DUF494 - PFAM28P - GREMLIN Contacts

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DUF494 - Protein of unknown function (DUF494)

PFAM:	PF04361	Sequences: MFDVLVYLFENYMEPDACPDRDELARELSAAGFEDDEISKALDWLDGLAEAQESPAAPAPPSSGSIRVYSDEEQERLDTECRGFLLFLEQAGVLDPAQRELVIDRAMALDGDEIDLEDLKWIVLMVLFNQPGQEPAYLWMEDLVFDDEPRLLH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	153 (151)
Sequences:	3922 (2326)
Seq/√Len:	189.3
META:	0.901

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
89_E	99_R	4.050	1.00
94_L	102_V	3.824	1.00
74_Q	82_R	3.786	1.00
81_C	119_L	3.187	1.00
69_Y	82_R	3.085	1.00
106_A	119_L	2.834	1.00
78_D	81_C	2.418	1.00
78_D	82_R	2.191	1.00
76_R	107_M	2.159	1.00
71_D	74_Q	2.159	1.00
85_L	102_V	2.146	1.00
135_P	139_W	2.128	1.00
5_L	9_F	1.997	1.00
79_T	83_G	1.984	1.00
119_L	123_V	1.944	1.00
69_Y	86_L	1.883	1.00
86_L	90_Q	1.857	1.00
84_F	116_L	1.799	1.00
105_R	108_A	1.793	1.00
106_A	122_I	1.757	1.00
89_E	96_P	1.687	1.00
87_F	91_A	1.664	1.00
137_Y	145_F	1.592	1.00
111_G	118_D	1.591	1.00
137_Y	140_M	1.584	1.00
83_G	90_Q	1.564	1.00
29_S	38_I	1.536	1.00
148_E	151_L	1.517	1.00
20_D	23_E	1.512	1.00
132_G	135_P	1.499	1.00
82_R	103_I	1.487	1.00
15_P	18_C	1.470	1.00
139_W	142_D	1.466	1.00
95_D	133_Q	1.458	1.00
115_D	118_D	1.457	1.00
142_D	145_F	1.404	1.00
131_P	136_A	1.395	1.00
106_A	114_I	1.384	1.00
141_E	145_F	1.373	1.00
95_D	98_Q	1.351	1.00
99_R	103_I	1.332	1.00
51_A	101_L	1.308	1.00
141_E	144_V	1.300	1.00
79_T	82_R	1.294	1.00
28_L	38_I	1.293	1.00
77_L	81_C	1.280	1.00
143_L	150_R	1.276	1.00
47_G	108_A	1.241	1.00
21_R	25_A	1.240	1.00
27_E	30_A	1.226	1.00
72_E	107_M	1.225	1.00
1_M	42_L	1.222	1.00
67_R	73_E	1.217	1.00
93_V	98_Q	1.217	1.00
69_Y	99_R	1.212	1.00
26_R	30_A	1.185	1.00
47_G	105_R	1.182	1.00
69_Y	89_E	1.173	1.00
28_L	32_G	1.172	1.00
77_L	106_A	1.169	1.00
76_R	113_E	1.121	1.00
147_D	150_R	1.115	1.00
87_F	90_Q	1.097	1.00
136_A	140_M	1.087	1.00
76_R	110_D	1.079	1.00
37_E	120_K	1.076	1.00
135_P	138_L	1.068	1.00
49_A	129_N	1.065	1.00
109_L	121_W	1.054	1.00
33_F	41_A	1.051	1.00
128_F	138_L	1.046	1.00
77_L	82_R	1.046	1.00
132_G	137_Y	1.044	1.00
145_F	149_P	1.041	1.00
84_F	87_F	1.030	1.00
138_L	143_L	1.026	1.00
134_E	137_Y	1.017	1.00
74_Q	79_T	1.017	1.00
133_Q	143_L	1.012	1.00
138_L	142_D	1.010	1.00
55_P	97_A	0.982	0.99
85_L	103_I	0.977	0.99
33_F	125_M	0.973	0.99
55_P	58_P	0.972	0.99
137_Y	141_E	0.967	0.99
102_V	123_V	0.959	0.99
124_L	128_F	0.940	0.99
51_A	55_P	0.932	0.99
139_W	143_L	0.932	0.99
45_L	100_E	0.926	0.99
55_P	60_P	0.925	0.99
121_W	124_L	0.923	0.99
138_L	145_F	0.912	0.99
85_L	99_R	0.908	0.99
144_V	148_E	0.900	0.99
83_G	86_L	0.894	0.99
145_F	150_R	0.892	0.99
77_L	119_L	0.889	0.99
102_V	119_L	0.877	0.99
9_F	125_M	0.869	0.99
34_E	37_E	0.868	0.99
61_P	95_D	0.855	0.98
40_K	110_D	0.854	0.98
131_P	134_E	0.852	0.98
101_L	125_M	0.852	0.98
28_L	33_F	0.851	0.98
46_D	50_E	0.851	0.98
37_E	105_R	0.850	0.98
114_I	147_D	0.847	0.98
102_V	122_I	0.846	0.98
69_Y	103_I	0.836	0.98
17_A	21_R	0.835	0.98
135_P	141_E	0.835	0.98
