DUF523 - PFAM28P - GREMLIN Contacts

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DUF523 - Protein of unknown function (DUF523)

PFAM:	PF04463	Sequences: IGVSACLLGENVRYDGGHKRDRFLTDTLGRLVKEEFVPVCPEVEGGLGTPREPARLGPRVTTKTGRDVTEAMLRGAEERLEELKEEGLDGAILKSRSPSCGMERVYDGTFSGPLRKGRGVFAALLMERGPLLPVEEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	137 (134)
Sequences:	14481 (10624)
Seq/√Len:	917.8
META:	0.843

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_R	126_M	3.528	1.00
43_V	49_T	2.874	1.00
11_N	18_H	2.750	1.00
52_E	64_T	2.392	1.00
102_M	126_M	2.372	1.00
123_A	127_E	2.361	1.00
5_A	10_E	2.320	1.00
59_R	67_D	2.089	1.00
118_R	123_A	2.056	1.00
124_L	127_E	1.993	1.00
54_A	68_V	1.958	1.00
93_L	122_A	1.948	1.00
52_E	63_K	1.894	1.00
103_E	118_R	1.893	1.00
13_R	19_K	1.839	1.00
45_G	71_A	1.826	1.00
104_R	116_K	1.804	1.00
52_E	62_T	1.674	1.00
20_R	25_T	1.673	1.00
84_K	128_R	1.642	1.00
77_E	124_L	1.637	1.00
2_G	91_A	1.628	1.00
10_E	38_P	1.626	1.00
90_G	131_L	1.625	1.00
90_G	133_P	1.601	1.00
32_V	36_F	1.560	1.00
47_L	68_V	1.555	1.00
62_T	66_R	1.535	1.00
126_M	134_V	1.462	1.00
95_S	134_V	1.446	1.00
68_V	71_A	1.431	1.00
74_R	78_E	1.418	1.00
66_R	71_A	1.403	1.00
124_L	128_R	1.402	1.00
94_K	135_E	1.370	1.00
58_P	123_A	1.311	1.00
96_R	114_L	1.293	1.00
44_E	79_R	1.280	1.00
56_L	123_A	1.268	1.00
52_E	61_T	1.267	1.00
78_E	81_E	1.236	1.00
79_R	121_F	1.233	1.00
8_L	38_P	1.232	1.00
81_E	128_R	1.230	1.00
8_L	36_F	1.221	1.00
96_R	104_R	1.220	1.00
101_G	105_V	1.200	1.00
45_G	75_G	1.195	1.00
70_E	74_R	1.195	1.00
39_V	44_E	1.180	1.00
76_A	124_L	1.145	1.00
91_A	130_P	1.139	1.00
78_E	82_E	1.139	1.00
107_D	111_S	1.130	1.00
73_L	124_L	1.129	1.00
80_L	128_R	1.123	1.00
93_L	125_L	1.120	1.00
53_P	62_T	1.120	1.00
53_P	63_K	1.112	1.00
61_T	66_R	1.109	1.00
95_S	103_E	1.107	1.00
2_G	83_L	1.103	1.00
45_G	54_A	1.098	1.00
81_E	84_K	1.093	1.00
107_D	110_F	1.079	1.00
54_A	62_T	1.075	1.00
25_T	29_G	1.070	1.00
54_A	72_M	1.067	1.00
125_L	132_L	1.061	1.00
22_R	26_D	1.037	1.00
61_T	68_V	1.037	1.00
2_G	88_L	1.036	1.00
29_G	32_V	1.030	1.00
79_R	82_E	1.027	1.00
73_L	77_E	1.023	1.00
54_A	60_V	1.013	1.00
95_S	136_E	1.007	1.00
47_L	54_A	1.001	1.00
21_D	24_L	0.997	1.00
102_M	134_V	0.993	1.00
61_T	65_G	0.992	1.00
73_L	120_V	0.991	1.00
81_E	85_E	0.990	1.00
61_T	64_T	0.988	1.00
72_M	99_S	0.986	1.00
80_L	124_L	0.970	1.00
3_V	36_F	0.963	1.00
102_M	132_L	0.953	1.00
56_L	120_V	0.943	1.00
75_G	79_R	0.935	1.00
20_R	29_G	0.920	1.00
107_D	112_G	0.917	1.00
15_D	19_K	0.911	1.00
20_R	26_D	0.906	1.00
79_R	125_L	0.890	1.00
45_G	72_M	0.889	1.00
31_L	36_F	0.880	1.00
107_D	113_P	0.869	1.00
39_V	75_G	0.848	1.00
23_F	27_T	0.844	1.00
88_L	91_A	0.844	1.00
