GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF523 - Protein of unknown function (DUF523)
Pfam: PF04463 (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: 143
Sequences: 850
Seq/Len: 5.94
HH_delta: 0.945 (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
123_S131_K0.359052.538
98_K140_E0.346792.451
13_R19_K0.336622.379
84_L129_L0.32572.302
11_N18_H0.319532.258
97_L127_A0.310242.193
2_L130_L0.305542.159
128_E132_E0.30482.154
8_L34_I0.299462.116
52_I72_V0.294862.084
87_L92_I0.275481.947
28_L34_I0.26731.889
107_E123_S0.263281.861
56_G61_I0.261511.848
129_L133_E0.260561.842
50_P67_P0.257171.818
97_L130_L0.255291.804
82_K85_E0.255151.803
99_S139_I0.252311.783
41_V47_V0.249671.765
112_D116_S0.249331.762
65_D70_R0.223061.576
8_L36_P0.222051.569
62_R71_D0.219181.549
106_V131_K0.216311.529
94_G138_P0.215511.523
43_A79_G0.215381.522
50_P66_T0.213511.509
78_E82_K0.212171.500
2_L95_F0.208421.473
76_L79_G0.199771.412
129_L132_E0.193281.366
100_K119_L0.190221.344
57_E61_I0.186541.318
84_L133_E0.186451.318
57_E77_L0.186131.315
21_D24_V0.181561.283
50_P65_D0.179431.268
52_I63_V0.175751.242
105_G109_T0.174221.231
74_E78_E0.171061.209
85_E133_E0.169581.199
53_R115_F0.166931.180
45_L75_E0.166481.177
88_K133_E0.164281.161
13_R18_H0.159671.128
26_E30_E0.158451.120
98_K142_E0.15761.114
95_F135_P0.156251.104
31_Y34_I0.155241.097
5_A9_G0.154771.094
83_Q130_L0.154231.090
99_S106_V0.152651.079
5_A10_E0.149921.060
108_R121_K0.148031.046
13_R17_G0.147441.042
106_V139_I0.145421.028
84_L134_G0.14491.024
53_R113_G0.144591.022
112_D117_G0.143831.017
37_V42_L0.143381.013
3_V24_V0.142721.009
57_E128_E0.142651.008
8_L28_L0.142451.007
63_V66_T0.142091.004
55_V64_I0.142031.004
91_G107_E0.139780.988
45_L72_V0.139190.984
2_L92_I0.139130.983
23_F32_V0.138040.976
97_L104_C0.134460.950
106_V123_S0.133610.944
76_L103_S0.133340.942
61_I128_E0.131470.929
10_E41_V0.131340.928
27_L30_E0.130450.922
81_E85_E0.129460.915
138_P142_E0.128770.910
7_L45_L0.128290.907
134_G137_L0.128030.905
1_I34_I0.127210.899
35_I56_G0.126690.895
82_K86_E0.12550.887
32_V46_G0.12540.886
70_R75_E0.124670.881
63_V86_E0.12440.879
7_L103_S0.123960.876
63_V69_G0.123620.874
54_L125_I0.123480.873
95_F126_F0.123320.872
94_G136_K0.123050.870
11_N20_R0.120190.849
121_K132_E0.120020.848
85_E88_K0.119760.846
22_E26_E0.119170.842
87_L95_F0.118960.841
107_E141_E0.118270.836
62_R74_E0.117890.833
17_G100_K0.117830.833
7_L16_G0.117230.829
54_L128_E0.117040.827
83_Q126_F0.116910.826
22_E25_K0.116590.824
14_Y48_P0.116020.820
75_E100_K0.11580.818
54_L61_I0.115730.818
53_R63_V0.115590.817
81_E129_L0.114750.811
28_L31_Y0.113880.805
106_V137_L0.113650.803
27_L34_I0.113650.803
77_L81_E0.113520.802
22_E121_K0.11240.794
63_V115_F0.112170.793
34_I92_I0.11180.790
53_R112_D0.111740.790
74_E121_K0.111380.787
95_F130_L0.110560.781
79_G103_S0.110360.780
109_T120_G0.109940.777
109_T123_S0.109840.776
134_G142_E0.10960.775
85_E118_E0.109480.774
9_G115_F0.109460.774
51_P66_T0.109050.771
35_I116_S0.108460.767
80_A83_Q0.108130.764
136_K142_E0.108120.764
99_S141_E0.107730.761
123_S139_I0.107370.759
12_C100_K0.107130.757
103_S126_F0.107120.757
25_K29_K0.106980.756
61_I77_L0.106810.755
18_H138_P0.106520.753
50_P74_E0.106350.752
42_L96_I0.105870.748
24_V84_L0.105650.747
22_E132_E0.105480.745
114_N118_E0.105420.745
2_L87_L0.103280.730
117_G122_G0.10310.729
80_A87_L0.102840.727
100_K108_R0.102540.725
5_A142_E0.102480.724
20_R25_K0.102090.722
131_K139_I0.102080.721
14_Y127_A0.101480.717
46_G50_P0.10120.715
37_V79_G0.101090.714
74_E81_E0.100930.713
1_I131_K0.100630.711
80_A134_G0.100330.709
87_L126_F0.099840.706
28_L32_V0.099820.705
99_S142_E0.099470.703
28_L138_P0.099440.703
52_I65_D0.099410.703
10_E70_R0.099240.701
23_F94_G0.099240.701
79_G129_L0.098990.700
92_I95_F0.098610.697
125_I129_L0.098040.693
1_I96_I0.097570.690
24_V28_L0.097310.688
80_A103_S0.09730.688
47_V71_D0.097210.687
9_G48_P0.097110.686
95_F125_I0.097050.686
67_P70_R0.096920.685
67_P74_E0.096670.683
119_L132_E0.095960.678
126_F138_P0.095950.678
62_R76_L0.095830.677
46_G64_I0.095750.677
2_L126_F0.09570.676
99_S140_E0.095460.675
64_I72_V0.095170.673
54_L109_T0.095160.673
104_C130_L0.09460.669
43_A72_V0.094120.665
25_K28_L0.093950.664
12_C41_V0.09370.662
41_V44_G0.093660.662
3_V71_D0.093560.661
56_G128_E0.093440.660
56_G78_E0.093250.659
52_I111_Y0.093190.659
31_Y93_D0.093120.658
15_D18_H0.093050.658
15_D19_K0.092840.656
36_P82_K0.092740.655
8_L12_C0.092550.654
80_A129_L0.092160.651
46_G52_I0.091940.650
28_L94_G0.09180.649
19_K47_V0.090830.642
69_G125_I0.090630.641
47_V62_R0.090620.640
96_I140_E0.090540.640
27_L100_K0.089880.635
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
4f02C0.188816.10.945
3rq4A0.8182160.945
4at7A0.867115.90.945
3s8pA0.811214.60.946
3q9kA0.3566120.948
2hjjA0.23088.20.951
3tm8A0.56647.70.952
3o3mB0.75527.30.952
2qq4A0.54555.60.954
4eb5C0.46155.50.955
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