GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DnaB_C - DnaB-like helicase C terminal domain
Pfam: PF03796 (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: CL0023
Length: 259
Sequences: 4181
Seq/Len: 16.14
HH_delta: 0.059 (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
75_P78_K0.890213.907
182_E185_D0.741863.256
4_T16_L0.689533.026
16_L39_I0.660042.897
50_P132_D0.61912.717
49_Y132_D0.611362.683
52_L124_L0.576122.529
210_L230_L0.575142.524
18_P170_N0.572592.513
40_A135_F0.551712.421
121_I134_V0.528312.319
9_L210_L0.519582.280
3_P10_D0.510512.241
181_R200_G0.507892.229
36_A176_L0.500332.196
23_V206_A0.496242.178
193_L209_V0.492642.162
13_L208_V0.483012.120
5_G10_D0.463572.035
40_A51_V0.455632.000
43_A133_V0.454951.997
22_T172_P0.448751.970
166_A173_V0.444441.951
39_I133_V0.428471.881
22_T208_V0.421971.852
216_E226_G0.415441.823
18_P132_D0.415081.822
190_R229_E0.40711.787
122_R165_L0.398941.751
20_E62_E0.392311.722
107_E120_K0.377751.658
135_F174_I0.377721.658
7_P11_R0.373781.641
3_P46_N0.373451.639
21_L162_L0.372371.634
12_L241_G0.369961.624
26_A212_L0.364271.599
51_V133_V0.360891.584
42_N46_N0.349691.535
211_F233_A0.348841.531
16_L172_P0.346991.523
40_A53_Y0.345861.518
133_V172_P0.343891.509
41_L71_L0.341941.501
8_A11_R0.340951.496
134_V171_I0.338341.485
155_I159_S0.322991.418
159_S205_D0.321131.409
36_A135_F0.320451.406
114_I161_E0.319511.402
133_V174_I0.317721.394
179_L211_F0.316311.388
35_F39_I0.316051.387
165_L169_L0.294271.292
121_I169_L0.293621.289
17_R20_E0.292811.285
105_Y124_L0.290151.273
212_L230_L0.286351.257
64_A68_L0.27981.228
208_V235_N0.277911.220
9_L13_L0.275221.208
30_V217_K0.274551.205
2_I43_A0.271311.191
43_A49_Y0.267941.176
235_N239_P0.266731.171
215_D229_E0.264541.161
235_N238_G0.264321.160
125_K130_K0.264261.160
156_G160_R0.262591.153
58_M236_R0.261211.146
24_I174_I0.260571.144
117_I142_L0.256731.127
212_L228_A0.256631.126
41_L70_R0.255751.122
105_Y129_K0.255231.120
29_G237_N0.255121.120
23_V202_I0.254741.118
35_F212_L0.252681.109
29_G234_K0.252281.107
16_L174_I0.250931.101
151_R154_E0.250511.099
159_S175_A0.249541.095
37_L67_L0.24941.095
61_E65_A0.24681.083
26_A30_V0.245211.076
2_I172_P0.244391.073
216_E227_E0.242881.066
151_R198_E0.241731.061
44_A104_L0.23861.047
52_L134_V0.237521.042
52_L131_V0.235621.034
53_Y135_F0.234311.028
149_D152_R0.231471.016
16_L133_V0.229781.009
163_K207_D0.22941.007
57_E178_Q0.229181.006
122_R168_E0.228181.001
50_P130_K0.227841.000
152_R156_G0.227841.000
150_N153_Q0.227640.999
35_F230_L0.227080.997
113_T148_S0.226710.995
34_A66_R0.225930.992
4_T10_D0.225060.988
155_I160_R0.224750.986
121_I173_V0.224730.986
125_K131_V0.224730.986
149_D153_Q0.221150.971
200_G203_E0.220210.967
210_L232_V0.219890.965
54_F121_I0.219870.965
30_V218_Y0.219540.964
36_A53_Y0.217850.956
156_G201_A0.215850.947
39_I174_I0.214590.942
50_P131_V0.213630.938
20_E237_N0.212740.934
215_D218_Y0.212370.932
44_A51_V0.212350.932
206_A209_V0.21080.925
152_R201_A0.210140.922
4_T39_I0.208910.917
19_G170_N0.20890.917
178_Q204_Q0.208830.917
117_I136_I0.206540.907
40_A44_A0.205060.900
158_I161_E0.205040.900
159_S163_K0.203620.894
215_D227_E0.203570.893
59_S62_E0.203470.893
29_G240_T0.202480.889
185_D192_S0.201030.882
26_A32_K0.200950.882
214_R226_G0.19920.874
190_R231_I0.198980.873
115_D161_E0.198830.873
207_D236_R0.198610.872
13_L232_V0.197810.868
77_N81_S0.196690.863
109_T117_I0.196170.861
186_R192_S0.195910.860
197_R200_G0.194670.854
14_G17_R0.193670.850
166_A172_P0.192930.847
32_K137_D0.190830.838
215_D219_D0.190530.836
216_E219_D0.189810.833
164_A167_K0.189270.831
41_L45_L0.189040.830
17_R208_V0.188730.828
214_R217_K0.18830.826
155_I158_I0.188060.825
160_R163_K0.187820.824
213_H231_I0.187570.823
143_K164_A0.18660.819
