DUF5061 - PFAM28P - GREMLIN Contacts

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DUF5061 - 17 kDa common-antigen outer membrane protein

PFAM:	PF16587	Sequences: LAALAALLLLAGCATTPGKSLDAADQALAAQAAQQALETAPTGQTSTWANPDSGNSGTVTPTRTYQAASGRYCRELTVTVGGGEAAYGTACRQPDGSWKIQPR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	103 (96)
Sequences:	563 (466)
Seq/√Len:	47.5
META:	0.86

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_A	28_L	2.653	1.00
66_Q	72_Y	2.590	1.00
65_Y	69_S	2.540	1.00
65_Y	68_A	2.490	1.00
77_T	80_V	2.408	1.00
93_Q	97_S	2.317	1.00
23_A	28_L	2.266	1.00
32_A	59_V	2.184	1.00
45_T	60_T	2.159	1.00
29_A	32_A	2.138	1.00
35_Q	39_T	2.027	0.99
69_S	89_T	1.920	0.99
36_A	40_A	1.726	0.98
38_E	92_R	1.712	0.98
73_C	91_C	1.681	0.98
34_Q	37_L	1.648	0.98
71_R	99_K	1.624	0.98
8_L	11_A	1.594	0.97
63_R	75_E	1.575	0.97
37_L	61_P	1.554	0.97
12_G	16_T	1.487	0.96
78_V	83_G	1.446	0.95
69_S	99_K	1.406	0.94
45_T	58_T	1.369	0.93
34_Q	90_A	1.365	0.93
27_A	68_A	1.350	0.93
37_L	67_A	1.319	0.92
53_S	88_G	1.308	0.92
73_C	98_W	1.286	0.91
6_A	11_A	1.241	0.89
78_V	87_Y	1.238	0.89
37_L	90_A	1.210	0.88
40_A	46_S	1.208	0.88
48_W	57_G	1.158	0.86
71_R	76_L	1.145	0.85
76_L	79_T	1.138	0.85
61_P	90_A	1.125	0.84
8_L	13_C	1.114	0.84
59_V	78_V	1.110	0.83
74_R	93_Q	1.106	0.83
50_N	57_G	1.101	0.83
33_A	36_A	1.092	0.82
64_T	74_R	1.085	0.82
14_A	17_P	1.068	0.81
33_A	68_A	1.057	0.80
79_T	84_E	1.046	0.80
50_N	53_S	1.042	0.79
27_A	31_Q	1.037	0.79
30_A	84_E	1.032	0.79
27_A	32_A	1.029	0.78
48_W	53_S	1.023	0.78
91_C	98_W	1.012	0.77
49_A	68_A	0.969	0.74
18_G	92_R	0.958	0.73
76_L	88_G	0.945	0.72
41_P	94_P	0.936	0.72
38_E	64_T	0.934	0.71
19_K	27_A	0.929	0.71
28_L	31_Q	0.921	0.70
18_G	21_L	0.915	0.70
74_R	96_G	0.896	0.68
24_A	27_A	0.895	0.68
7_L	15_T	0.893	0.68
13_C	68_A	0.891	0.68
11_A	17_P	0.885	0.67
65_Y	89_T	0.883	0.67
76_L	84_E	0.880	0.67
48_W	95_D	0.876	0.66
76_L	80_V	0.854	0.64
53_S	56_S	0.854	0.64
44_Q	47_T	0.846	0.64
33_A	37_L	0.843	0.63
76_L	100_I	0.842	0.63
69_S	76_L	0.842	0.63
43_G	53_S	0.837	0.63
66_Q	89_T	0.835	0.63
35_Q	67_A	0.833	0.63
36_A	61_P	0.831	0.62
37_L	42_T	0.803	0.60
86_A	99_K	0.800	0.59
26_Q	31_Q	0.790	0.58
23_A	27_A	0.788	0.58
93_Q	96_G	0.778	0.57
21_L	29_A	0.775	0.57
35_Q	97_S	0.772	0.57
90_A	95_D	0.768	0.56
80_V	83_G	0.767	0.56
6_A	9_L	0.739	0.53
35_Q	45_T	0.738	0.53
28_L	35_Q	0.738	0.53
24_A	30_A	0.737	0.53
52_D	94_P	0.729	0.52
30_A	39_T	0.724	0.52
27_A	30_A	0.722	0.52
76_L	83_G	0.716	0.51
51_P	54_G	0.710	0.50
39_T	71_R	0.710	0.50
50_N	55_N	0.704	0.50
25_D	57_G	0.697	0.49
32_A	36_A	0.689	0.48
20_S	23_A	0.688	0.48
78_V	88_G	0.686	0.48
81_G	85_A	0.678	0.47
53_S	74_R	0.674	0.47
53_S	89_T	0.668	0.46
68_A	71_R	0.665	0.46
44_Q	75_E	0.660	0.45
30_A	69_S	0.659	0.45
23_A	29_A	0.654	0.45
53_S	76_L	0.651	0.45
36_A	57_G	0.648	0.44
67_A	76_L	0.643	0.44
67_A	71_R	0.639	0.43
38_E	72_Y	0.639	0.43
39_T	72_Y	0.635	0.43
41_P	44_Q	0.617	0.41
7_L	11_A	0.603	0.40
80_V	84_E	0.603	0.40
62_T	69_S	0.600	0.40
77_T	81_G	0.597	0.39
8_L	78_V	0.596	0.39
10_L	72_Y	0.596	0.39
71_R	89_T	0.590	0.39
51_P	92_R	0.583	0.38
25_D	29_A	0.580	0.38
19_K	22_D	0.566	0.36
75_E	83_G	0.566	0.36
62_T	100_I	0.566	0.36
40_A	63_R	0.562	0.36
12_G	84_E	0.554	0.35
21_L	25_D	0.548	0.35
61_P	75_E	0.547	0.35
24_A	41_P	0.542	0.34
7_L	92_R	0.533	0.33
42_T	97_S	0.530	0.33
22_D	95_D	0.527	0.33
63_R	67_A	0.525	0.33
7_L	23_A	0.524	0.33
12_G	87_Y	0.523	0.33
24_A	82_G	0.521	0.32
23_A	30_A	0.520	0.32
46_S	68_A	0.509	0.31
36_A	44_Q	0.501	0.31
7_L	25_D	0.500	0.31

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
3zbiC	1	0.2621	26.2	0.878	Contact Map
1ru4A	1	0.9126	10.7	0.898	Contact Map
1w7fA	1	0.7087	10.2	0.899	Contact Map
3pmqA	1	0.4369	8.5	0.902	Contact Map
3draB	1	0.8932	6	0.909	Contact Map
3ucpA	1	0.534	5.2	0.911	Contact Map
1yr2A	1	0.699	5.2	0.911	Contact Map
4u6bA	3	0.4175	4.6	0.914	Contact Map
2mhkA	1	0.932	4.6	0.914	Contact Map
4fajA	1	0.5825	4.3	0.915	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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