GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RecO_N_2 - RecO N terminal
Pfam: PF13114 (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: CL0021
Length: 71
Sequences: 1320
Seq/Len: 18.59
HH_delta: 0.148 (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
3_G48_F0.689292.552
20_I30_Y0.666742.469
2_Q23_P0.621022.299
3_G20_I0.609932.258
20_I48_F0.570392.112
33_Y59_K0.537741.991
6_L42_L0.471491.746
3_G22_T0.46841.734
17_I57_L0.463391.716
22_T26_L0.427651.583
39_I63_V0.414731.536
19_T27_K0.408021.511
30_Y60_L0.399021.477
11_V31_R0.391721.450
31_R57_L0.389121.441
7_K19_T0.378831.403
10_K36_R0.371341.375
12_R15_D0.370361.371
49_E62_K0.370071.370
8_I16_L0.359771.332
29_L57_L0.355931.318
51_E61_R0.355241.315
12_R31_R0.350481.298
30_Y50_L0.343191.271
16_L35_A0.336261.245
10_K16_L0.323091.196
11_V17_I0.320561.187
9_Q17_I0.317331.175
2_Q45_K0.295061.092
11_V57_L0.292871.084
17_I29_L0.291851.081
2_Q47_D0.291131.078
14_E36_R0.286471.061
8_I18_V0.275711.021
32_F60_L0.274981.018
9_Q19_T0.263450.975
4_F45_K0.258330.956
26_L43_G0.257780.954
25_S50_L0.256440.949
6_L27_K0.254440.942
21_L26_L0.251880.933
25_S52_Q0.24320.900
19_T29_L0.242970.900
45_K67_G0.240390.890
18_V42_L0.239130.885
51_E59_K0.238550.883
40_I46_I0.23510.870
41_Q44_Y0.234820.869
20_I46_I0.229990.852
39_I42_L0.224740.832
15_D34_G0.223480.827
34_G37_H0.219930.814
6_L21_L0.217190.804
5_I41_Q0.213520.791
2_Q66_L0.211740.784
44_Y65_H0.202270.749
10_K17_I0.202060.748
6_L45_K0.201580.746
17_I31_R0.199260.738
9_Q29_L0.198490.735
22_T25_S0.196150.726
8_I42_L0.195910.725
39_I47_D0.195320.723
2_Q67_G0.192790.714
16_L41_Q0.191670.710
39_I46_I0.185360.686
46_I63_V0.184960.685
2_Q24_N0.183810.681
52_Q58_P0.182750.677
28_T32_F0.18220.675
39_I65_H0.182180.675
14_E34_G0.181510.672
40_I51_E0.178830.662
35_A38_S0.178780.662
40_I48_F0.178550.661
44_Y67_G0.178390.660
40_I44_Y0.173540.643
8_I12_R0.173080.641
11_V29_L0.172090.637
32_F63_V0.171880.636
18_V30_Y0.171390.635
27_K52_Q0.170410.631
25_S58_P0.170360.631
4_F65_H0.169870.629
25_S28_T0.168870.625
55_K58_P0.166970.618
47_D64_E0.166490.616
49_E61_R0.165470.613
64_E67_G0.164930.611
48_F67_G0.163770.606
14_E37_H0.163690.606
36_R47_D0.161780.599
28_T52_Q0.161310.597
23_P52_Q0.159370.590
30_Y52_Q0.158740.588
15_D37_H0.158560.587
18_V40_I0.158510.587
23_P26_L0.158420.587
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
3q8dA0.985999.50.148
1u5kA0.971899.50.177
4gs4A0.971820.20.86
4b5oA0.971890.88
2e5pA0.53525.20.891
3r8nR0.54935.10.891
2kbnA150.892
3bboQ0.436650.892
2k75A0.957740.896
4ag3A0.915540.896

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