GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SCPU - Spore Coat Protein U domain
Pfam: PF05229 (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: CL0204
Length: 139
Sequences: 704
Seq/Len: 5.06
HH_delta: 0.806 (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
38_T119_R0.371763.342
23_L41_G0.34193.074
23_L118_G0.325432.926
82_Y134_D0.288382.593
87_D117_Y0.266912.400
83_Q93_V0.265972.391
70_R79_Y0.255012.293
90_R119_R0.247262.223
25_F118_G0.244132.195
84_L116_I0.238472.144
60_G69_R0.215891.941
38_T90_R0.197421.775
86_Q94_W0.196841.770
85_Y90_R0.19281.733
29_S125_Q0.19031.711
86_Q92_T0.18391.653
62_N72_S0.182011.636
84_L136_V0.180841.626
57_L94_W0.176851.590
55_I114_L0.164791.481
109_G112_Q0.160561.443
17_V138_V0.152151.368
58_D61_N0.140321.261
72_S79_Y0.140261.261
53_Y114_L0.139321.253
42_T115_P0.136051.223
62_N79_Y0.135981.222
73_N130_G0.135891.222
59_G62_N0.135671.220
87_D90_R0.134131.206
45_V116_I0.133671.202
46_T111_S0.131881.186
18_S89_G0.129581.165
80_L120_I0.128151.152
96_S100_A0.127471.146
29_S32_L0.126131.134
78_N128_P0.125041.124
29_S80_L0.124531.120
39_A136_V0.122151.098
62_N70_R0.121111.089
45_V55_I0.118521.066
53_Y120_I0.11851.065
20_T41_G0.117521.057
8_S11_V0.117451.056
65_G83_Q0.116081.044
19_A136_V0.115831.041
61_N135_T0.115281.036
57_L136_V0.115071.034
99_N103_S0.114281.027
80_L93_V0.113781.023
85_Y119_R0.113251.018
40_S115_P0.111110.999
53_Y56_G0.111090.999
51_T111_S0.110740.996
60_G127_V0.110390.992
81_P124_Q0.108660.977
62_N133_T0.108390.974
80_L125_Q0.107280.964
86_Q90_R0.107180.964
87_D91_S0.105880.952
18_S22_T0.105850.952
58_D137_T0.105830.951
63_S66_G0.10510.945
23_L37_Q0.105080.945
9_A48_T0.103790.933
9_A80_L0.103290.929
55_I105_S0.102470.921
99_N102_T0.101490.912
95_G100_A0.101230.910
94_W102_T0.101070.909
20_T40_S0.100390.903
82_Y138_V0.099840.898
8_S12_A0.099410.894
14_S46_T0.099130.891
23_L96_S0.099040.890
85_Y118_G0.098970.890
134_D138_V0.098890.889
73_N128_P0.098080.882
57_L116_I0.097950.881
25_F60_G0.097890.880
101_T105_S0.09760.877
124_Q127_V0.097510.877
17_V38_T0.096670.869
58_D69_R0.095780.861
31_P80_L0.09570.860
22_T39_A0.095650.860
15_C47_C0.095370.857
46_T89_G0.095170.856
24_N138_V0.094910.853
71_M129_A0.094820.852
43_L113_T0.093890.844
56_G95_G0.093410.840
22_T40_S0.093370.839
56_G97_G0.092720.834
42_T114_L0.092680.833
90_R117_Y0.092180.829
65_G99_N0.092170.829
16_S102_T0.091860.826
11_V24_N0.091630.824
14_S49_N0.091580.823
44_T113_T0.091420.822
31_P127_V0.091210.820
35_S138_V0.090690.815
103_S106_T0.090450.813
43_L94_W0.090160.811
88_A117_Y0.09010.810
42_T91_S0.08970.806
103_S133_T0.089640.806
69_R118_G0.08940.804
94_W100_A0.089080.801
40_S81_P0.089010.800
85_Y91_S0.088690.797
10_T103_S0.088480.795
112_Q136_V0.088390.795
120_I124_Q0.088360.794
42_T113_T0.088320.794
9_A71_M0.087760.789
11_V14_S0.087570.787
85_Y124_Q0.087360.785
65_G96_S0.087130.783
86_Q95_G0.086670.779
49_N55_I0.086510.778
98_G104_G0.086440.777
86_Q135_T0.08640.777
55_I70_R0.086210.775
86_Q117_Y0.086170.775
48_T113_T0.086140.774
17_V48_T0.085920.772
97_G120_I0.085780.771
60_G63_S0.085640.770
83_Q121_P0.085450.768
80_L104_G0.085180.766
51_T136_V0.085120.765
16_S46_T0.085010.764
16_S24_N0.084490.760
73_N78_N0.084330.758
61_N127_V0.084320.758
50_G91_S0.083710.753
9_A12_A0.083450.750
102_T106_T0.083140.747
81_P88_A0.082330.740
50_G108_T0.082210.739
45_V53_Y0.081690.734
11_V136_V0.081660.734
53_Y112_Q0.081620.734
32_L124_Q0.081480.733
62_N65_G0.081430.732
60_G70_R0.081280.731
31_P66_G0.081150.730
53_Y98_G0.08110.729
130_G134_D0.080910.727
17_V67_T0.080890.727
9_A84_L0.08080.726
11_V48_T0.080590.725
22_T116_I0.080270.722
79_Y128_P0.080240.721
101_T104_G0.080210.721
41_G137_T0.08020.721
46_T137_T0.079890.718
23_L39_A0.079490.715
69_R85_Y0.079310.713
35_S113_T0.079160.712
97_G100_A0.079020.710
62_N134_D0.078650.707
61_N93_V0.07860.707
76_G137_T0.078460.705
11_V134_D0.078410.705
24_N92_T0.078350.704
28_S31_P0.078040.702
30_S33_S0.077860.700
33_S126_N0.077680.698
59_G93_V0.077580.697
32_L116_I0.077550.697
84_L117_Y0.07710.693
88_A115_P0.07680.690
86_Q102_T0.076410.687
41_G84_L0.07640.687
18_S46_T0.076370.687
23_L43_L0.076350.686
16_S49_N0.076090.684
58_D136_V0.075890.682
13_A51_T0.075810.682
57_L105_S0.075760.681
71_M77_S0.075660.680
24_N81_P0.075580.679
78_N91_S0.075460.678
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
2jmrA0.985696.20.806
4dwhB0.899395.90.812
3bfqG0.870595.90.813
3bwuF0.906595.40.819
3jwnH0.877795.20.822
1ze3H0.820194.90.826
2xg5B0.949694.80.826
2jtyA0.971294.40.829
2uy6B0.949693.40.837
1n12A0.892193.20.838
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