GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Chlam_OMP6 - Chlamydia cysteine-rich outer membrane protein 6
Pfam: PF03504 (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: 95
Sequences: 1027
Seq/Len: 10.81
HH_delta: 0.713 (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
20_Q51_Q1.172035.992
59_F62_S0.535452.737
82_G85_E0.505942.587
57_V93_V0.44562.278
40_G44_C0.409422.093
37_L86_K0.372271.903
31_P92_W0.361151.846
61_R92_W0.342411.751
36_I87_C0.338391.730
76_W89_I0.33241.699
81_L85_E0.331961.697
17_E39_Q0.329421.684
50_T75_V0.30641.566
14_C44_C0.306331.566
43_D83_Q0.302051.544
53_L93_V0.301581.542
46_N79_G0.29421.504
44_C47_V0.292351.495
66_T76_W0.271631.389
62_S91_V0.268941.375
43_D80_R0.268691.374
69_T74_L0.266261.361
78_I89_I0.246771.262
33_P90_T0.235781.205
76_W91_V0.230791.180
22_V25_Y0.229041.171
18_I34_I0.228741.169
74_L91_V0.226671.159
22_V32_Y0.223841.144
23_P33_P0.223131.141
71_D74_L0.218041.115
64_P76_W0.216271.106
14_C40_G0.214731.098
18_I36_I0.209391.070
24_K27_T0.206781.057
34_I51_Q0.20461.046
22_V57_V0.196471.004
17_E37_L0.19140.978
82_G88_K0.188190.962
18_I49_I0.185120.946
24_K30_S0.184130.941
23_P26_A0.18380.940
47_V81_L0.182760.934
47_V61_R0.182330.932
57_V91_V0.181250.927
59_F64_P0.181130.926
69_T72_G0.177130.906
67_T76_W0.17590.899
34_I38_A0.175560.898
47_V79_G0.175550.897
36_I67_T0.173810.889
20_Q47_V0.172130.880
48_V77_K0.171920.879
49_I78_I0.169410.866
60_V92_W0.165370.845
34_I49_I0.164350.840
31_P60_V0.163070.834
72_G75_V0.160310.820
42_K83_Q0.159610.816
63_D85_E0.15810.808
41_K83_Q0.156690.801
52_Q58_E0.156220.799
53_L57_V0.155940.797
42_K46_N0.154590.790
15_N39_Q0.15270.781
77_K80_R0.150170.768
35_E88_K0.150090.767
16_V41_K0.148570.760
15_N76_W0.147830.756
49_I69_T0.147810.756
55_C58_E0.14770.755
29_G32_Y0.146180.747
62_S66_T0.145550.744
50_T73_K0.145050.742
16_V87_C0.145020.741
30_S93_V0.144860.741
22_V26_A0.143830.735
35_E86_K0.143680.735
35_E90_T0.141420.723
34_I40_G0.140770.720
49_I89_I0.136060.696
16_V50_T0.135610.693
65_E83_Q0.135230.691
33_P92_W0.13270.678
59_F91_V0.131720.673
22_V60_V0.131280.671
15_N41_K0.130080.665
14_C41_K0.128030.655
34_I91_V0.126240.645
40_G83_Q0.124050.634
43_D82_G0.122350.625
30_S64_P0.121720.622
27_T71_D0.121640.622
36_I79_G0.120080.614
48_V75_V0.119770.612
64_P91_V0.119580.611
38_A41_K0.119430.611
46_N78_I0.118270.605
37_L55_C0.117330.600
42_K92_W0.116470.595
32_Y73_K0.115870.592
23_P91_V0.115650.591
48_V86_K0.11510.588
22_V62_S0.11470.586
44_C80_R0.1140.583
47_V87_C0.113460.580
18_I90_T0.112640.576
83_Q86_K0.111510.570
24_K52_Q0.110830.567
32_Y62_S0.110580.565
55_C63_D0.11040.564
15_N43_D0.109630.560
61_R91_V0.109540.560
23_P27_T0.109440.559
37_L85_E0.109360.559
46_N75_V0.108770.556
49_I56_E0.108620.555
28_V78_I0.108490.555
66_T80_R0.107950.552
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
3iduA0.810597.20.713
2l0dA0.726395.70.765
2kutA0.747494.90.778
3icgA0.989594.40.783
3kptA194.10.786
3qdhA0.873793.80.789
4fxkB0.863293.70.79
3ndzE0.852693.50.791
3ijeA0.936893.20.794
2iaaC0.8737930.795
If you are interested in a protein containing this domain,
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