43_V	48_G	0.843	1.00
5_A	38_P	0.842	1.00
12_V	43_V	0.837	1.00
58_P	120_V	0.837	1.00
95_S	102_M	0.835	1.00
39_V	79_R	0.832	1.00
56_L	60_V	0.831	1.00
99_S	121_F	0.828	1.00
72_M	75_G	0.819	1.00
62_T	65_G	0.814	1.00
105_V	118_R	0.813	1.00
73_L	123_A	0.810	1.00
5_A	12_V	0.805	1.00
102_M	118_R	0.795	1.00
76_A	80_L	0.782	1.00
27_T	30_R	0.770	1.00
45_G	68_V	0.762	1.00
96_R	136_E	0.762	1.00
55_R	106_Y	0.762	1.00
5_A	44_E	0.762	1.00
69_T	73_L	0.759	1.00
60_V	65_G	0.759	1.00
104_R	114_L	0.758	1.00
2_G	39_V	0.757	1.00
79_R	83_L	0.736	1.00
23_F	32_V	0.734	1.00
83_L	88_L	0.733	1.00
96_R	115_R	0.725	1.00
44_E	75_G	0.717	1.00
82_E	86_E	0.714	1.00
77_E	81_E	0.711	1.00
118_R	122_A	0.705	1.00
47_L	71_A	0.702	1.00
44_E	78_E	0.699	1.00
91_A	121_F	0.699	1.00
83_L	130_P	0.690	1.00
122_A	126_M	0.688	1.00
52_E	66_R	0.687	1.00
39_V	83_L	0.684	1.00
68_V	72_M	0.682	1.00
58_P	73_L	0.674	1.00
60_V	64_T	0.668	1.00
28_L	31_L	0.666	1.00
93_L	134_V	0.663	1.00
93_L	102_M	0.662	1.00
3_V	9_G	0.662	1.00
93_L	100_C	0.661	1.00
105_V	117_G	0.659	1.00
2_G	125_L	0.654	1.00
54_A	61_T	0.650	1.00
80_L	129_G	0.646	1.00
74_R	77_E	0.642	1.00
26_D	30_R	0.642	1.00
8_L	25_T	0.630	1.00
14_Y	53_P	0.629	1.00
57_G	73_L	0.624	1.00
104_R	136_E	0.623	1.00
10_E	43_V	0.620	1.00
14_Y	17_G	0.615	1.00
11_N	17_G	0.614	1.00
82_E	85_E	0.609	1.00
24_L	36_F	0.606	1.00
71_A	74_R	0.603	1.00
126_M	132_L	0.600	1.00
115_R	118_R	0.590	1.00
89_D	131_L	0.590	1.00
22_R	25_T	0.590	1.00
95_S	104_R	0.588	1.00
59_R	70_E	0.585	1.00
62_T	68_V	0.583	1.00
75_G	80_L	0.578	1.00
55_R	108_G	0.577	1.00
44_E	82_E	0.574	1.00
39_V	121_F	0.570	1.00
60_V	63_K	0.552	1.00
43_V	46_G	0.548	1.00
107_D	114_L	0.544	1.00
87_G	90_G	0.544	1.00
103_E	136_E	0.543	1.00
9_G	18_H	0.538	1.00
121_F	125_L	0.536	1.00
29_G	36_F	0.532	1.00
27_T	31_L	0.529	1.00
84_K	87_G	0.526	1.00
11_N	20_R	0.524	1.00
24_L	92_I	0.524	1.00
3_V	8_L	0.522	1.00
118_R	127_E	0.519	1.00
5_A	9_G	0.519	1.00
93_L	121_F	0.517	1.00
109_T	113_P	0.514	1.00
28_L	32_V	0.510	1.00
125_L	134_V	0.510	1.00
103_E	134_V	0.508	1.00
24_L	27_T	0.507	1.00
24_L	32_V	0.506	1.00
55_R	110_F	0.505	1.00
31_L	35_E	0.502	1.00
28_L	36_F	0.500	1.00
77_E	128_R	0.500	1.00

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
3tm8A	1	0.5693	8	0.937	Contact Map
4g7wA	1	0.3577	5.5	0.941	Contact Map
3pfnA	4	0.6204	4.7	0.943	Contact Map
3s8pA	1	0.8102	4.4	0.944	Contact Map
4g7xA	1	0.3212	4.3	0.944	Contact Map
2kswA	1	0.3577	3.7	0.946	Contact Map
4l6rA	1	0.2482	3.3	0.947	Contact Map
1u6tA	1	0.3212	3.1	0.947	Contact Map
2yynA	2	0.3066	2.4	0.95	Contact Map
2p2eA	1	0.5328	2.4	0.951	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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