GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-HC5HC2H_2 - PHD-zinc-finger like domain
Pfam: PF13832 (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: CL0390
Length: 110
Sequences: 1027
Seq/Len: 9.34
HH_delta: 0.508 (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
107_C110_H0.345082.483
80_F105_A0.343862.474
56_L70_K0.333012.396
53_R68_C0.310672.236
56_L79_A0.302742.178
5_L22_V0.289922.086
23_H26_C0.280812.021
32_E53_R0.280532.019
3_C6_C0.264621.904
58_C61_C0.251521.810
30_I53_R0.23711.706
70_K79_A0.232841.676
60_I90_L0.208351.499
58_C71_C0.206871.489
25_L82_P0.204321.470
27_A35_F0.192431.385
85_A92_F0.186541.342
70_K77_S0.185021.331
24_V35_F0.184761.330
85_A89_G0.178911.287
12_A16_T0.175711.264
61_C71_C0.175641.264
27_A33_V0.175581.263
36_N45_D0.174941.259
37_N41_M0.173031.245
83_T86_R0.17241.241
31_P70_K0.171861.237
66_G71_C0.171061.231
71_C76_C0.16761.206
36_N43_P0.167561.206
14_K24_V0.165281.189
2_S9_R0.162461.169
49_I72_S0.161881.165
25_L83_T0.161581.163
37_N42_E0.159691.149
21_W24_V0.155971.122
30_I68_C0.155561.119
37_N40_S0.153331.103
57_K64_S0.150161.081
29_W92_F0.149031.072
53_R56_L0.143441.032
66_G76_C0.142491.025
29_W86_R0.142071.022
64_S74_P0.141891.021
60_I77_S0.141491.018
9_R12_A0.141361.017
30_I82_P0.141181.016
59_S78_T0.14021.009
94_I105_A0.139971.007
12_A21_W0.139051.001
57_K75_G0.136390.981
24_V27_A0.1360.979
80_F92_F0.13590.978
29_W85_A0.134420.967
12_A15_R0.134250.966
30_I67_A0.134030.964
11_G18_D0.133630.962
22_V27_A0.133150.958
86_R91_Y0.132870.956
22_V82_P0.13260.954
22_V44_V0.131260.945
68_C82_P0.131260.945
58_C66_G0.126960.914
70_K82_P0.125530.903
67_A104_I0.124010.892
37_N43_P0.123980.892
103_F109_K0.123680.890
63_K108_P0.123010.885
43_P85_A0.122930.885
32_E51_P0.12290.884
8_K83_T0.122050.878
11_G94_I0.119560.860
47_S51_P0.119450.860
69_I72_S0.119280.858
55_K62_G0.118930.856
94_I103_F0.118440.852
30_I80_F0.117830.848
58_C81_H0.117650.847
61_C81_H0.117530.846
33_V77_S0.117450.845
16_T21_W0.116380.837
10_G13_L0.116310.837
103_F106_Y0.11630.837
10_G15_R0.11590.834
34_I47_S0.11570.833
66_G84_C0.115650.832
49_I53_R0.115450.831
74_P109_K0.115240.829
16_T19_G0.114530.824
50_P54_F0.114060.821
29_W69_I0.113940.820
49_I52_S0.113880.819
25_L28_L0.113780.819
50_P53_R0.113650.818
9_R13_L0.113560.817
91_Y94_I0.113440.816
59_S79_A0.111810.805
48_N55_K0.111670.804
4_V8_K0.111010.799
2_S62_G0.110910.798
57_K70_K0.110140.793
93_E104_I0.110060.792
2_S39_E0.109860.791
56_L75_G0.109340.787
71_C81_H0.108920.784
13_L40_S0.108390.780
61_C76_C0.108240.779
76_C84_C0.107610.774
44_V54_F0.107170.771
9_R29_W0.107010.770
106_Y110_H0.106990.770
4_V10_G0.10690.769
4_V21_W0.106380.766
29_W60_I0.105890.762
80_F85_A0.105840.762
75_G109_K0.105830.762
47_S63_K0.10520.757
85_A90_L0.105030.756
76_C81_H0.104880.755
35_F96_N0.104630.753
58_C76_C0.10440.751
18_D93_E0.103950.748
33_V52_S0.1030.741
86_R89_G0.102870.740
103_F108_P0.102870.740
36_N39_E0.102730.739
3_C26_C0.101970.734
13_L108_P0.101650.731
57_K77_S0.101560.731
40_S45_D0.101430.730
28_L39_E0.101320.729
4_V46_I0.101270.729
17_S48_N0.101020.727
61_C66_G0.100860.726
70_K74_P0.100730.725
40_S52_S0.100720.725
59_S64_S0.100340.722
11_G21_W0.100030.720
18_D39_E0.099780.718
20_Q56_L0.099780.718
21_W50_P0.099680.717
76_C107_C0.09940.715
33_V45_D0.099260.714
80_F90_L0.099190.714
55_K59_S0.099110.713
77_S108_P0.0990.712
59_S108_P0.098560.709
32_E50_P0.098220.707
34_I48_N0.098090.706
31_P47_S0.098080.706
5_L87_K0.097880.704
4_V18_D0.097860.704
32_E49_I0.097640.703
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
2lq6A0.654599.20.508
4gneA0.5364920.828
1wewA0.609189.80.837
2ri7A0.481889.40.838
3v43A0.827386.40.845
2xb1A0.585.50.847
1we9A0.472784.60.849
2rsdA0.545583.70.851
3kv4A0.4545830.852
1wepA0.518282.10.853
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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