DUF3739 - PFAM28P - GREMLIN Contacts

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DUF3739 - Filamentous haemagglutinin family outer membrane protein

PFAM:	PF12545	Sequences: GGDILIWSSNGDIDAGRGAKTAVSAPPPRVLIDADGNVTVDLAGLVTGSGIGTLATVPGVPPGDVDLIAPRGTVDAGDAGIRSGNLNIAALQVLNADNIQVGGTSTGVPV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	110 (110)
Sequences:	1501 (840)
Seq/√Len:	80.1
META:	0.869

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_V	88_I	4.282	1.00
32_I	38_V	4.096	1.00
52_G	82_R	3.766	1.00
66_D	87_N	3.609	1.00
86_L	101_V	2.983	1.00
33_D	37_N	2.735	1.00
18_G	49_S	2.634	1.00
10_N	71_R	2.579	1.00
12_D	73_T	2.578	1.00
101_V	105_S	2.427	1.00
76_A	81_I	2.345	1.00
81_I	99_I	2.336	1.00
68_I	89_A	2.318	1.00
14_D	75_D	2.314	1.00
73_T	92_Q	2.252	1.00
73_T	94_L	1.907	1.00
73_T	91_L	1.807	1.00
6_I	13_I	1.725	1.00
105_S	108_V	1.620	1.00
76_A	99_I	1.581	1.00
64_D	85_N	1.535	0.99
14_D	17_R	1.534	0.99
54_L	82_R	1.523	0.99
22_A	49_S	1.515	0.99
87_N	106_T	1.501	0.99
78_D	97_D	1.481	0.99
28_P	45_L	1.418	0.99
85_N	103_G	1.410	0.99
85_N	104_T	1.362	0.99
41_D	44_G	1.331	0.98
30_V	40_V	1.312	0.98
88_I	93_V	1.307	0.98
81_I	88_I	1.254	0.98
7_W	70_P	1.231	0.97
57_V	60_V	1.226	0.97
53_T	83_S	1.222	0.97
25_A	49_S	1.214	0.97
20_K	98_N	1.209	0.97
55_A	83_S	1.200	0.97
68_I	87_N	1.147	0.96
74_V	93_V	1.119	0.95
17_R	23_V	1.083	0.95
42_L	45_L	1.048	0.93
22_A	25_A	1.044	0.93
31_L	39_T	1.036	0.93
4_I	52_G	0.975	0.91
88_I	99_I	0.971	0.91
55_A	60_V	0.968	0.90
47_T	54_L	0.962	0.90
85_N	101_V	0.954	0.90
86_L	105_S	0.931	0.89
31_L	41_D	0.911	0.88
4_I	65_V	0.908	0.87
23_V	46_V	0.902	0.87
5_L	10_N	0.894	0.87
63_G	83_S	0.888	0.86
25_A	56_T	0.886	0.86
29_R	41_D	0.874	0.85
77_G	80_G	0.860	0.84
53_T	65_V	0.858	0.84
90_A	93_V	0.852	0.84
26_P	45_L	0.841	0.83
25_A	42_L	0.840	0.83
5_L	68_I	0.833	0.82
44_G	56_T	0.824	0.82
94_L	99_I	0.822	0.82
45_L	63_G	0.814	0.81
32_I	37_N	0.813	0.81
28_P	38_V	0.808	0.80
20_K	78_D	0.808	0.80
96_A	99_I	0.808	0.80
75_D	95_N	0.785	0.79
26_P	56_T	0.774	0.78
75_D	94_L	0.771	0.77
105_S	109_P	0.770	0.77
7_W	89_A	0.763	0.77
13_I	38_V	0.757	0.76
60_V	63_G	0.750	0.75
29_R	43_A	0.731	0.73
19_A	78_D	0.728	0.73
93_V	110_V	0.727	0.73
14_D	45_L	0.721	0.72
29_R	40_V	0.715	0.72
95_N	98_N	0.714	0.72
