DUF479 - PFAM28P - GREMLIN Contacts

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DUF479 - Protein of unknown function, DUF479

PFAM:	PF04336	Sequences: YDHFLAKNWSRYSDEPLEDFTQRVYALLEENYDLLPERLQRMLPYMIEQNWLYSYATLEGIERALEGMSRRTKRPSPLAEAIEELEEHYDELEEDFREFFPELIA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (104)
Sequences:	8948 (6983)
Seq/√Len:	684.7
META:	0.878

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_L	86_E	2.830	1.00
29_E	47_I	2.791	1.00
50_N	53_Y	2.789	1.00
32_Y	40_Q	2.339	1.00
93_E	97_R	2.152	1.00
88_H	91_E	2.047	1.00
62_E	66_E	2.041	1.00
11_R	97_R	1.973	1.00
1_Y	95_D	1.934	1.00
12_Y	97_R	1.899	1.00
8_N	97_R	1.866	1.00
77_P	80_E	1.853	1.00
15_E	23_R	1.845	1.00
3_H	89_Y	1.759	1.00
8_N	11_R	1.758	1.00
21_T	53_Y	1.738	1.00
8_N	93_E	1.730	1.00
63_R	67_G	1.694	1.00
62_E	82_I	1.634	1.00
18_E	53_Y	1.623	1.00
31_N	34_L	1.613	1.00
25_Y	50_N	1.607	1.00
64_A	67_G	1.533	1.00
91_E	95_D	1.498	1.00
4_F	89_Y	1.495	1.00
57_T	60_G	1.479	1.00
6_A	17_L	1.474	1.00
67_G	70_R	1.416	1.00
43_L	47_I	1.413	1.00
7_K	93_E	1.362	1.00
69_S	79_A	1.361	1.00
17_L	21_T	1.323	1.00
72_T	76_S	1.310	1.00
18_E	22_Q	1.284	1.00
69_S	76_S	1.255	1.00
53_Y	56_A	1.236	1.00
45_Y	49_Q	1.194	1.00
94_E	98_E	1.191	1.00
16_P	19_D	1.175	1.00
58_L	89_Y	1.162	1.00
89_Y	93_E	1.138	1.00
20_F	24_V	1.135	1.00
7_K	89_Y	1.130	1.00
83_E	87_E	1.129	1.00
58_L	82_I	1.124	1.00
96_F	100_F	1.117	1.00
92_L	95_D	1.111	1.00
42_M	51_W	1.082	1.00
41_R	45_Y	1.073	1.00
91_E	94_E	1.057	1.00
3_H	7_K	1.046	1.00
18_E	50_N	1.038	1.00
90_D	93_E	1.033	1.00
6_A	56_A	1.021	1.00
101_P	104_I	1.010	1.00
21_T	50_N	0.988	1.00
29_E	43_L	0.984	1.00
27_L	31_N	0.980	1.00
64_A	68_M	0.980	1.00
24_V	28_L	0.976	1.00
80_E	83_E	0.974	1.00
39_L	44_P	0.971	1.00
44_P	48_E	0.952	1.00
37_E	41_R	0.948	1.00
23_R	27_L	0.940	1.00
97_R	101_P	0.939	1.00
88_H	92_L	0.937	1.00
72_T	75_P	0.937	1.00
84_E	88_H	0.932	1.00
82_I	86_E	0.931	1.00
29_E	32_Y	0.908	1.00
26_A	30_E	0.901	1.00
65_L	81_A	0.901	1.00
69_S	78_L	0.899	1.00
35_L	43_L	0.881	1.00
21_T	25_Y	0.867	1.00
100_F	103_L	0.860	1.00
98_E	101_P	0.853	1.00
55_Y	64_A	0.851	1.00
39_L	42_M	0.841	1.00
46_M	51_W	0.841	1.00
18_E	21_T	0.819	1.00
83_E	86_E	0.802	1.00
6_A	21_T	0.792	1.00
54_S	57_T	0.789	1.00
51_W	67_G	0.788	1.00
58_L	62_E	0.787	1.00
98_E	102_E	0.779	1.00
9_W	12_Y	0.778	1.00
60_G	64_A	0.773	1.00
32_Y	35_L	0.769	1.00
19_D	23_R	0.759	1.00
21_T	52_L	0.756	1.00
4_F	93_E	0.756	1.00
59_E	62_E	0.736	1.00
66_E	69_S	0.729	1.00
84_E	87_E	0.722	1.00
90_D	94_E	0.717	1.00
28_L	43_L	0.712	1.00
15_E	19_D	0.711	1.00
37_E	40_Q	0.710	1.00
61_I	65_L	0.707	1.00
51_W	64_A	0.702	1.00
24_V	27_L	0.700	1.00
58_L	85_L	0.693	1.00
69_S	73_K	0.692	1.00
39_L	43_L	0.678	1.00
27_L	30_E	0.676	1.00
85_L	89_Y	0.673	1.00
13_S	100_F	0.672	1.00
8_N	12_Y	0.667	1.00
40_Q	44_P	0.665	1.00
66_E	79_A	0.665	1.00
74_R	77_P	0.662	1.00
73_K	76_S	0.655	1.00
46_M	52_L	0.650	1.00
82_I	85_L	0.640	1.00
49_Q	67_G	0.637	1.00
45_Y	48_E	0.636	1.00
54_S	64_A	0.632	1.00
42_M	45_Y	0.628	1.00
66_E	70_R	0.620	1.00
35_L	39_L	0.613	1.00
4_F	8_N	0.605	1.00
42_M	46_M	0.603	1.00
99_F	102_E	0.602	1.00
3_H	6_A	0.599	1.00
63_R	66_E	0.597	1.00
66_E	80_E	0.595	1.00
21_T	24_V	0.589	1.00
12_Y	17_L	0.587	1.00
28_L	35_L	0.584	1.00
88_H	95_D	0.580	1.00
75_P	79_A	0.574	1.00
45_Y	67_G	0.568	1.00
86_E	89_Y	0.567	1.00
38_R	42_M	0.565	1.00
78_L	84_E	0.563	1.00
25_Y	47_I	0.562	1.00
55_Y	68_M	0.555	1.00
58_L	61_I	0.554	1.00
54_S	63_R	0.553	1.00
94_E	97_R	0.551	1.00
45_Y	51_W	0.548	1.00
100_F	104_I	0.547	1.00
4_F	85_L	0.546	1.00
95_D	98_E	0.543	1.00
23_R	26_A	0.539	1.00
32_Y	44_P	0.531	1.00
12_Y	100_F	0.522	1.00
69_S	75_P	0.516	0.99
99_F	103_L	0.508	0.99
62_E	86_E	0.508	0.99
18_E	56_A	0.501	0.99
38_R	41_R	0.500	0.99
4_F	92_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
1wa5C	1	1	13.3	0.896	Contact Map
4hpqC	2	0.9619	6.3	0.91	Contact Map
1h2vC	1	0.4095	5.5	0.913	Contact Map
3zqeA	1	0.9143	5.2	0.914	Contact Map
3gjxA	1	0.9524	4.7	0.916	Contact Map
4ow8A	2	0.7333	4.7	0.916	Contact Map
4fgvA	1	0.9524	4.4	0.917	Contact Map
3a6pA	1	0.9524	4.2	0.918	Contact Map
1g1eB	1	0.8476	4.1	0.918	Contact Map
4po5B	3	0.6381	4	0.918	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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