DUF3433 - PFAM28P - GREMLIN Contacts

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DUF3433 - Protein of unknown function (DUF3433)

PFAM:	PF11915	Sequences: FLWTYLPTLLAVLLALLWQSIDFAVRRLQPFAQLSRGGAPASRSLLLDYLSLLPLLVLFKALRNRHWLVALSSLASLLASLLTILASG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	88 (87)
Sequences:	2053 (1693)
Seq/√Len:	181.5
META:	0.478

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_Q	33_Q	3.785	1.00
22_D	26_R	3.690	1.00
25_V	72_S	2.760	1.00
22_D	72_S	2.669	1.00
33_Q	66_H	2.570	1.00
39_A	44_S	2.548	1.00
24_A	27_R	2.429	1.00
61_A	70_A	2.375	1.00
62_L	70_A	2.104	1.00
49_Y	66_H	1.903	1.00
43_R	64_N	1.745	1.00
67_W	70_A	1.583	1.00
11_A	86_A	1.529	1.00
3_W	11_A	1.503	1.00
41_A	46_L	1.500	1.00
52_L	60_K	1.490	1.00
41_A	44_S	1.443	1.00
79_A	82_L	1.433	1.00
49_Y	69_V	1.386	1.00
34_L	45_L	1.369	1.00
80_S	84_I	1.369	1.00
41_A	45_L	1.314	1.00
80_S	86_A	1.314	1.00
22_D	73_S	1.295	1.00
40_P	43_R	1.289	1.00
29_Q	66_H	1.286	1.00
33_Q	43_R	1.282	1.00
61_A	69_V	1.263	1.00
2_L	6_L	1.227	1.00
29_Q	32_A	1.182	1.00
83_T	87_S	1.135	1.00
67_W	71_L	1.134	1.00
16_L	19_Q	1.130	1.00
58_L	73_S	1.129	1.00
39_A	43_R	1.123	1.00
53_L	56_L	1.123	1.00
79_A	84_I	1.113	1.00
17_L	20_S	1.091	1.00
47_L	66_H	1.067	1.00
31_F	79_A	1.045	1.00
18_W	72_S	1.043	1.00
3_W	7_P	1.042	1.00
80_S	83_T	1.034	1.00
81_L	84_I	1.029	1.00
23_F	50_L	1.019	0.99
49_Y	64_N	0.988	0.99
59_F	63_R	0.971	0.99
13_L	17_L	0.970	0.99
15_A	83_T	0.934	0.99
8_T	20_S	0.932	0.99
25_V	68_L	0.917	0.99
33_Q	44_S	0.913	0.99
58_L	61_A	0.890	0.99
15_A	19_Q	0.889	0.99
56_L	60_K	0.883	0.99
2_L	7_P	0.878	0.98
20_S	31_F	0.877	0.98
52_L	56_L	0.875	0.98
5_Y	12_V	0.859	0.98
23_F	69_V	0.855	0.98
8_T	11_A	0.853	0.98
37_G	43_R	0.846	0.98
29_Q	68_L	0.843	0.98
18_W	75_A	0.841	0.98
13_L	18_W	0.841	0.98
28_L	82_L	0.827	0.98
1_F	6_L	0.822	0.98
77_L	80_S	0.821	0.98
72_S	76_S	0.812	0.97
55_L	58_L	0.808	0.97
26_R	69_V	0.797	0.97
22_D	69_V	0.796	0.97
35_S	53_L	0.793	0.97
20_S	24_A	0.786	0.97
14_L	33_Q	0.782	0.97
9_L	35_S	0.765	0.96
44_S	47_L	0.759	0.96
55_L	59_F	0.746	0.96
19_Q	23_F	0.745	0.96
11_A	83_T	0.742	0.96
28_L	32_A	0.738	0.96
78_L	85_L	0.725	0.95
17_L	78_L	0.719	0.95
76_S	80_S	0.717	0.95
23_F	31_F	0.694	0.94
19_Q	72_S	0.688	0.93
78_L	82_L	0.680	0.93
64_N	67_W	0.673	0.93
29_Q	49_Y	0.665	0.92
76_S	83_T	0.658	0.92
23_F	27_R	0.639	0.91
10_L	63_R	0.634	0.90
20_S	83_T	0.632	0.90
32_A	35_S	0.630	0.90
25_V	69_V	0.618	0.89
19_Q	57_V	0.613	0.89
57_V	65_R	0.606	0.88
34_L	75_A	0.597	0.88
2_L	82_L	0.597	0.88
34_L	77_L	0.595	0.87
67_W	78_L	0.594	0.87
37_G	41_A	0.592	0.87
29_Q	73_S	0.592	0.87
69_V	78_L	0.586	0.87
60_K	63_R	0.570	0.85
16_L	70_A	0.569	0.85
59_F	62_L	0.563	0.84
16_L	26_R	0.561	0.84
33_Q	58_L	0.557	0.84
54_P	58_L	0.555	0.84
8_T	12_V	0.553	0.83
34_L	38_G	0.552	0.83
26_R	57_V	0.551	0.83
1_F	4_T	0.545	0.82
6_L	13_L	0.542	0.82
7_P	69_V	0.540	0.82
68_L	72_S	0.537	0.82
24_A	31_F	0.536	0.81
36_R	39_A	0.535	0.81
25_V	28_L	0.532	0.81
64_N	70_A	0.532	0.81
52_L	71_L	0.526	0.80
40_P	45_L	0.525	0.80
6_L	11_A	0.523	0.80
1_F	85_L	0.520	0.79
81_L	86_A	0.512	0.78
75_A	78_L	0.511	0.78
12_V	17_L	0.510	0.78
48_D	69_V	0.509	0.78
10_L	34_L	0.500	0.77

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
4wl1A	3	0	5.6	0.877	Contact Map
3w9iA	3	0.8523	3.9	0.886	Contact Map
4dx5A	3	0.8523	3.4	0.89	Contact Map
4mt1A	3	0.8523	3.3	0.89	Contact Map
4k0jA	3	0.8295	2.9	0.893	Contact Map
2dw3A	1	0.5455	2.4	0.898	Contact Map
3aqpA	1	0.8523	2.1	0.901	Contact Map
3mqzA	1	0.3409	1.9	0.903	Contact Map
3ne5A	3	0.9659	1.7	0.906	Contact Map
3b5xA	2	0.4205	1.6	0.907	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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