Chlam_OMP6 - PFAM28P - GREMLIN Contacts

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Chlam_OMP6 - Chlamydia cysteine-rich outer membrane protein 6

PFAM:	PF03504	Sequences: MYTTTVNDDADVTITKTAPAEATVGSTYTITVTNTGPSDATNVVVTDTLPAGVTFVSATPAATVTAGGTLTWNIGTLAAGESATITVTVKP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (78)
Sequences:	779 (681)
Seq/√Len:	77.1
META:	0.935

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_F	58_A	5.520	1.00
49_L	53_V	3.633	1.00
30_I	34_N	3.327	1.00
28_Y	34_N	3.315	1.00
62_A	70_L	3.084	1.00
78_A	81_E	2.386	1.00
70_L	87_V	2.348	1.00
45_V	85_I	2.055	1.00
32_V	83_A	1.945	1.00
63_T	72_W	1.825	1.00
23_T	26_S	1.783	1.00
12_V	16_K	1.715	1.00
30_I	36_G	1.704	1.00
57_S	88_T	1.617	1.00
39_D	76_T	1.603	1.00
58_A	62_A	1.602	1.00
31_T	84_T	1.579	0.99
16_K	47_D	1.519	0.99
72_W	85_I	1.286	0.98
20_A	25_G	1.260	0.97
49_L	70_L	1.260	0.97
12_V	40_A	1.249	0.97
41_T	81_E	1.176	0.96
65_T	70_L	1.126	0.95
43_V	75_G	1.116	0.95
32_V	36_G	1.097	0.94
29_T	47_D	1.097	0.94
53_V	89_V	1.091	0.94
62_A	72_W	1.084	0.94
19_P	22_A	1.035	0.92
22_A	33_T	1.019	0.92
15_T	31_T	1.002	0.91
47_D	70_L	0.987	0.90
32_V	45_V	0.967	0.90
21_E	25_G	0.966	0.89
40_A	43_V	0.961	0.89
83_A	87_V	0.954	0.89
28_Y	32_V	0.925	0.87
40_A	79_A	0.908	0.86
70_L	74_I	0.906	0.86
64_V	68_G	0.901	0.86
64_V	67_G	0.895	0.86
72_W	87_V	0.880	0.85
60_P	64_V	0.868	0.84
59_T	86_T	0.857	0.83
53_V	87_V	0.852	0.83
26_S	51_A	0.838	0.82
21_E	26_S	0.799	0.78
25_G	75_G	0.797	0.78
28_Y	53_V	0.791	0.78
68_G	71_T	0.790	0.78
14_I	52_G	0.788	0.77
34_N	37_P	0.782	0.77
64_V	72_W	0.776	0.76
40_A	52_G	0.773	0.76
48_T	54_T	0.768	0.76
39_D	78_A	0.768	0.76
48_T	69_T	0.762	0.75
20_A	23_T	0.751	0.74
28_Y	44_V	0.746	0.73
43_V	85_I	0.741	0.73
37_P	69_T	0.731	0.72
29_T	86_T	0.730	0.72
36_G	40_A	0.720	0.71
47_D	69_T	0.715	0.70
50_P	54_T	0.707	0.69
63_T	69_T	0.698	0.68
29_T	84_T	0.695	0.68
38_S	79_A	0.693	0.68
60_P	72_W	0.681	0.67
66_A	69_T	0.668	0.65
65_T	69_T	0.663	0.65
16_K	25_G	0.661	0.64
44_V	81_E	0.655	0.64
53_V	79_A	0.654	0.63
31_T	58_A	0.652	0.63
44_V	71_T	0.651	0.63
63_T	70_L	0.646	0.62
45_V	75_G	0.645	0.62
64_V	70_L	0.645	0.62
44_V	83_A	0.642	0.62
55_F	72_W	0.639	0.62
27_T	56_V	0.635	0.61
45_V	67_G	0.632	0.61
22_A	68_G	0.632	0.61
56_V	61_A	0.630	0.61
44_V	56_V	0.620	0.59
34_N	77_L	0.608	0.58
16_K	19_P	0.602	0.57
49_L	89_V	0.601	0.57
63_T	84_T	0.597	0.56
22_A	26_S	0.595	0.56
24_V	85_I	0.591	0.56
20_A	43_V	0.586	0.55
42_N	84_T	0.582	0.55
54_T	65_T	0.579	0.54
85_I	88_T	0.577	0.54
20_A	24_V	0.574	0.54
61_A	82_S	0.572	0.53
33_T	37_P	0.568	0.53
26_S	76_T	0.561	0.52
50_P	53_V	0.558	0.52
74_I	85_I	0.549	0.50
59_T	88_T	0.549	0.50
13_T	23_T	0.546	0.50
37_P	49_L	0.545	0.50
36_G	41_T	0.543	0.50
13_T	52_G	0.542	0.50
18_A	23_T	0.531	0.48
42_N	61_A	0.529	0.48
27_T	57_S	0.527	0.48
35_T	53_V	0.522	0.47
33_T	82_S	0.521	0.47
12_V	17_T	0.520	0.47
38_S	51_A	0.516	0.46
18_A	24_V	0.509	0.45
21_E	24_V	0.500	0.44

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3iduA	1	0.7912	95.4	0.775	Contact Map
2l0dA	1	0.7582	93.3	0.796	Contact Map
2kutA	1	0.7802	90.2	0.813	Contact Map
4phzA	3	0.956	89.1	0.817	Contact Map
4ziqA	2	0.989	81.7	0.835	Contact Map
4hsqA	1	0.8681	81.2	0.836	Contact Map
2iaaC	1	0.9121	77.3	0.842	Contact Map
4tshB	1	1	77.1	0.842	Contact Map
1cuoA	1	0.8462	75.4	0.844	Contact Map
1yewA	3	0.956	75	0.845	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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