GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_1 - Transposase DDE domain
Pfam: PF01609 (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: 213
Sequences: 3613
Seq/Len: 16.96
HH_delta: 0.495 (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
94_L99_I0.488933.137
48_P212_N0.463112.971
81_A103_I0.41962.692
38_H54_T0.356252.285
92_E96_E0.343322.202
64_L90_N0.337342.164
38_H85_Y0.333972.142
69_E97_R0.316152.028
78_L102_V0.306961.969
12_T184_K0.29861.916
69_E93_A0.296981.905
51_V205_F0.291851.872
135_Q138_K0.290221.862
181_R185_Q0.289091.855
48_P208_L0.285381.831
163_P166_T0.276321.773
91_L103_I0.26581.705
180_F184_K0.251711.615
121_W124_F0.251261.612
100_H158_N0.248361.593
197_P201_E0.245971.578
52_K70_R0.244541.569
173_R177_E0.239191.534
65_P93_A0.238311.529
80_V169_L0.23761.524
79_V94_L0.233811.500
87_S90_N0.232531.492
50_S70_R0.231331.484
170_Y173_R0.23041.478
176_I180_F0.220861.417
39_L180_F0.219551.408
34_G56_G0.218951.405
93_A97_R0.216071.386
177_E184_K0.213891.372
192_L203_H0.213221.368
194_V199_R0.208891.340
11_G60_D0.208151.335
63_A66_E0.206211.323
11_G85_Y0.204751.314
204_L208_L0.20221.297
162_L166_T0.200391.286
175_Q178_R0.199141.278
9_I64_L0.193291.240
119_K122_K0.192781.237
11_G84_G0.191381.228
83_R104_R0.189661.217
54_T63_A0.189651.217
196_S199_R0.189341.215
174_W178_R0.188661.210
42_D45_S0.18711.200
94_L97_R0.185271.189
36_K60_D0.18511.187
102_V169_L0.185021.187
203_H207_T0.1851.187
94_L101_F0.18391.180
181_R184_K0.183511.177
185_Q190_E0.183481.177
128_S133_P0.182491.171
135_Q139_R0.182331.170
189_L207_T0.180781.160
155_L158_N0.17861.146
127_R130_R0.17781.141
127_R133_P0.177781.140
127_R132_K0.177341.138
194_V203_H0.177131.136
41_V176_I0.176191.130
58_V63_A0.175171.124
108_N111_K0.174531.120
95_K101_F0.173831.115
129_A133_P0.173441.113
51_V208_L0.172551.107
179_F211_Y0.171921.103
131_K135_Q0.171871.103
25_Y28_G0.169451.087
25_Y29_K0.169311.086
48_P51_V0.169291.086
86_D103_I0.169241.086
156_V159_I0.168961.084
164_R167_A0.167581.075
157_T160_T0.167121.072
74_R77_D0.1671.071
102_V170_Y0.166981.071
161_T165_D0.166871.070
181_R186_F0.166291.067
139_R142_V0.165731.063
50_S67_L0.165581.062
138_K144_I0.164911.058
136_K140_V0.164231.054
120_F124_F0.164071.053
28_G32_G0.163761.051
27_K31_R0.16231.041
59_H62_K0.162261.041
199_R202_A0.162151.040
13_T35_Y0.161921.039
81_A84_G0.161661.037
13_T17_P0.160921.032
52_K201_E0.160171.028
90_N93_A0.159051.020
200_I203_H0.157111.008
78_L169_L0.15570.999
24_R28_G0.155620.998
11_G16_T0.15460.992
183_L207_T0.154490.991
60_D84_G0.153580.985
202_A206_L0.153410.984
59_H84_G0.153290.983
182_E211_Y0.153150.982
121_W125_D0.153130.982
61_S87_S0.152540.979
155_L159_I0.152040.975
9_I85_Y0.151990.975
65_P90_N0.151880.974
122_K125_D0.151240.970
48_P179_F0.150260.964
52_K67_L0.150170.963
52_K63_A0.14940.958
17_P33_F0.149360.958
26_K34_G0.148910.955
80_V102_V0.148210.951
113_I116_I0.147770.948
195_R203_H0.145680.935
187_L211_Y0.144540.927
54_T85_Y0.14430.926
126_R129_A0.143930.923
58_V62_K0.143250.919
145_R148_Q0.14320.919
189_L203_H0.142680.915
94_L103_I0.142670.915
165_D168_A0.142510.914
41_V179_F0.14220.912
173_R180_F0.142170.912
133_P136_K0.142160.912
147_E150_K0.142050.911
125_D134_K0.141480.908
115_K119_K0.141250.906
178_R182_E0.140910.904
142_V150_K0.140660.902
26_K29_K0.140630.902
29_K32_G0.140210.899
105_L108_N0.140170.899
11_G36_K0.140130.899
205_F212_N0.140020.898
192_L211_Y0.139970.898
204_L207_T0.139310.894
86_D106_K0.139310.894
107_K111_K0.138710.890
194_V207_T0.13830.887
159_I162_L0.137940.885
77_D99_I0.137420.882
