Fil_haemagg_2 - PFAM28P - GREMLIN Contacts

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Fil_haemagg_2 - Haemagluttinin repeat

PFAM:	PF13332	Sequences: IGSSKSKSTSTSSSTTAVGSTLSAGGNVTITAGGGDITVQGSQVSAGGDVTLSAGNDINLLAAQNTSSSSSSNSSSGASVGVSVGLGGGGGGIGVTAGASKGKGKSNGDSTTQTNSTVGAGGNVTINSGGDTTLKGAQVSAGDVTADAGGNLNIESAQDTSTYSSKQSSA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	170 (161)
Sequences:	6285 (4839)
Seq/√Len:	381.3
META:	0.555

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_I	126_I	3.286	1.00
38_T	59_N	3.150	1.00
130_G	150_G	3.056	1.00
37_I	52_L	3.031	1.00
39_V	42_S	3.021	1.00
46_A	50_V	2.976	1.00
133_T	153_N	2.902	1.00
128_S	132_T	2.713	1.00
124_V	139_V	2.667	1.00
53_S	127_N	2.455	1.00
34_G	56_N	2.452	1.00
134_L	137_A	2.246	1.00
51_T	125_T	2.110	1.00
40_Q	61_L	2.073	1.00
141_A	144_V	2.062	1.00
62_A	113_Q	2.056	1.00
57_D	130_G	1.988	1.00
50_V	118_V	1.918	1.00
65_N	114_T	1.916	1.00
28_V	44_V	1.897	1.00
17_A	65_N	1.877	1.00
135_K	155_E	1.871	1.00
60_L	116_S	1.861	1.00
56_N	130_G	1.859	1.00
115_N	137_A	1.853	1.00
32_A	37_I	1.790	1.00
38_T	61_L	1.785	1.00
14_S	67_S	1.734	1.00
21_T	43_Q	1.725	1.00
144_V	148_A	1.715	1.00
62_A	157_A	1.702	1.00
113_Q	157_A	1.700	1.00
131_D	151_N	1.695	1.00
24_A	28_V	1.679	1.00
110_S	161_S	1.648	1.00
36_D	56_N	1.583	1.00
26_G	48_G	1.578	1.00
64_Q	113_Q	1.572	1.00
45_S	119_G	1.547	1.00
59_N	133_T	1.546	1.00
39_V	60_L	1.537	1.00
115_N	138_Q	1.513	1.00
43_Q	117_T	1.505	1.00
132_T	146_A	1.500	1.00
64_Q	111_T	1.460	1.00
63_A	114_T	1.452	1.00
29_T	51_T	1.450	1.00
36_D	57_D	1.418	1.00
113_Q	159_D	1.410	1.00
17_A	63_A	1.359	1.00
39_V	44_V	1.345	1.00
54_A	129_G	1.344	1.00
120_A	124_V	1.320	1.00
23_S	45_S	1.302	1.00
123_N	143_D	1.285	1.00
13_S	68_S	1.279	1.00
86_L	89_G	1.275	1.00
131_D	150_G	1.233	1.00
132_T	148_A	1.221	1.00
135_K	157_A	1.212	1.00
127_N	147_D	1.206	1.00
68_S	109_D	1.200	1.00
58_I	128_S	1.192	1.00
77_G	100_S	1.191	1.00
124_V	141_A	1.185	1.00
41_G	63_A	1.171	1.00
113_Q	136_G	1.170	1.00
31_T	53_S	1.150	1.00
27_N	48_G	1.124	1.00
30_I	37_I	1.119	1.00
49_D	123_N	1.111	1.00
78_A	82_V	1.103	1.00
117_T	138_Q	1.092	1.00
60_L	134_L	1.086	1.00
126_I	146_A	1.086	1.00
125_T	145_T	1.073	1.00
50_V	124_V	1.055	1.00
10_S	71_S	1.053	1.00
15_T	66_T	1.040	1.00
75_S	102_G	1.039	1.00
19_G	42_S	1.039	1.00
143_D	146_A	1.029	1.00
134_L	154_I	1.027	1.00
20_S	42_S	1.021	1.00
40_Q	63_A	1.012	1.00
148_A	152_L	1.001	1.00
43_Q	114_T	1.000	1.00
133_T	155_E	0.998	1.00
122_G	142_G	0.970	1.00
37_I	58_I	0.969	1.00
109_D	162_T	0.942	1.00
60_L	137_A	0.938	1.00
17_A	41_G	0.918	1.00
50_V	53_S	0.886	1.00
119_G	140_S	0.881	1.00
8_S	73_N	0.869	1.00
44_V	118_V	0.863	1.00
73_N	104_G	0.853	1.00
142_G	145_T	0.847	1.00
19_G	43_Q	0.829	1.00
15_T	18_V	0.827	1.00
37_I	54_A	0.818	1.00
12_S	69_S	0.812	1.00
79_S	83_S	0.809	1.00
5_K	76_S	0.804	1.00
139_V	154_I	0.803	1.00
116_S	137_A	0.801	1.00
49_D	125_T	0.795	1.00
48_G	122_G	0.790	1.00
61_L	135_K	0.789	1.00
36_D	54_A	0.781	1.00
67_S	110_S	0.780	1.00
86_L	92_G	0.776	1.00
108_G	163_Y	0.774	1.00
106_S	165_S	0.773	1.00
31_T	127_N	0.773	1.00
123_N	145_T	0.771	1.00
52_L	126_I	0.769	1.00
28_V	50_V	0.766	1.00
85_G	89_G	0.752	1.00
46_A	49_D	0.750	1.00