144_V	151_L	0.833	0.98
19_P	24_L	0.825	0.98
98_Q	130_Q	0.823	0.98
26_R	29_S	0.815	0.98
63_S	97_A	0.812	0.98
2_F	97_A	0.810	0.98
127_L	130_Q	0.807	0.98
140_M	143_L	0.804	0.98
41_A	105_R	0.785	0.97
129_N	133_Q	0.780	0.97
85_L	119_L	0.771	0.97
145_F	148_E	0.763	0.97
104_D	108_A	0.755	0.97
147_D	151_L	0.753	0.96
89_E	94_L	0.753	0.96
84_F	88_L	0.751	0.96
57_A	97_A	0.739	0.96
29_S	151_L	0.738	0.96
125_M	128_F	0.738	0.96
32_G	38_I	0.737	0.96
108_A	122_I	0.735	0.96
43_D	47_G	0.730	0.96
57_A	60_P	0.726	0.96
12_Y	33_F	0.726	0.96
33_F	38_I	0.726	0.96
133_Q	145_F	0.723	0.96
9_F	13_M	0.721	0.95
88_L	123_V	0.719	0.95
136_A	139_W	0.706	0.95
45_L	48_L	0.704	0.95
10_E	117_E	0.703	0.95
25_A	29_S	0.700	0.95
146_D	150_R	0.695	0.94
8_L	124_L	0.695	0.94
21_R	24_L	0.689	0.94
106_A	150_R	0.684	0.94
134_E	140_M	0.684	0.94
2_F	5_L	0.683	0.94
139_W	151_L	0.672	0.93
140_M	145_F	0.665	0.93
101_L	130_Q	0.663	0.93
55_P	59_A	0.663	0.93
139_W	144_V	0.663	0.93
7_Y	100_E	0.661	0.93
122_I	125_M	0.659	0.93
58_P	75_E	0.659	0.93
2_F	18_C	0.652	0.92
4_V	33_F	0.650	0.92
13_M	111_G	0.648	0.92
1_M	128_F	0.647	0.92
109_L	113_E	0.643	0.92
146_D	151_L	0.637	0.92
132_G	140_M	0.636	0.91
139_W	150_R	0.636	0.91
5_L	96_P	0.634	0.91
146_D	149_P	0.629	0.91
12_Y	27_E	0.626	0.91
138_L	141_E	0.621	0.90
8_L	127_L	0.621	0.90
6_V	9_F	0.620	0.90
123_V	133_Q	0.616	0.90
39_S	43_D	0.608	0.90
1_M	118_D	0.607	0.89
136_A	150_R	0.596	0.89
137_Y	147_D	0.590	0.88
48_L	88_L	0.586	0.88
135_P	140_M	0.585	0.88
31_A	70_S	0.580	0.87
7_Y	27_E	0.577	0.87
44_W	105_R	0.576	0.87
136_A	145_F	0.574	0.87
1_M	138_L	0.573	0.87
137_Y	142_D	0.572	0.87
130_Q	133_Q	0.568	0.86
56_A	97_A	0.567	0.86
4_V	8_L	0.566	0.86
98_Q	129_N	0.566	0.86
3_D	145_F	0.564	0.86
7_Y	31_A	0.560	0.85
51_A	54_S	0.560	0.85
71_D	75_E	0.559	0.85
107_M	112_D	0.559	0.85
22_D	79_T	0.551	0.84
27_E	31_A	0.548	0.84
10_E	124_L	0.547	0.84
41_A	44_W	0.547	0.84
54_S	59_A	0.546	0.84
143_L	151_L	0.546	0.84
139_W	145_F	0.545	0.84
135_P	149_P	0.543	0.84
39_S	66_I	0.542	0.83
64_G	112_D	0.538	0.83
137_Y	146_D	0.536	0.83
84_F	120_K	0.536	0.83
129_N	135_P	0.536	0.83
30_A	34_E	0.532	0.82
69_Y	83_G	0.532	0.82
28_L	45_L	0.529	0.82
34_E	91_A	0.526	0.82
17_A	29_S	0.524	0.81
10_E	27_E	0.521	0.81
62_S	71_D	0.521	0.81
8_L	39_S	0.517	0.81
39_S	42_L	0.514	0.80
41_A	104_D	0.513	0.80
133_Q	137_Y	0.509	0.80
16_D	19_P	0.508	0.79
7_Y	13_M	0.507	0.79
6_V	10_E	0.506	0.79
23_E	30_A	0.505	0.79
84_F	96_P	0.503	0.79
11_N	27_E	0.502	0.79
110_D	113_E	0.500	0.78

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
2dakA	1	0.3399	43	0.904	Contact Map
2jujA	1	0.366	42.1	0.905	Contact Map
4un2B	1	0.2026	37.3	0.907	Contact Map
4dbgB	1	0.3333	36.2	0.908	Contact Map
1z96A	1	0.1765	35.1	0.909	Contact Map
3qr0A	1	0.9935	34.3	0.909	Contact Map
2dahA	1	0.2745	34.3	0.909	Contact Map
1dv0A	1	0.2222	33.9	0.909	Contact Map
2g3qA	1	0.2092	32	0.911	Contact Map
2ragA	2	0.3922	31.9	0.911	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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