Fil_haemagg - PFAM28P - GREMLIN Contacts

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Fil_haemagg - Haemagluttinin repeat

PFAM:	PF05594	Sequences: VSAGALTVNAAGVSALGGLLNNQGGLLSSGGGLTLTAAGLDNNGGTLSSGGALTLTAASLDNNGGTISAQGDLDLSG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (69)
Sequences:	7345 (5901)
Seq/√Len:	710.4
META:	0.592

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_G	75_L	4.903	1.00
29_S	33_L	2.349	1.00
6_L	10_A	2.310	1.00
30_G	50_G	2.232	1.00
49_S	53_L	2.197	1.00
65_G	68_S	2.126	1.00
69_A	75_L	1.930	1.00
23_Q	41_D	1.767	1.00
60_L	63_N	1.764	1.00
31_G	51_G	1.747	1.00
32_G	52_A	1.654	1.00
32_G	51_G	1.584	1.00
43_N	61_D	1.569	1.00
65_G	69_A	1.568	1.00
19_L	22_N	1.565	1.00
20_L	23_Q	1.462	1.00
37_A	40_L	1.434	1.00
19_L	39_G	1.426	1.00
24_G	44_G	1.400	1.00
28_S	48_S	1.380	1.00
36_T	56_T	1.359	1.00
69_A	73_L	1.340	1.00
39_G	59_S	1.283	1.00
37_A	57_A	1.223	1.00
50_G	70_Q	1.213	1.00
26_L	46_T	1.149	1.00
5_A	32_G	1.132	1.00
38_A	58_A	1.102	1.00
23_Q	43_N	1.079	1.00
61_D	64_G	1.070	1.00
34_T	54_T	1.052	1.00
5_A	31_G	1.052	1.00
35_L	47_L	1.035	1.00
60_L	64_G	1.021	1.00
57_A	63_N	0.989	1.00
37_A	41_D	0.977	1.00
52_A	55_L	0.952	1.00
20_L	27_L	0.938	1.00
54_T	57_A	0.928	1.00
57_A	60_L	0.922	1.00
69_A	72_D	0.915	1.00
53_L	57_A	0.905	1.00
18_G	39_G	0.900	1.00
8_V	11_A	0.892	1.00
25_G	29_S	0.874	1.00
9_N	36_T	0.852	1.00
5_A	8_V	0.840	1.00
21_N	24_G	0.836	1.00
7_T	34_T	0.831	1.00
3_A	6_L	0.828	1.00
39_G	58_A	0.828	1.00
34_T	56_T	0.827	1.00
43_N	62_N	0.815	1.00
4_G	7_T	0.782	1.00
44_G	64_G	0.777	1.00
68_S	75_L	0.776	1.00
28_S	50_G	0.775	1.00
36_T	54_T	0.772	1.00
46_T	66_T	0.766	1.00
52_A	72_D	0.758	1.00
70_Q	75_L	0.753	1.00
22_N	42_N	0.752	1.00
67_I	75_L	0.729	1.00
3_A	30_G	0.725	1.00
6_L	11_A	0.724	1.00
43_N	64_G	0.719	1.00
55_L	59_S	0.714	1.00
46_T	50_G	0.709	1.00
32_G	54_T	0.704	1.00
5_A	10_A	0.698	1.00
40_L	47_L	0.698	1.00
57_A	69_A	0.698	1.00
38_A	42_N	0.687	1.00
7_T	10_A	0.677	1.00
48_S	68_S	0.657	1.00
45_G	55_L	0.647	1.00
4_G	8_V	0.638	1.00
33_L	53_L	0.631	1.00
40_L	43_N	0.628	1.00
48_S	70_Q	0.618	1.00
54_T	74_D	0.609	1.00
46_T	49_S	0.606	1.00
30_G	34_T	0.606	1.00
49_S	52_A	0.603	1.00
28_S	46_T	0.601	1.00
23_Q	27_L	0.599	1.00
3_A	10_A	0.597	1.00
11_A	39_G	0.596	1.00
29_S	32_G	0.594	1.00
59_S	63_N	0.590	1.00
23_Q	42_N	0.580	1.00
4_G	11_A	0.573	1.00
29_S	49_S	0.570	1.00
65_G	76_S	0.552	1.00
66_T	69_A	0.536	1.00
19_L	38_A	0.532	1.00
66_T	70_Q	0.531	1.00
66_T	72_D	0.530	1.00
54_T	71_G	0.523	1.00
3_A	29_S	0.512	1.00
43_N	63_N	0.511	1.00
51_G	71_G	0.503	0.99
32_G	49_S	0.502	0.99
70_Q	73_L	0.500	0.99

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	0.9351	81.6	0.621	Contact Map
4i84A	1	0.987	8.6	0.792	Contact Map
4peuA	1	0.9351	7.6	0.796	Contact Map
1wxrA	1	0.9481	6.6	0.802	Contact Map
3h09A	1	0.8831	4.8	0.815	Contact Map
2odlA	1	0.987	4.8	0.815	Contact Map
4nu3A	2	0.6883	4.4	0.818	Contact Map
3vn3A	1	0.6753	4.4	0.818	Contact Map
4mtkA	4	0.8961	3.6	0.826	Contact Map
4nuhA	1	0.6753	3.2	0.829	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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