DUF4833 - PFAM28P - GREMLIN Contacts

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DUF4833 - Domain of unknown function (DUF4833)

PFAM:	PF16117	Sequences: FYIQRSKNANTVVYDANLDADGKLDPKEPVHVYWIRYAEDGQREELNFIQRKFAYGIKVKPIGNGSYELRLVAYKKRPITLRKDADGKYRAYTTINGKPAILERIYVKAEGGSFWLPKVEYVELFGTDLATGKPVYER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	138 (138)
Sequences:	2112 (1719)
Seq/√Len:	146.3
META:	0.929

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_D	33_Y	3.255	1.00
95_I	100_A	3.068	1.00
79_I	91_A	3.035	1.00
123_E	138_R	3.023	1.00
83_K	89_Y	2.589	1.00
128_D	131_T	2.572	1.00
6_S	109_A	2.517	1.00
6_S	108_K	2.474	1.00
98_K	128_D	2.399	1.00
16_A	24_L	2.198	1.00
100_A	135_V	2.169	1.00
108_K	120_E	2.165	1.00
90_R	101_I	2.150	1.00
9_A	38_A	2.130	1.00
4_Q	11_T	2.116	1.00
69_L	91_A	2.024	1.00
68_E	78_P	2.022	1.00
39_E	42_Q	1.920	1.00
77_R	137_E	1.915	1.00
19_D	23_K	1.825	1.00
103_E	127_T	1.818	1.00
11_T	37_Y	1.777	1.00
26_P	61_P	1.722	1.00
110_E	120_E	1.721	1.00
125_F	136_Y	1.694	1.00
70_R	78_P	1.691	1.00
15_D	31_H	1.649	1.00
31_H	43_R	1.625	1.00
108_K	121_Y	1.622	1.00
2_Y	11_T	1.615	1.00
123_E	136_Y	1.599	1.00
7_K	109_A	1.591	1.00
36_R	50_Q	1.561	1.00
36_R	44_E	1.536	1.00
61_P	67_Y	1.521	1.00
101_I	129_L	1.501	1.00
47_N	50_Q	1.449	1.00
31_H	45_E	1.430	1.00
17_N	31_H	1.409	1.00
19_D	25_D	1.402	1.00
32_V	46_L	1.362	1.00
5_R	8_N	1.342	1.00
66_S	82_R	1.334	1.00
32_V	57_I	1.329	1.00
81_L	91_A	1.300	1.00
17_N	25_D	1.274	1.00
102_L	105_I	1.266	1.00
94_T	99_P	1.244	1.00
77_R	124_L	1.221	1.00
112_G	115_W	1.215	1.00
19_D	26_P	1.176	1.00
104_R	125_F	1.173	1.00
68_E	80_T	1.137	0.99
36_R	47_N	1.129	0.99
84_D	90_R	1.126	0.99
3_I	55_Y	1.121	0.99
36_R	39_E	1.116	0.99
36_R	42_Q	1.108	0.99
4_Q	104_R	1.108	0.99
28_E	31_H	1.106	0.99
66_S	80_T	1.096	0.99
127_T	134_P	1.089	0.99
4_Q	106_Y	1.084	0.99
95_I	126_G	1.070	0.99
77_R	93_T	1.062	0.99
12_V	34_W	1.056	0.99
2_Y	13_V	1.045	0.99
63_G	66_S	1.039	0.99
30_V	81_L	1.019	0.99
16_A	89_Y	1.017	0.99
30_V	69_L	1.017	0.99
82_R	99_P	0.993	0.99
44_E	47_N	0.976	0.98
69_L	79_I	0.964	0.98
26_P	67_Y	0.948	0.98
5_R	12_V	0.944	0.98
79_I	102_L	0.938	0.98
55_Y	73_A	0.934	0.98
46_L	50_Q	0.928	0.98
111_G	117_P	0.927	0.98
59_V	69_L	0.914	0.98
60_K	68_E	0.913	0.98
101_I	127_T	0.897	0.97
7_K	11_T	0.894	0.97
38_A	42_Q	0.892	0.97
125_F	134_P	0.877	0.97
4_Q	37_Y	0.874	0.97
58_K	72_V	0.869	0.97
25_D	28_E	0.861	0.96
50_Q	57_I	0.859	0.96
128_D	133_K	0.846	0.96
8_N	45_E	0.846	0.96
102_L	124_L	0.828	0.96
3_I	6_S	0.825	0.96
57_I	71_L	0.812	0.95
82_R	92_Y	0.787	0.94
111_G	120_E	0.780	0.94
3_I	14_Y	0.777	0.94
37_Y	41_G	0.775	0.94
121_Y	138_R	0.773	0.94
74_Y	105_I	0.771	0.94
5_R	9_A	0.769	0.94
128_D	135_V	0.755	0.93
13_V	37_Y	0.753	0.93
2_Y	37_Y	0.752	0.93
