GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CRS1_YhbY - CRS1 YhbY (CRM) domain
Pfam: PF01985 (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. )
Length: 84
Sequences: 976
Seq/Len: 11.62
HH_delta: -0.031 (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
13_A81_V0.809453.920
36_D84_R0.752623.645
8_F12_L0.577772.798
3_S6_R0.479592.323
19_V38_A0.438512.124
63_Q67_K0.406321.968
3_S7_K0.386081.870
58_K62_E0.378481.833
35_I64_L0.372711.805
65_A82_L0.357811.733
57_R78_R0.305751.481
20_V31_V0.298851.447
32_I64_L0.282341.367
48_K79_T0.279631.354
74_Q81_V0.272911.322
61_A80_I0.259061.255
36_D40_E0.257721.248
65_A72_V0.253591.228
65_A70_A0.249271.207
56_D59_E0.241481.170
10_R74_Q0.236141.144
32_I67_K0.233121.129
37_D41_K0.232871.128
26_G55_E0.231961.123
13_A16_L0.231531.121
7_K10_R0.229541.112
1_L5_E0.227751.103
61_A75_V0.226041.095
12_L43_E0.225081.090
61_A72_V0.221451.073
36_D39_L0.220921.070
19_V42_H0.219691.064
46_K77_G0.218931.060
24_K50_L0.214581.039
62_E66_E0.214461.039
53_C57_R0.212881.031
20_V34_E0.209631.015
47_V80_I0.208771.011
2_T5_E0.207651.006
53_C60_I0.207121.003
5_E8_F0.201820.977
66_E69_G0.201340.975
34_E78_R0.199770.968
49_V80_I0.199080.964
64_L82_L0.197790.958
20_V47_V0.197120.955
27_L31_V0.193140.935
19_V45_V0.192630.933
33_E36_D0.190520.923
30_G33_E0.189730.919
10_R44_L0.18840.912
61_A65_A0.187910.910
64_L80_I0.187570.908
72_V75_V0.185810.900
16_L42_H0.185250.897
13_A76_I0.183510.889
55_E60_I0.183470.889
14_H44_L0.18320.887
20_V48_K0.182040.882
29_D33_E0.180850.876
39_L70_A0.178580.865
31_V47_V0.17780.861
58_K75_V0.175670.851
53_C56_D0.172110.834
28_T48_K0.171640.831
18_P44_L0.169690.822
33_E37_D0.169630.822
13_A73_V0.168770.817
34_E37_D0.168370.815
7_K11_K0.168080.814
14_H79_T0.16690.808
32_I68_T0.166240.805
71_E81_V0.166030.804
49_V60_I0.164430.796
21_Q50_L0.163760.793
15_H47_V0.162260.786
24_K56_D0.160870.779
62_E72_V0.160470.777
9_L43_E0.160030.775
27_L60_I0.158240.766
46_K76_I0.157950.765
20_V35_I0.157320.762
54_R57_R0.157140.761
2_T58_K0.15590.755
22_I64_L0.154510.748
34_E54_R0.154380.748
60_I80_I0.154240.747
30_G66_E0.153650.744
51_G60_I0.153510.743
8_F43_E0.152530.739
35_I68_T0.152480.738
49_V78_R0.151790.735
10_R72_V0.151540.734
59_E63_Q0.150710.730
78_R81_V0.150170.727
29_D66_E0.149850.726
49_V53_C0.149540.724
35_I47_V0.148620.720
73_V76_I0.148450.719
55_E59_E0.148420.719
11_K74_Q0.14770.715
21_Q24_K0.147370.714
2_T8_F0.147350.714
59_E66_E0.146860.711
17_K33_E0.146840.711
65_A75_V0.146260.708
58_K69_G0.145910.707
17_K42_H0.145730.706
31_V48_K0.145370.704
7_K58_K0.144910.702
21_Q48_K0.144790.701
25_N83_Y0.143290.694
12_L16_L0.142630.691
17_K62_E0.141440.685
72_V80_I0.140980.683
14_H57_R0.140780.682
9_L78_R0.140480.680
17_K78_R0.140030.678
15_H82_L0.139860.677
31_V35_I0.139580.676
34_E53_C0.139540.676
35_I45_V0.13950.676
25_N55_E0.139280.675
23_G82_L0.138860.673
25_N40_E0.13880.672
35_I39_L0.138790.672
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
1jo0A199.9-0.031
1rq8A199.9-0.028
3j21k0.976242.10.883
2f1fA0.845239.90.885
3a1yG0.964339.50.885
3iygZ0.86937.20.886
1nbwB0.845237.10.887
2pc6A0.8452370.887
1zavA0.916735.70.887
2j01J0.9286350.888

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