GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-C5HC2 - C5HC2 zinc finger
Pfam: PF02928 (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: 54
Sequences: 269
Seq/Len: 4.98
HH_delta: 0.522 (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_C34_C0.26232.119
1_C4_C0.222561.798
12_A42_R0.187361.514
29_K33_S0.178211.440
20_D33_S0.176471.426
14_T40_T0.17581.420
15_C32_C0.175341.416
46_D49_E0.154291.246
13_V28_A0.144921.171
51_E54_V0.144191.165
46_D50_L0.143831.162
25_L43_Y0.143361.158
23_V31_L0.14271.153
1_C9_Y0.14091.138
33_S39_H0.137571.111
39_H43_Y0.137271.109
10_L44_R0.134161.084
4_C24_C0.132531.071
1_C15_C0.13091.057
48_E52_S0.129921.050
8_C22_V0.129361.045
12_A19_P0.129291.044
32_C50_L0.127951.034
1_C24_C0.126691.023
47_D51_E0.126171.019
5_K8_C0.125051.010
6_A9_Y0.124851.009
11_S29_K0.124631.007
14_T20_D0.124451.005
12_A45_Y0.1241.002
16_S40_T0.123931.001
28_A33_S0.123710.999
39_H48_E0.122540.990
43_Y46_D0.122250.988
26_R30_E0.121690.983
12_A22_V0.121670.983
7_Y47_D0.12160.982
2_S49_E0.119660.967
40_T43_Y0.119550.966
9_Y27_H0.119470.965
4_C15_C0.11840.956
5_K9_Y0.117450.949
3_I21_K0.114880.928
21_K48_E0.114510.925
8_C46_D0.113790.919
16_S21_K0.113790.919
31_L45_Y0.113380.916
31_L50_L0.112960.912
16_S38_N0.112640.910
10_L27_H0.110980.897
20_D29_K0.110590.893
8_C14_T0.108310.875
3_I20_D0.108270.875
8_C53_L0.10790.872
11_S45_Y0.107360.867
9_Y24_C0.107250.866
50_L54_V0.107130.865
9_Y44_R0.107040.865
3_I33_S0.105620.853
27_H31_L0.105280.850
36_C50_L0.105110.849
18_K39_H0.104660.845
26_R39_H0.104020.840
49_E54_V0.103940.840
4_C9_Y0.103760.838
41_L52_S0.103620.837
40_T51_E0.103180.833
3_I30_E0.102340.827
5_K21_K0.100340.811
2_S38_N0.099640.805
37_S53_L0.099460.803
23_V26_R0.099090.800
12_A34_C0.099080.800
20_D52_S0.09880.798
20_D30_E0.098740.798
45_Y49_E0.098380.795
22_V47_D0.098290.794
30_E33_S0.097970.791
18_K28_A0.096870.783
7_Y22_V0.095440.771
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
3avrA0.981597.80.522
4askA0.981541.40.812
1wflA0.870423.40.833
1wfhA0.8333180.841
1wffA0.944417.10.842
1wfpA0.833314.70.846
1vq0A0.907413.50.849
1vzyA0.7778130.851
1i7fA0.7778130.851
1wg2A0.833312.60.851
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