GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SIR2_2 - SIR2-like domain
Pfam: PF13289 (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: CL0085
Length: 143
Sequences: 1101
Seq/Len: 7.7
HH_delta: 0.807 (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
47_K51_S0.399493.485
8_Y61_L0.359773.139
13_E47_K0.332382.900
4_I83_L0.287322.507
10_D14_K0.245812.145
61_L65_D0.214091.868
78_N81_R0.191191.668
4_I48_L0.186971.631
14_K17_E0.185881.622
49_H66_Y0.185361.617
7_N49_H0.18071.576
2_T44_P0.176991.544
6_T98_D0.174471.522
49_H101_I0.161781.411
49_H98_D0.160441.400
66_Y91_F0.160321.399
8_Y66_Y0.151451.321
91_F119_H0.151181.319
6_T94_Y0.150881.316
28_S31_D0.146411.277
119_H123_I0.146271.276
62_T65_D0.146031.274
96_F121_I0.145521.270
96_F102_R0.145441.269
94_Y97_N0.14341.251
49_H100_D0.141131.231
16_L45_I0.140891.229
68_E106_R0.139421.216
60_V66_Y0.139061.213
16_L23_F0.138611.209
49_H95_S0.137931.203
5_T48_L0.135511.182
64_D68_E0.134151.170
88_T118_R0.132981.160
2_T83_L0.132121.153
8_Y65_D0.131171.144
5_T47_K0.130091.135
47_K76_F0.129781.132
69_Y99_P0.128031.117
4_I46_Y0.127881.116
91_F121_I0.126751.106
81_R85_R0.12661.104
94_Y102_R0.126391.103
102_R105_L0.124621.087
10_D54_W0.12361.078
12_L45_I0.121941.064
8_Y100_D0.120851.054
48_L69_Y0.118931.038
94_Y98_D0.118871.037
8_Y51_S0.118761.036
43_P48_L0.11851.034
4_I76_F0.118111.030
51_S61_L0.117941.029
98_D101_I0.117471.025
89_L94_Y0.116771.019
85_R111_N0.116241.014
11_L49_H0.116191.014
73_N77_P0.115171.005
2_T46_Y0.114751.001
52_L58_S0.113960.994
29_D74_P0.113830.993
63_E67_E0.112270.979
87_K114_K0.112060.978
48_L106_R0.111820.976
94_Y100_D0.111430.972
6_T47_K0.111050.969
113_G125_D0.10950.955
15_A82_S0.109390.954
12_L16_L0.109340.954
3_I38_S0.109270.953
66_Y92_I0.108720.949
5_T13_E0.108660.948
101_I105_L0.10780.940
90_L119_H0.106930.933
3_I16_L0.106850.932
45_I51_S0.106160.926
20_G23_F0.105840.923
51_S54_W0.105670.922
45_I73_N0.105360.919
47_K61_L0.104820.914
66_Y96_F0.104590.912
69_Y100_D0.104580.912
47_K101_I0.10340.902
95_S98_D0.103350.902
91_F120_Y0.103180.900
60_V68_E0.102540.895
120_Y126_P0.102540.895
87_K92_I0.101950.889
14_K79_F0.101890.889
55_D120_Y0.100530.877
44_P79_F0.100510.877
13_E100_D0.100150.874
70_Y103_Q0.10010.873
17_E20_G0.099490.868
10_D52_L0.099440.868
118_R124_P0.099430.867
123_I126_P0.099180.865
12_L69_Y0.099140.865
8_Y49_H0.098810.862
20_G37_R0.098770.862
119_H124_P0.098640.861
62_T73_N0.098240.857
18_E39_S0.098220.857
71_S74_P0.097890.854
89_L119_H0.097490.851
24_I28_S0.09680.845
24_I44_P0.095860.836
77_P106_R0.095720.835
61_L69_Y0.095240.831
96_F100_D0.0950.829
18_E37_R0.094660.826
65_D98_D0.093750.818
46_Y65_D0.093660.817
3_I13_E0.09330.814
13_E123_I0.09320.813
3_I45_I0.092920.811
2_T37_R0.092780.809
17_E23_F0.092670.808
97_N102_R0.092520.807
62_T67_E0.092370.806
69_Y75_W0.091940.802
13_E98_D0.091610.799
80_L104_L0.091250.796
68_E71_S0.091120.795
58_S73_N0.091010.794
15_A31_D0.09070.791
3_I12_L0.090270.788
99_P103_Q0.089620.782
67_E107_S0.089540.781
114_K126_P0.089060.777
4_I84_L0.088880.775
43_P83_L0.088850.775
65_D108_A0.087940.767
13_E51_S0.08790.767
2_T87_K0.087810.766
113_G118_R0.087670.765
94_Y121_I0.08740.763
65_D100_D0.087350.762
38_S81_R0.087290.762
64_D99_P0.087290.762
8_Y94_Y0.087170.760
51_S101_I0.087130.760
5_T98_D0.087020.759
44_P101_I0.0870.759
27_I31_D0.086850.758
59_I96_F0.086810.757
20_G28_S0.086610.756
113_G120_Y0.086410.754
52_L63_E0.086360.753
7_N13_E0.086010.750
77_P81_R0.085990.750
72_S106_R0.085940.750
6_T70_Y0.085930.750
61_L67_E0.085280.744
80_L103_Q0.08520.743
29_D32_F0.08510.742
119_H125_D0.084950.741
106_R110_E0.084690.739
75_W108_A0.084350.736
56_P85_R0.084240.735
7_N95_S0.083940.732
33_S126_P0.083470.728
13_E17_E0.083420.728
37_R92_I0.083380.727
58_S124_P0.083380.727
16_L127_D0.08330.727
75_W78_N0.083230.726
19_A43_P0.0830.724
30_E81_R0.082970.724
105_L109_L0.08290.723
46_Y83_L0.082770.722
27_I32_F0.082530.720
54_W120_Y0.082490.720
13_E97_N0.082190.717
48_L126_P0.082160.717
42_R95_S0.082060.716
9_D49_H0.081850.714
62_T74_P0.081430.710
6_T92_I0.081380.710
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
1yc5A0.909196.10.807
1m2kA0.9231960.809
1s5pA0.902195.40.818
1ma3A0.923195.30.82
4i5iA0.748393.50.835
3riyA0.923192.10.842
3pkiA0.923191.70.845
2hjhA0.916191.20.846
3k35A0.923191.10.847
3zgoA0.909187.90.856
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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