118_E161_E0.186230.817
18_P49_Y0.186060.817
158_I163_K0.185030.812
45_L48_G0.18480.811
197_R204_Q0.184570.810
69_A79_I0.183790.807
46_N71_L0.183780.807
121_I125_K0.182950.803
33_T63_L0.182420.801
24_I210_L0.182210.800
139_L202_I0.181970.799
27_R30_V0.181260.796
38_Q42_N0.180680.793
213_H229_E0.180520.792
125_K170_N0.180430.792
60_E64_A0.180210.791
119_S123_R0.178940.785
50_P129_K0.178770.785
42_N45_L0.178680.784
196_L209_V0.177280.778
154_E197_R0.176840.776
43_A51_V0.176550.775
13_L17_R0.176030.773
181_R203_E0.175740.771
157_E161_E0.175340.770
9_L232_V0.175250.769
31_G137_D0.17460.766
39_I43_A0.174180.764
12_L235_N0.171250.752
176_L181_R0.171010.751
51_V135_F0.170640.749
156_G163_K0.17060.749
32_K57_E0.170360.748
19_G59_S0.169780.745
141_L205_D0.169460.744
55_S58_M0.168880.741
28_P31_G0.168590.740
138_Y178_Q0.167260.734
155_I199_S0.166470.731
201_A205_D0.165690.727
118_E168_E0.165680.727
134_V173_V0.165240.725
183_A186_R0.164920.724
24_I36_A0.163760.719
156_G161_E0.163640.718
29_G193_L0.163630.718
28_P203_E0.161650.709
33_T37_L0.161620.709
25_A196_L0.161560.709
125_K132_D0.161450.709
183_A217_K0.16140.708
112_L117_I0.159490.700
24_I35_F0.159420.700
53_Y104_L0.158920.698
55_S138_Y0.158680.696
21_L163_K0.158050.694
55_S177_S0.157260.690
52_L81_S0.156910.689
28_P206_A0.156720.688
216_E220_E0.156320.686
136_I162_L0.156130.685
12_L232_V0.155920.684
27_R184_E0.155650.683
138_Y176_L0.155350.682
131_V171_I0.15530.682
162_L173_V0.155270.681
121_I165_L0.155020.680
232_V235_N0.154570.678
33_T178_Q0.154490.678
150_N241_G0.154280.677
203_E209_V0.153630.674
6_F38_Q0.153520.674
6_F116_D0.153360.673
70_R76_Y0.152880.671
216_E228_A0.152590.670
162_L166_A0.152470.669
14_G29_G0.152270.668
26_A31_G0.152090.668
28_P32_K0.151850.666
58_M66_R0.15150.665
186_R191_P0.151380.664
186_R190_R0.151330.664
214_R218_Y0.151060.663
30_V228_A0.150990.663
196_L203_E0.15090.662
178_Q198_E0.149960.658
21_L207_D0.149850.658
180_N217_K0.149390.656
17_R235_N0.149280.655
29_G32_K0.149280.655
3_P75_P0.148680.653
173_V181_R0.148680.653
121_I131_V0.148610.652
165_L168_E0.147040.645
65_A126_R0.146740.644
180_N183_A0.146220.642
213_H218_Y0.14590.640
38_Q41_L0.145710.640
56_L141_L0.145690.639
24_I133_V0.145330.638
77_N239_P0.144830.636
27_R211_F0.144480.634
151_R190_R0.144220.633
20_E235_N0.144120.633
54_F134_V0.144040.632
145_E157_E0.143640.630
177_S196_L0.143620.630
21_L159_S0.14310.628
124_L127_E0.142420.625
211_F229_E0.142360.625
151_R155_I0.141840.623
39_I42_N0.141190.620
27_R204_Q0.141090.619
143_K157_E0.14060.617
109_T112_L0.140050.615
140_Q177_S0.140050.615
146_D149_D0.139360.612
115_D118_E0.138660.609
165_L172_P0.138320.607
17_R22_T0.1380.606
27_R32_K0.13780.605
152_R155_I0.136780.600
125_K129_K0.136740.600
32_K178_Q0.136350.598
145_E149_D0.135580.595
140_Q155_I0.135520.595
150_N154_E0.135420.594
155_I163_K0.135170.593
156_G159_S0.135080.593
56_L142_L0.13490.592
23_V175_A0.134420.590
211_F215_D0.13440.590
69_A74_V0.13410.589
157_E160_R0.133640.587
36_A174_I0.13340.585
48_G132_D0.132660.582
25_A211_F0.13210.580
23_V209_V0.131720.578
152_R159_S0.131650.578
25_A179_L0.130780.574
214_R228_A0.130490.573
37_L53_Y0.130430.572
14_G81_S0.130180.571
56_L112_L0.130170.571
190_R213_H0.130120.571
73_G78_K0.130050.571
2_I46_N0.129970.570
3_P7_P0.129680.569
144_S157_E0.129650.569
16_L208_V0.129630.569
112_L116_D0.129470.568
67_L71_L0.129250.567
209_V236_R0.129170.567
193_L233_A0.129010.566
10_D15_G0.128670.565
109_T164_A0.128380.563
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
4a1fA0.99611000.059
3bgwA0.99231000.075
2q6tA0.99611000.094
3bh0A0.99231000.099
2r6aA0.99611000.129
1q57A0.96911000.166
1cr0A0.9731000.337
2ztsA0.91121000.39
3cmuA0.8611000.392
3cmwA0.8611000.402

Page generated in 0.0183 seconds.