6_S	106_Y	0.751	0.93
92_Y	99_P	0.747	0.93
10_N	50_Q	0.745	0.92
12_V	36_R	0.744	0.92
111_G	115_W	0.744	0.92
44_E	107_V	0.741	0.92
5_R	34_W	0.741	0.92
27_K	75_K	0.737	0.92
83_K	88_K	0.734	0.92
30_V	57_I	0.732	0.92
27_K	60_K	0.728	0.92
107_V	121_Y	0.720	0.91
59_V	62_I	0.717	0.91
112_G	117_P	0.716	0.91
7_K	10_N	0.716	0.91
47_N	51_R	0.713	0.91
42_Q	50_Q	0.709	0.90
36_R	41_G	0.706	0.90
84_D	87_G	0.704	0.90
16_A	83_K	0.703	0.90
48_F	52_K	0.703	0.90
16_A	30_V	0.702	0.90
110_E	114_F	0.700	0.90
84_D	88_K	0.700	0.90
62_I	65_G	0.698	0.90
107_V	116_L	0.681	0.89
112_G	116_L	0.678	0.88
127_T	132_G	0.675	0.88
52_K	72_V	0.668	0.88
83_K	87_G	0.666	0.87
77_R	100_A	0.662	0.87
57_I	69_L	0.661	0.87
5_R	109_A	0.657	0.87
92_Y	129_L	0.646	0.86
70_R	75_K	0.640	0.85
62_I	66_S	0.639	0.85
13_V	33_Y	0.631	0.85
84_D	101_I	0.631	0.85
103_E	134_P	0.628	0.84
74_Y	77_R	0.628	0.84
23_K	61_P	0.626	0.84
54_A	67_Y	0.620	0.84
128_D	132_G	0.615	0.83
111_G	114_F	0.615	0.83
96_N	137_E	0.614	0.83
100_A	124_L	0.609	0.82
71_L	122_V	0.604	0.82
71_L	75_K	0.601	0.82
96_N	135_V	0.601	0.82
49_I	111_G	0.597	0.81
84_D	92_Y	0.597	0.81
11_T	15_D	0.590	0.80
1_F	5_R	0.590	0.80
55_Y	72_V	0.589	0.80
126_G	129_L	0.589	0.80
95_I	137_E	0.587	0.80
63_G	68_E	0.586	0.80
60_K	70_R	0.582	0.80
113_S	122_V	0.582	0.80
11_T	16_A	0.580	0.79
20_A	27_K	0.579	0.79
36_R	45_E	0.577	0.79
34_W	117_P	0.572	0.78
12_V	105_I	0.572	0.78
14_Y	32_V	0.568	0.78
61_P	64_N	0.565	0.78
10_N	36_R	0.564	0.77
93_T	102_L	0.562	0.77
39_E	44_E	0.560	0.77
78_P	93_T	0.558	0.77
15_D	22_G	0.553	0.76
82_R	101_I	0.552	0.76
50_Q	89_Y	0.552	0.76
35_I	43_R	0.546	0.75
39_E	46_L	0.545	0.75
48_F	53_F	0.545	0.75
31_H	57_I	0.544	0.75
35_I	41_G	0.543	0.75
42_Q	45_E	0.543	0.75
35_I	89_Y	0.543	0.75
62_I	68_E	0.543	0.75
46_L	108_K	0.542	0.75
82_R	90_R	0.542	0.75
10_N	38_A	0.537	0.74
98_K	130_A	0.536	0.74
24_L	93_T	0.534	0.73
53_F	119_V	0.533	0.73
13_V	17_N	0.533	0.73
75_K	79_I	0.532	0.73
2_Y	67_Y	0.529	0.73
15_D	35_I	0.524	0.72
13_V	18_L	0.519	0.71
107_V	122_V	0.519	0.71
120_E	123_E	0.518	0.71
3_I	13_V	0.516	0.71
28_E	82_R	0.516	0.71
79_I	93_T	0.512	0.70
77_R	97_G	0.509	0.70
121_Y	136_Y	0.507	0.70
109_A	112_G	0.505	0.69
53_F	116_L	0.502	0.69
49_I	136_Y	0.500	0.69

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
1uebA	1	0.3768	9.2	0.935	Contact Map
3cpfA	1	0.3913	8.5	0.936	Contact Map
3a5zB	1	0.3768	7.2	0.939	Contact Map
3oyyA	1	0.3986	7.1	0.939	Contact Map
3treA	1	0.3768	6.1	0.94	Contact Map
3f6yA	2	0.6667	5.5	0.942	Contact Map
1bkbA	3	0.442	4.7	0.944	Contact Map
3payA	4	0.3768	3.8	0.946	Contact Map
1isiA	2	0.6667	3.6	0.947	Contact Map
1khiA	1	0.413	3.1	0.948	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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