.688
169_A173_G0.07610.688
13_E95_D0.076090.688
147_A150_Q0.075920.686
84_D124_I0.075560.683
64_V88_L0.075540.683
142_K173_G0.075530.683
182_D186_I0.075530.683
93_L98_L0.07550.683
176_R180_R0.075430.682
49_Y52_G0.075410.682
91_S100_G0.075010.678
27_M135_I0.074770.676
71_I123_G0.074460.673
14_R59_I0.074180.671
97_L130_T0.074160.670
48_Q57_P0.074010.669
17_Q142_K0.073950.668
32_D53_K0.073710.666
149_H152_S0.073660.666
34_M83_N0.073620.666
71_I184_A0.073370.663
117_G121_A0.073260.662
92_P95_D0.072990.660
31_I73_H0.072970.660
98_L168_F0.072810.658
61_L71_I0.072270.653
33_C151_E0.071970.651
133_K150_Q0.071580.647
14_R99_Q0.071540.647
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
4fw1A0.76118.90.953
1c0mA0.756113.70.956
3kksA0.663413.50.956
3qv2A0.292712.70.956
2c7pA0.292710.20.958
2qrvA0.2927100.958
1ef5A0.32280.96
3rf0A0.34157.80.96
4hdeA0.44397.30.96
2wbrA0.21956.40.961
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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