49_D	122_G	0.749	1.00
136_G	157_A	0.742	1.00
79_S	98_G	0.741	1.00
17_A	40_Q	0.730	1.00
85_G	88_G	0.730	1.00
33_G	37_I	0.730	1.00
83_S	86_L	0.730	1.00
87_G	90_G	0.730	1.00
27_N	46_A	0.721	1.00
76_S	101_K	0.716	1.00
27_N	120_A	0.712	1.00
120_A	123_N	0.708	1.00
126_I	139_V	0.707	1.00
142_G	147_D	0.706	1.00
124_V	144_V	0.706	1.00
54_A	58_I	0.703	1.00
52_L	118_V	0.702	1.00
28_V	46_A	0.698	0.99
47_G	121_G	0.695	0.99
24_A	27_N	0.682	0.99
132_T	149_G	0.681	0.99
12_S	67_S	0.680	0.99
53_S	56_N	0.677	0.99
115_N	157_A	0.676	0.99
123_N	142_G	0.668	0.99
33_G	55_G	0.663	0.99
36_D	129_G	0.663	0.99
87_G	92_G	0.663	0.99
101_K	105_K	0.660	0.99
17_A	114_T	0.652	0.99
126_I	132_T	0.650	0.99
143_D	148_A	0.650	0.99
32_A	56_N	0.645	0.99
27_N	49_D	0.644	0.99
92_G	95_V	0.643	0.99
22_L	28_V	0.640	0.99
26_G	47_G	0.637	0.99
15_T	65_N	0.637	0.99
111_T	160_T	0.635	0.99
16_T	65_N	0.626	0.99
128_S	148_A	0.624	0.99
32_A	55_G	0.618	0.99
54_A	128_S	0.617	0.99
34_G	55_G	0.614	0.99
20_S	39_V	0.611	0.99
50_V	120_A	0.610	0.99
136_G	158_Q	0.610	0.99
144_V	152_L	0.608	0.99
22_L	30_I	0.607	0.99
83_S	94_G	0.604	0.99
36_D	55_G	0.603	0.98
84_V	93_I	0.602	0.98
19_G	114_T	0.600	0.98
77_G	102_G	0.595	0.98
84_V	87_G	0.594	0.98
7_K	11_T	0.591	0.98
81_G	84_V	0.590	0.98
85_G	90_G	0.588	0.98
132_T	152_L	0.587	0.98
144_V	147_D	0.584	0.98
149_G	152_L	0.584	0.98
60_L	118_V	0.583	0.98
66_T	111_T	0.581	0.98
89_G	92_G	0.581	0.98
20_S	23_S	0.579	0.98
30_I	44_V	0.573	0.98
83_S	96_T	0.570	0.98
83_S	89_G	0.568	0.98
162_T	166_K	0.567	0.98
70_S	107_N	0.566	0.98
77_G	80_V	0.566	0.98
42_S	116_S	0.565	0.98
80_V	83_S	0.563	0.98
54_A	57_D	0.562	0.98
86_L	90_G	0.559	0.98
5_K	8_S	0.558	0.98
88_G	96_T	0.557	0.97
88_G	93_I	0.557	0.97
116_S	119_G	0.556	0.97
71_S	75_S	0.552	0.97
156_S	159_D	0.552	0.97
103_K	107_N	0.551	0.97
83_S	87_G	0.551	0.97
134_L	139_V	0.549	0.97
69_S	107_N	0.548	0.97
94_G	97_A	0.547	0.97
70_S	109_D	0.546	0.97
78_A	81_G	0.546	0.97
144_V	150_G	0.545	0.97
131_D	153_N	0.544	0.97
118_V	139_V	0.544	0.97
128_S	150_G	0.543	0.97
94_G	98_G	0.542	0.97
5_K	9_T	0.534	0.97
83_S	92_G	0.532	0.97
57_D	131_D	0.532	0.97
19_G	22_L	0.531	0.97
135_K	138_Q	0.531	0.97
44_V	50_V	0.530	0.97
84_V	89_G	0.528	0.97
144_V	149_G	0.527	0.97
106_S	163_Y	0.525	0.96
24_A	46_A	0.525	0.96
95_V	99_A	0.524	0.96
74_S	79_S	0.523	0.96
109_D	164_S	0.522	0.96
28_V	32_A	0.520	0.96
108_G	161_S	0.519	0.96
145_T	148_A	0.518	0.96
7_K	74_S	0.518	0.96
71_S	106_S	0.514	0.96
102_G	106_S	0.509	0.96
80_V	84_V	0.508	0.96
24_A	47_G	0.507	0.96
131_D	149_G	0.505	0.96
61_L	64_Q	0.504	0.96
32_A	54_A	0.503	0.95
31_T	51_T	0.503	0.95
18_V	21_T	0.502	0.95
9_T	13_S	0.502	0.95
88_G	92_G	0.500	0.95

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
1wthA	3	0.4882	17.5	0.875	Contact Map
4i84A	1	0.7647	8.3	0.892	Contact Map
4ku0A	3	0.4059	5.7	0.9	Contact Map
4mtkA	4	0.6118	2.4	0.917	Contact Map
4peuA	1	0.8588	2.1	0.92	Contact Map
1s7mA	5	0.3176	1.3	0.928	Contact Map
1rwrA	1	0.5412	1.1	0.932	Contact Map
3a1mA	5	0.4941	1	0.933	Contact Map
2jcbA	1	0.3176	0.9	0.936	Contact Map
1wxrA	1	0.9588	0.5	0.947	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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