GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fcf1 - Fcf1
Pfam: PF04900 (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: CL0280
Length: 101
Sequences: 484
Seq/Len: 4.79
HH_delta: 0.599 (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
15_C56_C0.312212.653
81_R99_E0.281042.388
69_V80_L0.265612.257
57_I69_V0.259572.205
44_C56_C0.255542.171
15_C44_C0.229451.950
46_H56_C0.21361.815
54_D71_T0.200941.707
72_Q91_L0.200611.704
15_C46_H0.190821.621
71_T76_L0.190691.620
19_E76_L0.189241.608
16_V19_E0.180491.534
55_D79_R0.177741.510
13_T56_C0.166751.417
58_L79_R0.162961.385
77_R90_Y0.159441.355
19_E23_L0.15771.340
54_D76_L0.157141.335
81_R90_Y0.15681.332
19_E53_A0.156341.328
16_V53_A0.155511.321
18_E45_N0.151371.286
9_K45_N0.150681.280
57_I80_L0.148561.262
5_G33_I0.143061.216
75_E78_R0.141851.205
2_K5_G0.141611.203
69_V73_D0.138611.178
19_E54_D0.137831.171
88_V92_R0.137311.167
89_I96_L0.136051.156
52_S55_D0.133671.136
67_Y70_A0.128331.090
9_K100_P0.127771.086
61_A69_V0.127331.082
25_K28_K0.127271.081
13_T67_Y0.126731.077
62_G65_N0.120651.025
11_Y40_E0.120251.022
3_L96_L0.119631.016
11_Y34_A0.118231.005
96_L100_P0.11781.001
13_T46_H0.117180.996
18_E21_E0.117170.996
76_L79_R0.11710.995
2_K8_V0.116180.987
46_H67_Y0.115760.984
19_E73_D0.115590.982
11_Y43_K0.11540.981
31_L35_K0.114810.975
85_G99_E0.114340.971
18_E22_S0.112810.958
72_Q97_I0.11280.958
56_C67_Y0.110720.941
92_R97_I0.110470.939
21_E31_L0.108650.923
77_R93_R0.108550.922
20_L34_A0.108550.922
4_L89_I0.108180.919
59_D63_K0.108130.919
19_E52_S0.107770.916
33_I74_K0.107650.915
72_Q92_R0.106770.907
80_L94_N0.106590.906
13_T44_C0.106410.904
9_K40_E0.105330.895
11_Y91_L0.105250.894
90_Y94_N0.103980.883
54_D79_R0.10350.879
15_C67_Y0.102110.868
29_G65_N0.101660.864
42_R46_H0.101640.864
20_L69_V0.101380.861
46_H70_A0.100980.858
58_L61_A0.100790.856
18_E34_A0.100690.856
45_N93_R0.100260.852
21_E24_G0.099690.847
30_A33_I0.099570.846
14_Q43_K0.098850.840
33_I36_R0.098210.834
70_A81_R0.098090.833
3_L12_V0.097470.828
22_S75_E0.097370.827
26_K72_Q0.096910.823
20_L48_E0.09680.822
63_K94_N0.096780.822
14_Q18_E0.096580.821
54_D58_L0.096490.820
16_V73_D0.096290.818
36_R71_T0.096050.816
70_A75_E0.095220.809
2_K96_L0.095180.809
7_K89_I0.095080.808
35_K75_E0.09420.800
29_G32_R0.093720.796
83_I87_P0.092720.788
68_I89_I0.092450.786
5_G76_L0.09240.785
16_V77_R0.091860.780
63_K66_K0.091610.778
17_L65_N0.091560.778
26_K31_L0.090460.769
11_Y96_L0.090210.766
70_A87_P0.089350.759
9_K59_D0.089260.758
16_V23_L0.088650.753
42_R97_I0.088110.749
41_R69_V0.087430.743
57_I98_L0.086310.733
24_G30_A0.086090.731
68_I99_E0.085760.729
24_G27_F0.085160.724
74_K78_R0.084950.722
17_L45_N0.084680.719
43_K93_R0.084650.719
42_R60_L0.084450.718
42_R98_L0.084210.715
23_L73_D0.084110.715
59_D62_G0.083920.713
19_E22_S0.083920.713
93_R96_L0.083520.710
59_D97_I0.083410.709
54_D74_K0.083340.708
29_G74_K0.082970.705
47_K59_D0.082960.705
29_G91_L0.082440.700
91_L97_I0.082270.699
4_L76_L0.081830.695
58_L63_K0.08180.695
45_N92_R0.081410.692
56_C70_A0.081230.690
27_F31_L0.08120.690
53_A76_L0.080930.688
34_A61_A0.080830.687
9_K42_R0.080680.686
17_L33_I0.080630.685
78_R81_R0.080490.684
25_K63_K0.080270.682
42_R45_N0.080010.680
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
1o4wA0.891198.80.599
3ix7A0.960498.60.63
3i8oA0.920898.10.687
2dokA0.950597.60.729
2lcqA0.950595.10.805
2fe1A0.831747.70.884
2dk4A0.554542.40.888
2wp8J0.990134.60.893
2hwyA0.891124.40.9
2fm8C0.811920.10.904
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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