GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TSCPD - TSCPD domain
Pfam: PF12637 (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: 95
Sequences: 529
Seq/Len: 5.57
HH_delta: 0.885 (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
65_R92_E0.716814.207
68_R71_P0.383112.249
42_A84_P0.366842.153
3_T6_G0.349892.054
37_S41_E0.333821.959
7_C83_C0.323731.900
12_V32_K0.321071.884
68_R73_G0.31691.860
7_C36_C0.30841.810
11_Y27_F0.293111.720
40_L43_I0.280441.646
36_C83_C0.27771.630
7_C69_C0.249251.463
36_C69_C0.240781.413
13_T31_G0.239671.407
32_K87_I0.23871.401
41_E68_R0.231561.359
61_I91_L0.229141.345
47_I60_I0.229081.344
43_I46_L0.222251.304
69_C83_C0.221131.298
7_C35_G0.213831.255
19_D56_P0.211821.243
45_R67_I0.211631.242
66_G85_D0.210751.237
2_K10_L0.208141.222
46_L60_I0.202731.190
35_G83_C0.199781.173
14_V53_S0.19821.163
55_V63_Q0.196351.152
26_V56_P0.195971.150
35_G69_C0.187871.103
70_G73_G0.182561.071
39_N83_C0.175611.031
2_K11_Y0.173361.017
17_D28_I0.172661.013
45_R63_Q0.17221.011
56_P59_E0.171931.009
42_A67_I0.167990.986
3_T10_L0.159640.937
57_P73_G0.159360.935
13_T33_A0.159110.934
15_N27_F0.152680.896
10_L34_G0.152460.895
29_N60_I0.151280.888
60_I64_L0.149280.876
45_R65_R0.147210.864
53_S58_E0.145360.853
30_V44_A0.143740.844
36_C74_T0.141640.831
46_L64_L0.141260.829
18_E62_D0.140770.826
13_T37_S0.140650.825
41_E67_I0.140330.824
61_I84_P0.139180.817
9_K42_A0.138690.814
3_T12_V0.138170.811
27_F87_I0.137240.805
38_G85_D0.134940.792
82_S85_D0.134750.791
40_L84_P0.134710.791
11_Y14_V0.133760.785
4_K9_K0.132030.775
13_T27_F0.131210.770
17_D26_V0.130950.769
33_A37_S0.130420.765
56_P89_K0.129760.762
74_T84_P0.12960.761
43_I47_I0.129320.759
6_G57_P0.129210.758
29_N56_P0.125180.735
2_K33_A0.124870.733
53_S86_A0.123080.722
71_P93_E0.122210.717
31_G88_A0.12160.714
31_G62_D0.11990.704
55_V73_G0.119660.702
58_E61_I0.119210.700
9_K12_V0.118790.697
11_Y89_K0.117720.691
88_A92_E0.117440.689
29_N41_E0.116850.686
3_T87_I0.116580.684
31_G34_G0.116390.683
33_A67_I0.116360.683
2_K13_T0.115830.680
29_N92_E0.115350.677
71_P89_K0.114590.673
9_K72_S0.114280.671
34_G85_D0.113630.667
38_G86_A0.113430.666
6_G10_L0.113050.664
11_Y26_V0.112850.662
62_D93_E0.112550.661
59_E62_D0.111740.656
11_Y33_A0.11160.655
74_T90_A0.111010.652
33_A41_E0.110660.649
59_E90_A0.110560.649
34_G66_G0.110130.646
64_L92_E0.110020.646
45_R68_R0.109790.644
30_V34_G0.108280.636
2_K56_P0.106910.627
15_N26_V0.106840.627
12_V28_I0.106370.624
53_S56_P0.10580.621
39_N46_L0.105310.618
30_V74_T0.105210.617
11_Y19_D0.105160.617
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
1zkrA0.668.40.885
1utgA0.589554.20.895
3r07C0.842153.80.895
1ccdA0.610549.90.897
3fmuA0.842144.90.9
2z7eA0.894744.40.9
3q3uA0.842136.10.905
2ccaA0.863235.50.905
3iz5V0.831634.10.906
3j3bP0.821132.80.907
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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