GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YcxB - YcxB-like protein
Pfam: PF14317 (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: 62
Sequences: 455
Seq/Len: 7.34
HH_delta: 0.736 (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
27_E46_K0.472483.372
5_G19_W0.458153.270
49_F57_F0.422973.019
35_Y41_A0.282272.015
32_F58_R0.254631.817
22_I34_L0.251531.795
7_I16_R0.214491.531
19_W45_P0.202111.442
41_A45_P0.20021.429
27_E58_R0.198211.415
9_E14_S0.184271.315
28_T35_Y0.182651.304
6_I50_S0.181211.293
2_D19_W0.17861.275
24_K52_E0.17851.274
48_A57_F0.178081.271
46_K54_K0.17641.259
31_Y44_I0.171341.223
23_K42_F0.167851.198
6_I57_F0.164381.173
5_G16_R0.15841.130
2_D5_G0.157631.125
7_I14_S0.15761.125
8_I33_Y0.150631.075
22_I26_V0.143961.027
45_P48_A0.141261.008
41_A44_I0.137280.980
53_E56_E0.136230.972
36_L40_Q0.134730.962
17_I43_I0.133960.956
33_Y41_A0.128930.920
3_E51_E0.126560.903
42_F53_E0.126350.902
36_L42_F0.12520.894
9_E50_S0.124930.892
43_I47_R0.124610.889
3_E30_D0.124250.887
33_Y55_E0.123340.880
52_E55_E0.122950.877
23_K36_L0.120450.860
6_I42_F0.120270.858
54_K58_R0.119840.855
21_D50_S0.11870.847
8_I38_K0.116240.830
28_T46_K0.115750.826
22_I36_L0.114830.820
35_Y46_K0.112710.804
41_A53_E0.11270.804
25_V34_L0.111990.799
25_V53_E0.11060.789
25_V58_R0.110310.787
51_E54_K0.108240.773
28_T31_Y0.107940.770
15_S52_E0.107370.766
17_I22_I0.106810.762
12_N55_E0.105520.753
24_K35_Y0.104870.748
23_K30_D0.104270.744
32_F46_K0.103020.735
16_R20_S0.10240.731
20_S30_D0.102360.731
9_E38_K0.101170.722
19_W58_R0.097250.694
9_E39_N0.096460.688
8_I15_S0.096280.687
41_A56_E0.095720.683
30_D55_E0.095610.682
4_D14_S0.095350.681
21_D48_A0.095340.680
50_S53_E0.094880.677
3_E42_F0.09480.677
3_E9_E0.094790.677
15_S31_Y0.094560.675
5_G14_S0.094420.674
24_K59_E0.094170.672
13_G16_R0.094130.672
24_K27_E0.09390.670
10_S26_V0.093780.669
11_G37_G0.093710.669
4_D24_K0.093050.664
32_F54_K0.09270.662
6_I40_Q0.092630.661
7_I38_K0.092470.660
30_D37_G0.092320.659
10_S21_D0.091740.655
11_G15_S0.091680.654
8_I42_F0.090850.648
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
2i1jA0.951669.80.736
1h4rA0.951669.20.737
1ef1A0.951665.30.743
1mixA0.951657.40.756
3qijA146.40.77
4f7gA0.951646.40.77
3au4A0.903242.80.775
3ivfA0.951642.40.775
2cs7A0.806542.20.776
4khbD138.10.781
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