GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Tissue_fac - Tissue factor
Pfam: PF01108 (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: CL0159
Length: 107
Sequences: 5955
Seq/Len: 55.65
HH_delta: 0.227 (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
56_Q95_R1.635554.077
52_T99_E1.151522.871
54_T97_R1.026572.559
81_L94_A1.02312.551
54_T99_E1.01012.518
27_N42_D0.99142.472
99_E104_T0.963982.403
58_K93_Y0.95612.384
57_Y94_A0.922272.299
97_R104_T0.89362.228
100_V103_Q0.815962.034
54_T104_T0.776921.937
39_L94_A0.772131.925
53_Y98_A0.69941.744
65_W95_R0.678571.692
56_Q97_R0.664431.656
43_P53_Y0.654151.631
81_L84_E0.645211.608
55_V79_C0.643941.605
38_I80_D0.626241.561
31_D40_R0.567761.415
98_A105_S0.56771.415
57_Y81_L0.55851.392
37_H94_A0.55541.385
56_Q67_D0.554611.383
58_K65_W0.55181.376
28_V39_L0.541831.351
55_V96_V0.503421.255
59_K90_E0.499671.246
29_T40_R0.487321.215
39_L55_V0.459661.146
28_V96_V0.430131.072
23_P105_S0.42771.066
38_I78_S0.422511.053
41_W53_Y0.406141.012
79_C83_D0.4021.002
26_Q42_D0.401361.001
58_K95_R0.398360.993
30_V33_V0.382770.954
29_T42_D0.369850.922
44_G47_S0.368360.918
51_V101_G0.366680.914
60_Y91_S0.359480.896
41_W96_V0.348240.868
22_L103_Q0.337850.842
79_C84_E0.337440.841
55_V81_L0.336040.838
65_W68_V0.334490.834
25_P105_S0.333990.833
31_D38_I0.333550.832
44_G53_Y0.333290.831
97_R105_S0.327510.816
51_V100_V0.326490.814
40_R78_S0.325030.810
35_F88_P0.323910.807
56_Q65_W0.320850.800
89_S92_Y0.319750.797
58_K62_S0.313870.782
57_Y68_V0.313540.782
47_S50_N0.313350.781
23_P44_G0.312520.779
60_Y63_S0.310560.774
61_G93_Y0.309210.771
30_V37_H0.307910.768
60_Y93_Y0.30650.764
44_G50_N0.300660.750
80_D83_D0.298250.744
100_V105_S0.298090.743
54_T67_D0.297630.742
32_S38_I0.295160.736
36_K80_D0.293910.733
48_P100_V0.292350.729
49_P100_V0.286940.715
46_G49_P0.283860.708
52_T104_T0.283090.706
50_N98_A0.279280.696
50_N53_Y0.276520.689
41_W55_V0.276170.688
23_P45_P0.272460.679
44_G49_P0.271990.678
77_T83_D0.270470.674
83_D94_A0.269310.671
33_V37_H0.269260.671
34_N88_P0.260520.649
37_H81_L0.259760.648
61_G90_E0.258960.646
22_L105_S0.257850.643
21_S105_S0.256490.639
23_P26_Q0.254880.635
19_S102_N0.254670.635
84_E90_E0.254380.634
33_V36_K0.253970.633
35_F89_S0.252930.631
33_V38_I0.251550.627
39_L96_V0.248430.619
22_L100_V0.248280.619
88_P92_Y0.247320.617
30_V39_L0.246750.615
32_S36_K0.241610.602
25_P98_A0.240590.600
25_P96_V0.239470.597
43_P77_T0.239410.597
73_N99_E0.234360.584
60_Y64_S0.233750.583
32_S37_H0.23320.581
20_A23_P0.231420.577
69_P79_C0.227530.567
59_K73_N0.224840.561
84_E94_A0.223980.558
39_L105_S0.222450.555
37_H84_E0.221340.552
61_G64_S0.220570.550
21_S24_A0.216730.540
57_Y66_K0.216080.539
50_N100_V0.214240.534
68_V75_T0.212690.530
44_G105_S0.212150.529
28_V41_W0.209950.523
60_Y66_K0.207480.517
42_D46_G0.207360.517
31_D78_S0.207120.516
22_L102_N0.207110.516
35_F72_Q0.206750.515
59_K63_S0.204650.510
21_S100_V0.201960.503
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
3s98A0.822499.30.227
3utoA0.841199.30.233
3g9vA0.869299.20.251
3se4A0.859899.20.252
4dohR0.878599.20.265
4dohB0.850599.20.269
2crzA0.831899.10.278
1v5jA0.841199.10.284
1n26A0.962699.10.286
2d9qB0.97299.10.29

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