105_L116_I0.136310.874
68_L94_L0.135990.872
67_L70_R0.135660.870
63_A67_L0.135090.867
199_R206_L0.134930.866
140_V143_V0.134830.865
128_S131_K0.134650.864
84_G87_S0.134450.863
132_K135_Q0.134240.861
140_V145_R0.133980.860
119_K124_F0.133930.859
189_L204_L0.133850.859
81_A85_Y0.133780.858
55_P58_V0.13370.858
132_K139_R0.133620.857
107_K110_K0.133460.856
130_R139_R0.133430.856
207_T210_A0.132860.852
187_L207_T0.132810.852
106_K109_R0.132560.850
60_D85_Y0.131660.845
205_F208_L0.131240.842
208_L212_N0.131220.842
14_I17_P0.1310.840
36_K54_T0.130630.838
169_L174_W0.129890.833
78_L100_H0.129360.830
113_I124_F0.129320.830
40_A67_L0.129310.830
76_P99_I0.129090.828
35_Y197_P0.128530.825
34_G38_H0.128350.823
127_R135_Q0.128320.823
95_K100_H0.128010.821
179_F182_E0.127930.821
85_Y173_R0.127870.820
128_S135_Q0.127860.820
11_G17_P0.127380.817
61_S106_K0.126970.815
64_L68_L0.126940.814
30_K33_F0.126610.812
183_L208_L0.126570.812
53_V201_E0.126340.810
160_T166_T0.126180.809
193_R203_H0.125970.808
101_F158_N0.124730.800
100_H169_L0.124720.800
12_T104_R0.124650.800
143_V155_L0.124090.796
124_F164_R0.124010.796
192_L195_R0.12380.794
188_G191_R0.123750.794
79_V103_I0.123740.794
201_E205_F0.123540.793
134_K138_K0.123460.792
56_G59_H0.123410.792
73_G76_P0.123320.791
86_D105_L0.123270.791
82_D85_Y0.123230.791
46_G51_V0.122770.788
79_V99_I0.122750.787
119_K125_D0.121860.782
138_K152_G0.121550.780
178_R181_R0.121450.779
37_L204_L0.121160.777
9_I79_V0.120920.776
152_G156_V0.120890.776
198_E202_A0.120880.775
172_R175_Q0.120840.775
137_S141_R0.120560.773
182_E186_F0.120420.773
24_R27_K0.120190.771
28_G31_R0.120060.770
137_S149_K0.119930.769
131_K137_S0.119740.768
162_L165_D0.119620.767
135_Q140_V0.119610.767
133_P137_S0.119410.766
80_V173_R0.119230.765
104_R156_V0.118970.763
68_L97_R0.118830.762
24_R29_K0.118680.761
83_R170_Y0.118480.760
78_L159_I0.1180.757
177_E180_F0.117860.756
164_R168_A0.117740.755
140_V144_I0.117680.755
75_K98_G0.117340.753
129_A134_K0.117060.751
13_T32_G0.116990.751
197_P200_I0.116890.750
192_L200_I0.116560.748
25_Y34_G0.116420.747
120_F125_D0.115670.742
83_R86_D0.115470.741
132_K136_K0.115460.741
27_K34_G0.115450.741
132_K137_S0.115370.740
175_Q184_K0.115230.739
16_T192_L0.11490.737
61_S64_L0.114040.732
131_K144_I0.11370.729
115_K123_S0.113310.727
9_I17_P0.113210.726
139_R150_K0.1130.725
88_A92_E0.112630.723
135_Q141_R0.11240.721
144_I149_K0.112250.720
86_D91_L0.112010.719
156_V161_T0.111970.718
118_N121_W0.111590.716
150_K153_Y0.111290.714
24_R30_K0.111220.713
112_K116_I0.110980.712
154_F157_T0.110820.711
95_K198_E0.110750.710
27_K38_H0.110750.710
32_G37_L0.110690.710
163_P167_A0.110480.709
11_G38_H0.110330.708
89_E93_A0.110030.706
180_F185_Q0.109720.704
176_I207_T0.109670.704
118_N123_S0.109560.703
137_S140_V0.109260.701
152_G155_L0.109250.701
91_L105_L0.108910.699
192_L204_L0.108890.699
143_V146_K0.108830.698
123_S127_R0.10880.698
170_Y174_W0.108490.696
113_I117_E0.108410.695
154_F158_N0.107940.692
189_L193_R0.107790.691
75_K97_R0.107780.691
127_R131_K0.107540.690
126_R138_K0.107450.689
65_P69_E0.107430.689
144_I148_Q0.107370.689
130_R135_Q0.107170.688
131_K142_V0.10710.687
61_S65_P0.107070.687
136_K139_R0.106990.686
37_L53_V0.106670.684
146_K149_K0.106570.684
151_K155_L0.106510.683
116_I120_F0.106350.682
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
1musA199.60.495
3av9A0.605688.90.866
1ex4A0.605688.50.867
1c0mA0.633886.90.87
1cxqA0.638585.60.872
1c6vA0.605685.60.872
1bcoA0.8498840.875
1k6yA0.605682.20.878
3hphA0.600981.80.878
4fw1A0.624478.80.882

Page generated in 0.1265 seconds.