GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF606 - Protein of unknown function DUF606
Pfam: PF04657 (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: CL0184
Length: 138
Sequences: 966
Seq/Len: 7
HH_delta: 0.854 (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
34_S75_V0.291372.391
35_F42_F0.269282.210
22_Q25_K0.266182.185
75_V78_V0.24962.049
130_A134_A0.232381.907
69_L72_L0.222541.826
21_G82_I0.211461.735
106_L129_L0.194981.600
13_I101_Q0.187271.537
79_L83_I0.186291.529
131_L138_L0.186021.527
99_A133_I0.183231.504
64_P67_A0.182851.501
16_Q37_S0.180991.485
48_I52_T0.176981.453
96_L135_G0.175481.440
34_S38_F0.172281.414
5_L99_A0.170711.401
108_I113_L0.170121.396
81_N93_T0.168831.386
14_A85_V0.166621.367
90_A96_L0.165871.361
77_F97_I0.163791.344
126_I130_A0.163691.343
24_G27_L0.161331.324
52_T55_P0.159931.313
6_A84_L0.159031.305
81_N97_I0.157121.290
34_S37_S0.154261.266
88_L92_L0.153341.258
37_S74_G0.15191.247
38_F41_G0.15151.243
112_G115_G0.149251.225
107_L111_F0.149181.224
118_K126_I0.146561.203
127_L131_L0.146481.202
120_P123_L0.145571.195
110_H125_R0.145021.190
17_A85_V0.143951.181
47_I51_I0.142021.166
94_T98_V0.141711.163
14_A37_S0.139281.143
122_S125_R0.139121.142
128_G135_G0.13781.131
91_A125_R0.136721.122
43_I47_I0.13571.114
31_L79_L0.133611.097
34_S79_L0.13221.085
96_L107_L0.131821.082
123_L130_A0.131681.081
23_L70_G0.131421.079
91_A98_V0.131231.077
14_A18_A0.130481.071
17_A90_A0.129911.066
95_I105_S0.128821.057
91_A94_T0.128141.052
94_T135_G0.127621.047
63_V67_A0.127221.044
35_F39_G0.126831.041
23_L33_A0.1261.034
8_L127_L0.125821.033
62_S137_I0.125761.032
28_G32_V0.125531.030
69_L73_L0.124681.023
41_G82_I0.123311.012
8_L126_I0.123251.012
18_A116_A0.123241.011
112_G118_K0.123181.011
67_A90_A0.122931.009
4_L8_L0.121911.001
107_L129_L0.121070.994
37_S45_L0.120730.991
56_S59_S0.120340.988
23_L86_P0.119890.984
6_A94_T0.119460.980
43_I52_T0.119110.978
106_L121_F0.118520.973
86_P100_G0.118410.972
17_A24_G0.117850.967
124_R134_A0.117850.967
123_L126_I0.117480.964
85_V88_L0.117310.963
110_H121_F0.117070.961
15_L19_F0.117020.960
43_I51_I0.1170.960
17_A81_N0.116540.956
16_Q68_Y0.116430.956
115_G132_M0.115620.949
19_F41_G0.115410.947
41_G74_G0.115020.944
103_I133_I0.11480.942
85_V132_M0.112980.927
19_F23_L0.112490.923
129_L132_M0.111920.919
13_I42_F0.11180.918
34_S105_S0.111710.917
7_L64_P0.111530.915
122_S130_A0.111260.913
103_I106_L0.110960.911
24_G82_I0.110750.909
121_F126_I0.110630.908
68_Y128_G0.109970.903
31_L83_I0.109650.900
41_G93_T0.109620.900
91_A132_M0.109250.897
14_A70_G0.109190.896
117_P127_L0.108880.894
9_A13_I0.108370.889
120_P126_I0.108330.889
65_W68_Y0.108260.889
102_L111_F0.107780.885
3_I21_G0.107650.884
89_G98_V0.107380.881
37_S112_G0.107190.880
35_F102_L0.106980.878
4_L40_V0.106390.873
73_L132_M0.10610.871
6_A80_S0.105520.866
46_L103_I0.105470.866
16_Q20_N0.105280.864
127_L133_I0.104310.856
4_L45_L0.104280.856
17_A77_F0.10420.855
64_P68_Y0.103580.850
27_L36_I0.103570.850
39_G47_I0.103440.849
75_V82_I0.103250.847
26_A34_S0.102550.842
28_G76_F0.102420.841
41_G78_V0.10240.840
18_A99_A0.102210.839
17_A84_L0.101930.837
8_L46_L0.101840.836
42_F46_L0.101770.835
22_Q26_A0.101450.833
95_I116_A0.101150.830
24_G65_W0.101120.830
9_A80_S0.100920.828
18_A66_W0.100910.828
16_Q82_I0.100610.826
110_H122_S0.100420.824
125_R129_L0.100390.824
16_Q89_G0.100150.822
115_G138_L0.100150.822
46_L51_I0.100120.822
25_K33_A0.099930.820
56_S61_S0.09970.818
9_A12_L0.099590.817
122_S126_I0.09950.817
128_G136_V0.099140.814
31_L50_L0.099010.813
36_I107_L0.098770.811
105_S116_A0.098370.807
34_S45_L0.097970.804
30_P35_F0.09780.803
24_G49_L0.097470.800
96_L136_V0.097320.799
27_L32_V0.097210.798
117_P120_P0.097090.797
103_I123_L0.096490.792
95_I108_I0.096410.791
21_G88_L0.096340.791
25_K59_S0.09590.787
27_L80_S0.095760.786
48_I65_W0.095630.785
28_G127_L0.095610.785
14_A90_A0.095570.784
37_S71_G0.095280.782
27_L33_A0.094980.780
126_I133_I0.094940.779
81_N84_L0.094740.778
91_A109_D0.094620.777
133_I137_I0.09460.776
40_V44_L0.094480.775
56_S130_A0.094370.775
22_Q31_L0.094360.774
61_S127_L0.09430.774
46_L61_S0.094270.774
49_L138_L0.094240.773
10_G20_N0.094160.773
103_I134_A0.094110.772
51_I61_S0.094040.772
23_L27_L0.093970.771
78_V97_I0.093590.768
51_I130_A0.093340.766
8_L122_S0.093210.765
42_F45_L0.093020.763
103_I118_K0.092940.763
121_F129_L0.092890.762
13_I17_A0.092840.762
13_I128_G0.092760.761
20_N70_G0.092690.761
27_L41_G0.092680.761
85_V93_T0.092340.758
56_S127_L0.092310.758
33_A40_V0.092160.756
74_G90_A0.092090.756
79_L102_L0.09190.754
49_L105_S0.091830.754
35_F130_A0.091770.753
47_I56_S0.091510.751
90_A136_V0.09150.751
125_R136_V0.09150.751
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
2i68A0.717493.50.854
3b5dA0.717486.50.875
1u7gA0.833314.50.926
2xutA0.60145.30.939
2b2hA0.95654.60.94
2cfqA0.53623.70.943
3tijA0.36231.80.951
4gc0A0.68121.70.952
1pw4A0.88411.70.952
4fc4A0.42751.60.952
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