GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_int_SAM_4 - Phage integrase N-terminal SAM-like domain
Pfam: PF13495 (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: CL0469
Length: 85
Sequences: 15147
Seq/Len: 178.2
HH_delta: 0.001 (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
42_T45_D2.742653.143
53_L67_Y2.074862.377
25_H70_A1.799692.062
32_F52_Y1.79862.061
36_K45_D1.769192.027
25_H66_Q1.697641.945
77_W81_R1.666941.910
50_L68_L1.632861.871
28_R67_Y1.604081.838
74_F78_L1.595051.828
18_T22_Y1.467941.682
62_S66_Q1.460521.674
41_I75_F1.389481.592
23_R27_K1.316451.508
68_L72_R1.232781.413
32_F49_Y1.123541.287
25_H67_Y1.121341.285
17_K20_K1.116931.280
47_E51_N1.10961.271
22_Y70_A1.106891.268
43_P47_E1.096561.256
54_Q64_I1.06041.215
49_Y67_Y1.033411.184
78_L83_Y1.027991.178
46_I71_L1.017661.166
37_P40_E1.013331.161
15_S18_T1.012791.160
21_N66_Q0.973251.115
16_E19_I0.971831.114
17_K21_N0.966311.107
74_F77_W0.957961.098
63_T67_Y0.955421.095
50_L54_Q0.951171.090
14_L19_I0.942511.080
59_L67_Y0.936961.074
16_E20_K0.934961.071
65_N69_S0.919251.053
53_L64_I0.909911.043
29_F75_F0.89311.023
19_I23_R0.870710.998
29_F49_Y0.855040.980
20_K24_Y0.852510.977
49_Y53_L0.843470.966
46_I68_L0.828650.949
66_Q69_S0.818220.938
61_P65_N0.817050.936
21_N25_H0.811520.930
75_F79_L0.788450.903
73_S77_W0.785070.900
72_R76_R0.765360.877
29_F71_L0.758980.870
59_L64_I0.755010.865
21_N24_Y0.743480.852
51_N54_Q0.720430.825
59_L63_T0.719490.824
54_Q61_P0.714980.819
60_S63_T0.713530.818
33_L49_Y0.712280.816
27_K31_R0.704670.807
52_Y57_R0.699840.802
33_L45_D0.699270.801
26_L74_F0.68890.789
14_L22_Y0.682190.782
32_F48_Q0.681590.781
49_Y52_Y0.681230.781
76_R79_L0.679830.779
45_D48_Q0.676250.775
48_Q52_Y0.644810.739
49_Y71_L0.63990.733
46_I75_F0.628440.720
77_W83_Y0.628030.720
41_I46_I0.626750.718
62_S65_N0.62550.717
64_I68_L0.624020.715
36_K40_E0.623420.714
43_P80_E0.621590.712
44_E48_Q0.620110.711
24_Y28_R0.614320.704
38_P75_F0.605710.694
53_L59_L0.598530.686
33_L41_I0.594730.681
28_R31_R0.592160.679
38_P78_L0.587110.673
69_S73_S0.58570.671
26_L30_L0.580660.665
47_E50_L0.577620.662
27_K30_L0.572860.656
28_R59_L0.571170.654
28_R57_R0.565440.648
14_L18_T0.562070.644
66_Q70_A0.556690.638
13_G19_I0.551980.632
26_L70_A0.551680.632
79_L82_G0.547950.628
30_L34_G0.543730.623
22_Y66_Q0.538340.617
20_K23_R0.535210.613
76_R80_E0.529690.607
22_Y25_H0.528470.606
18_T21_N0.525050.602
73_S76_R0.525040.602
29_F33_L0.522230.598
52_Y56_E0.518910.595
33_L36_K0.516550.592
70_A73_S0.512020.587
25_H28_R0.509470.584
47_E81_R0.508660.583
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
3nrwA0.976598.90.001
3lysA0.976598.80.045
2keyA0.988298.80.051
2khqA0.976598.70.06
2kkpA0.988298.70.063
1z19A0.976598.70.064
1z1bA0.976598.70.065
1a0pA0.988298.70.073
2kd1A0.976598.70.085
2oxoA0.976598.70.087

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