38_V	87_N	0.713	0.72
58_P	61_P	0.709	0.71
65_V	70_P	0.708	0.71
27_P	54_L	0.706	0.71
74_V	86_L	0.704	0.71
45_L	53_T	0.700	0.70
33_D	39_T	0.697	0.70
68_I	74_V	0.688	0.69
6_I	9_S	0.687	0.69
97_D	100_Q	0.687	0.69
91_L	102_G	0.686	0.69
74_V	81_I	0.686	0.69
3_D	66_D	0.680	0.68
60_V	64_D	0.677	0.68
76_A	88_I	0.677	0.68
92_Q	97_D	0.669	0.67
28_P	42_L	0.666	0.66
74_V	92_Q	0.666	0.66
17_R	49_S	0.664	0.66
14_D	49_S	0.660	0.66
23_V	56_T	0.655	0.65
6_I	110_V	0.650	0.65
46_V	66_D	0.649	0.64
81_I	95_N	0.643	0.64
61_P	83_S	0.631	0.62
89_A	93_V	0.631	0.62
15_A	18_G	0.630	0.62
25_A	28_P	0.626	0.62
82_R	95_N	0.624	0.61
100_Q	104_T	0.622	0.61
96_A	100_Q	0.620	0.61
93_V	99_I	0.620	0.61
84_G	93_V	0.616	0.60
45_L	52_G	0.611	0.60
46_V	55_A	0.610	0.60
4_I	51_I	0.609	0.59
55_A	62_P	0.605	0.59
55_A	59_G	0.601	0.58
20_K	101_V	0.597	0.58
21_T	54_L	0.591	0.57
19_A	56_T	0.589	0.57
14_D	18_G	0.587	0.57
77_G	95_N	0.584	0.56
82_R	100_Q	0.584	0.56
56_T	60_V	0.579	0.56
9_S	61_P	0.569	0.54
51_I	67_L	0.566	0.54
47_T	52_G	0.562	0.54
57_V	63_G	0.562	0.54
17_R	22_A	0.558	0.53
66_D	85_N	0.557	0.53
14_D	23_V	0.554	0.52
62_P	84_G	0.553	0.52
55_A	63_G	0.551	0.52
18_G	23_V	0.546	0.51
44_G	47_T	0.546	0.51
28_P	36_G	0.546	0.51
104_T	110_V	0.545	0.51
18_G	28_P	0.544	0.51
62_P	83_S	0.542	0.51
25_A	44_G	0.541	0.51
37_N	46_V	0.540	0.51
7_W	67_L	0.540	0.51
21_T	90_A	0.536	0.50
23_V	43_A	0.536	0.50
19_A	28_P	0.533	0.50
23_V	45_L	0.530	0.49
67_L	74_V	0.529	0.49
33_D	36_G	0.526	0.49
24_S	43_A	0.526	0.49
29_R	32_I	0.523	0.48
87_N	91_L	0.519	0.48
94_L	97_D	0.517	0.48
37_N	49_S	0.514	0.47
53_T	63_G	0.510	0.47
65_V	86_L	0.508	0.47
49_S	52_G	0.508	0.47
23_V	54_L	0.503	0.46
46_V	54_L	0.502	0.46
83_S	86_L	0.502	0.46
60_V	83_S	0.500	0.45

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
1rwrA	1	0.9727	9.3	0.939	Contact Map
2odlA	1	0.9455	7.4	0.942	Contact Map
2v2fA	1	0.1364	2.9	0.952	Contact Map
1v1hA	3	0.3273	2.7	0.953	Contact Map
4i84A	1	0.8091	2.5	0.954	Contact Map
3vsfA	1	0.1545	1.8	0.957	Contact Map
2q07A	1	0.9	1.6	0.958	Contact Map
3a0cA	2	0.6	1.5	0.959	Contact Map
3tekA	1	0.3364	1.3	0.96	Contact Map
4e01A	3	0.2273	1.2	0.961	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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