DUF260 - PFAM28P - GREMLIN Contacts

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DUF260 - Protein of unknown function DUF260

PFAM:	PF03195	Sequences: PCAACKFLRRKCTPDCVFAPYFPADQPQKFANVHKVFGASNVSKLLQELPPHQRADAVNSLVYEANARLRDPVYGCVGLISALQQQVCQLQAELAAAQQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	99 (98)
Sequences:	1026 (487)
Seq/√Len:	49.2
META:	0.044

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
49_L	57_A	5.999	1.00
33_V	42_V	5.665	1.00
76_C	80_I	2.789	1.00
40_S	44_K	2.635	1.00
8_L	39_A	2.124	1.00
6_K	11_K	2.087	1.00
68_R	73_V	2.015	1.00
61_L	65_A	1.986	0.99
71_D	78_G	1.899	0.99
93_E	97_A	1.817	0.99
30_F	39_A	1.763	0.99
41_N	44_K	1.757	0.99
1_P	39_A	1.646	0.98
32_N	66_N	1.581	0.97
6_K	9_R	1.576	0.97
83_L	86_Q	1.521	0.97
18_F	43_S	1.508	0.96
22_F	30_F	1.476	0.96
74_Y	77_V	1.470	0.96
2_C	5_C	1.467	0.96
26_Q	29_K	1.393	0.95
88_C	92_A	1.373	0.94
80_I	83_L	1.353	0.94
61_L	66_N	1.351	0.94
3_A	23_P	1.345	0.93
35_K	65_A	1.323	0.93
38_G	41_N	1.298	0.92
60_S	78_G	1.268	0.91
10_R	14_P	1.250	0.91
87_V	90_L	1.241	0.90
95_A	98_Q	1.237	0.90
29_K	66_N	1.230	0.90
7_F	18_F	1.213	0.89
55_A	59_N	1.180	0.88
68_R	76_C	1.166	0.87
19_A	22_F	1.157	0.87
1_P	8_L	1.152	0.87
56_D	63_Y	1.141	0.86
90_L	93_E	1.138	0.86
53_Q	70_R	1.138	0.86
18_F	39_A	1.125	0.85
66_N	86_Q	1.106	0.84
30_F	41_N	1.104	0.84
62_V	67_A	1.090	0.83
7_F	45_L	1.090	0.83
50_P	53_Q	1.087	0.83
43_S	62_V	1.076	0.83
22_F	33_V	1.039	0.80
74_Y	78_G	1.034	0.80
71_D	80_I	1.024	0.79
4_A	9_R	1.015	0.79
71_D	91_Q	1.006	0.78
68_R	72_P	0.978	0.76
33_V	65_A	0.960	0.75
17_V	46_L	0.956	0.74
34_H	42_V	0.954	0.74
27_P	31_A	0.946	0.74
14_P	17_V	0.946	0.74
39_A	43_S	0.922	0.72
77_V	82_A	0.901	0.70
63_Y	70_R	0.876	0.68
86_Q	89_Q	0.866	0.67
92_A	96_A	0.839	0.64
6_K	10_R	0.828	0.63
2_C	22_F	0.828	0.63
27_P	61_L	0.807	0.61
36_V	91_Q	0.798	0.61
6_K	87_V	0.795	0.60
61_L	81_S	0.795	0.60
32_N	45_L	0.795	0.60
91_Q	96_A	0.788	0.60
50_P	84_Q	0.779	0.59
91_Q	98_Q	0.779	0.59
61_L	87_V	0.771	0.58
21_Y	44_K	0.769	0.58
29_K	58_V	0.756	0.56
12_C	16_C	0.755	0.56
87_V	98_Q	0.749	0.56
64_E	76_C	0.748	0.56
50_P	91_Q	0.743	0.55
89_Q	93_E	0.742	0.55
8_L	69_L	0.742	0.55
53_Q	61_L	0.739	0.55
21_Y	25_D	0.734	0.54
62_V	66_N	0.729	0.54
21_Y	55_A	0.727	0.53
5_C	12_C	0.727	0.53
37_F	81_S	0.721	0.53
87_V	91_Q	0.716	0.52
92_A	95_A	0.707	0.51
24_A	89_Q	0.701	0.51
26_Q	70_R	0.689	0.50
69_L	74_Y	0.687	0.49
7_F	59_N	0.681	0.49
28_Q	55_A	0.679	0.49
38_G	57_A	0.673	0.48
65_A	90_L	0.673	0.48
2_C	12_C	0.672	0.48
3_A	33_V	0.672	0.48
32_N	42_V	0.666	0.47
85_Q	88_C	0.661	0.47
1_P	18_F	0.654	0.46
75_G	80_I	0.650	0.46
46_L	68_R	0.635	0.44
31_A	40_S	0.634	0.44
52_H	70_R	0.631	0.44
4_A	14_P	0.630	0.44
84_Q	87_V	0.628	0.43
34_H	38_G	0.627	0.43
34_H	41_N	0.625	0.43
46_L	57_A	0.624	0.43
20_P	76_C	0.617	0.42
68_R	74_Y	0.604	0.41
48_E	59_N	0.599	0.41
45_L	57_A	0.599	0.41
47_Q	62_V	0.598	0.40
19_A	36_V	0.598	0.40
24_A	87_V	0.598	0.40
36_V	79_L	0.593	0.40
23_P	78_G	0.592	0.40
27_P	53_Q	0.589	0.40
63_Y	80_I	0.577	0.38
88_C	97_A	0.575	0.38
69_L	85_Q	0.575	0.38
91_Q	95_A	0.571	0.38
29_K	71_D	0.570	0.38
55_A	98_Q	0.569	0.38
47_Q	94_L	0.566	0.37
49_L	97_A	0.559	0.37
26_Q	90_L	0.559	0.37
55_A	82_A	0.556	0.36
81_S	85_Q	0.555	0.36
73_V	94_L	0.542	0.35
29_K	46_L	0.538	0.35
88_C	95_A	0.537	0.35
82_A	86_Q	0.523	0.33
76_C	86_Q	0.522	0.33
17_V	65_A	0.521	0.33
29_K	97_A	0.520	0.33
65_A	76_C	0.514	0.33
26_Q	49_L	0.514	0.33
51_P	62_V	0.512	0.32
12_C	20_P	0.508	0.32
18_F	45_L	0.504	0.32
36_V	39_A	0.501	0.31
20_P	40_S	0.500	0.31
21_Y	58_V	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
2er8A	1	0.6465	19.5	0.919	Contact Map
1zmeC	2	0.6364	19.5	0.919	Contact Map
3i00A	2	0.5253	16.7	0.922	Contact Map
4dznA	3	0.2222	14.8	0.924	Contact Map
2ic6A	1	0.2424	13.9	0.925	Contact Map
1hwtC	2	0.6465	11.7	0.927	Contact Map
4y66B	1	0.8889	10.7	0.929	Contact Map
1pyiA	2	0.6465	8.9	0.931	Contact Map
1am9A	2	0.6566	8.4	0.932	Contact Map
1z0jB	1	0.4848	8.1	0.932	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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