GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Helicase_C_3 - Helicase conserved C-terminal domain
Pfam: PF13625 (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: 129
Sequences: 690
Seq/Len: 5.35
HH_delta: 0.823 (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
10_I42_L0.29472.672
101_C107_L0.230972.094
61_I80_I0.198481.799
12_V17_P0.187221.697
90_V106_L0.184231.670
30_E49_R0.18291.658
2_L12_V0.179771.630
31_L38_H0.178311.616
18_S117_A0.176881.604
10_I25_L0.176531.600
30_E43_T0.172111.560
61_I81_E0.170041.541
43_T46_S0.169171.534
28_F64_L0.167831.521
58_E81_E0.158191.434
93_Y100_E0.157111.424
74_Q78_Q0.155581.410
61_I77_E0.155231.407
65_E77_E0.154741.403
47_L60_I0.15011.361
25_L63_F0.149411.354
54_G90_V0.148371.345
50_A60_I0.147781.340
56_T59_E0.147361.336
63_F67_Y0.144821.313
58_E76_V0.143831.304
30_E38_H0.143381.300
5_Q11_L0.141321.281
29_A41_R0.140191.271
48_W51_A0.136071.234
4_V10_I0.135641.230
62_E66_R0.134781.222
23_W46_S0.134081.216
65_E70_N0.134051.215
29_A40_Y0.13181.195
55_L60_I0.130891.187
10_I64_L0.130571.184
103_D106_L0.130461.183
9_E82_D0.130021.179
60_I84_A0.129251.172
21_D80_I0.128921.169
5_Q9_E0.128891.168
27_R53_A0.125291.136
42_L64_L0.124211.126
55_L59_E0.123441.119
18_S63_F0.123171.117
108_D112_A0.121861.105
10_I22_A0.120991.097
77_E81_E0.120581.093
32_K39_V0.116681.058
104_P108_D0.116421.055
91_R102_D0.115891.051
34_P64_L0.115511.047
37_M78_Q0.115191.044
39_V88_G0.113731.031
84_A88_G0.113581.030
93_Y98_L0.113521.029
25_L65_E0.113251.027
65_E103_D0.112951.024
105_E108_D0.112281.018
32_K51_A0.111831.014
11_L19_P0.111031.007
44_P83_W0.111011.006
81_E85_R0.110891.005
52_S91_R0.110651.003
41_R88_G0.109420.992
80_I97_Y0.108430.983
28_F89_R0.1080.979
55_L101_C0.10680.968
14_P41_R0.106740.968
18_S55_L0.106310.964
100_E110_L0.106290.964
23_W42_L0.104630.949
47_L111_L0.103930.942
109_E114_P0.10260.930
28_F34_P0.101760.923
34_P42_L0.101320.919
41_R87_Y0.101310.918
4_V42_L0.10130.918
47_L88_G0.100710.913
12_V38_H0.100650.912
3_I40_Y0.100630.912
110_L113_D0.100610.912
2_L38_H0.099940.906
47_L92_L0.099430.901
78_Q82_D0.099240.900
12_V22_A0.09910.898
42_L46_S0.098870.896
91_R100_E0.09860.894
76_V82_D0.098220.890
35_D73_P0.097850.887
14_P35_D0.097630.885
65_E104_P0.09730.882
18_S111_L0.096870.878
6_P35_D0.096810.878
40_Y92_L0.096770.877
6_P98_L0.096550.875
113_D116_L0.096480.875
114_P117_A0.096380.874
27_R63_F0.095860.869
60_I91_R0.095590.867
22_A43_T0.094770.859
64_L98_L0.094670.858
65_E72_L0.094470.856
48_W88_G0.094380.856
57_A84_A0.094330.855
59_E86_R0.094190.854
9_E103_D0.094090.853
12_V28_F0.093290.846
26_A89_R0.093120.844
92_L99_L0.092860.842
8_F75_N0.092410.838
69_K72_L0.092390.838
61_I64_L0.092290.837
43_T47_L0.092220.836
17_P101_C0.091880.833
4_V72_L0.091570.830
18_S21_D0.091480.829
30_E110_L0.091250.827
27_R45_A0.091120.826
34_P38_H0.090440.820
2_L67_Y0.090220.818
79_S83_W0.089890.815
18_S57_A0.089710.813
41_R71_P0.089670.813
93_Y110_L0.088930.806
22_A55_L0.088810.805
71_P118_K0.088620.803
24_F28_F0.088140.799
24_F60_I0.088020.798
69_K96_A0.087760.796
55_L111_L0.087470.793
76_V107_L0.087030.789
19_P75_N0.086470.784
62_E80_I0.086150.781
89_R113_D0.085860.778
96_A99_L0.085720.777
91_R98_L0.085710.777
43_T65_E0.084940.770
20_A111_L0.084880.769
115_E118_K0.08480.769
10_I46_S0.084630.767
26_A106_L0.084470.766
46_S50_A0.084340.765
102_D108_D0.084210.763
57_A68_S0.084110.762
103_D107_L0.08410.762
11_L32_K0.082980.752
90_V102_D0.082110.744
16_H48_W0.082030.744
52_S87_Y0.081840.742
18_S66_R0.081410.738
14_P21_D0.081150.736
50_A55_L0.080720.732
11_L31_L0.08070.732
73_P80_I0.079940.725
45_A49_R0.079860.724
32_K41_R0.079810.724
76_V83_W0.079660.722
34_P88_G0.079640.722
7_D88_G0.079540.721
4_V25_L0.079450.720
40_Y116_L0.079450.720
66_R118_K0.079350.719
74_Q85_R0.079210.718
62_E65_E0.079130.717
83_W106_L0.078880.715
38_H49_R0.078830.715
38_H69_K0.078710.714
30_E92_L0.078660.713
108_D111_L0.078640.713
75_N85_R0.078530.712
72_L81_E0.078410.711
42_L80_I0.078260.709
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
3domA0.658995.80.823
3dgpA0.441992.70.849
2nn6H0.651253.70.897
4ifdH0.674426.70.913
2pxgA0.790724.50.914
1b0nB0.418622.50.915
2dunA0.9302220.916
3memA0.899219.10.918
2fe1A0.922518.50.918
3dgpB0.294618.30.919
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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