GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-LITAF-like - LITAF-like zinc ribbon domain
Pfam: PF10601 (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: 73
Sequences: 535
Seq/Len: 7.33
HH_delta: 0.847 (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
17_V62_P0.595033.368
21_V57_V0.554353.137
30_Y49_F0.527622.986
26_G56_D0.514262.911
33_A49_F0.415582.352
5_P18_Q0.398262.254
20_R60_Y0.364592.063
19_T59_H0.362492.052
24_K58_Y0.361812.048
40_G43_P0.306211.733
8_I68_L0.290481.644
43_P46_C0.262011.483
30_Y33_A0.25631.451
23_Y57_V0.253481.435
9_Y16_Q0.250391.417
36_L48_P0.249931.415
12_Y66_A0.245821.391
58_Y70_T0.218091.234
20_R65_G0.213151.206
36_L54_C0.211271.196
36_L41_C0.208991.183
61_C64_C0.204641.158
26_G55_K0.204441.157
10_C13_C0.199321.128
34_A37_C0.198251.122
58_Y67_F0.19681.114
15_Q63_N0.189531.073
8_I17_V0.184051.042
29_T54_C0.17991.018
29_T48_P0.173920.984
29_T33_A0.168370.953
17_V65_G0.167890.950
27_T31_I0.166330.941
55_K58_Y0.166150.940
7_R16_Q0.163120.923
25_S29_T0.16120.912
56_D70_T0.160090.906
25_S55_K0.160030.906
48_P54_C0.159340.902
29_T49_F0.158930.899
17_V68_L0.157870.893
67_F71_Y0.157090.889
8_I12_Y0.15160.858
4_E66_A0.150750.853
33_A45_C0.150420.851
15_Q23_Y0.149360.845
15_Q62_P0.148810.842
41_C44_C0.147420.834
22_E35_L0.147070.832
22_E60_Y0.145980.826
17_V57_V0.144420.817
56_D72_K0.143610.813
27_T38_L0.140480.795
3_P54_C0.140470.795
15_Q27_T0.136370.772
32_C41_C0.134780.763
57_V71_Y0.133550.756
33_A37_C0.132710.751
4_E22_E0.132440.750
31_I67_F0.131580.745
28_M32_C0.131470.744
18_Q25_S0.130060.736
12_Y67_F0.128860.729
47_I51_C0.128820.729
11_P68_L0.128270.726
29_T55_K0.127570.722
23_Y52_D0.126980.719
24_K51_C0.126480.716
60_Y67_F0.124280.703
44_C72_K0.123930.701
56_D59_H0.122160.691
67_F70_T0.122140.691
24_K39_F0.121930.690
28_M54_C0.121730.689
43_P51_C0.12140.687
27_T56_D0.119390.676
11_P65_G0.118780.672
14_Q21_V0.118540.671
29_T36_L0.118480.671
25_S31_I0.118210.669
6_V17_V0.117820.667
53_S71_Y0.117330.664
8_I19_T0.116070.657
38_L41_C0.115520.654
27_T34_A0.11530.653
44_C47_I0.1150.651
40_G51_C0.113940.645
37_C41_C0.113560.643
34_A67_F0.113270.641
45_C48_P0.112220.635
3_P35_L0.11160.632
32_C35_L0.11080.627
6_V40_G0.110490.625
34_A42_W0.109240.618
17_V39_F0.109130.618
14_Q20_R0.108940.617
38_L45_C0.108890.616
23_Y54_C0.108860.616
30_Y44_C0.10860.615
6_V69_G0.108070.612
52_D55_K0.107110.606
22_E27_T0.106660.604
16_Q21_V0.105390.596
40_G45_C0.105050.595
26_G47_I0.104920.594
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
2jrpA0.876748.40.847
1k3xA0.452140.90.853
2xzfA0.465837.40.856
2fiyA0.808237.10.857
1twfL0.534233.20.86
1k82A0.452132.80.861
1h7bA0.547932.10.861
3u6pA0.452128.90.864
1weoA0.876727.90.865
3o9xA0.684924.70.868
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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