DUF4245 - PFAM28P - GREMLIN Contacts

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DUF4245 - Protein of unknown function (DUF4245)

PFAM:	PF14030	Sequences: RGRQTVRDMVLSLAVLLVVVLVLVLFVPRPSFDPGPVPTVDYAAALAAAARAAGFPVLAPGLPEGWRATSARFDGGGGVPTWHVGYLTPDGQYVGLEQSDAAAAALVAAVLGGAAPTGTVTVGGRTWQVYTEGGGETALVRTAGGVTVVVTGTASDAELRTLAAAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	166 (164)
Sequences:	2426 (1857)
Seq/√Len:	145.0
META:	0.666

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
83_H	97_E	4.408	1.00
42_Y	86_Y	4.102	1.00
7_R	11_L	3.662	1.00
94_V	162_L	3.602	1.00
92_Q	153_T	2.723	1.00
70_S	85_G	2.655	1.00
121_T	126_T	2.588	1.00
39_T	67_R	2.448	1.00
120_V	160_R	2.403	1.00
160_R	164_A	2.293	1.00
158_E	161_T	2.190	1.00
8_D	12_S	2.075	1.00
8_D	11_L	2.053	1.00
111_L	138_A	2.046	1.00
46_L	82_W	2.044	1.00
67_R	91_G	1.994	1.00
90_D	158_E	1.861	1.00
120_V	129_V	1.748	1.00
73_F	80_P	1.687	1.00
156_D	160_R	1.674	1.00
121_T	124_G	1.672	1.00
66_W	162_L	1.636	1.00
45_A	71_A	1.593	1.00
17_L	20_V	1.583	1.00
25_L	29_R	1.582	1.00
125_R	141_R	1.574	1.00
88_T	158_E	1.560	1.00
119_T	126_T	1.542	1.00
132_E	135_G	1.539	1.00
11_L	14_A	1.530	1.00
157_A	160_R	1.524	1.00
21_L	25_L	1.514	1.00
137_T	156_D	1.480	1.00
61_G	89_P	1.476	1.00
154_A	158_E	1.436	1.00
150_V	159_L	1.431	1.00
2_G	8_D	1.429	1.00
6_V	10_V	1.395	1.00
25_L	28_P	1.392	1.00
142_T	147_T	1.381	1.00
30_P	34_P	1.371	1.00
18_V	22_V	1.349	1.00
46_L	84_V	1.344	1.00
62_L	89_P	1.328	1.00
7_R	12_S	1.326	1.00
26_F	29_R	1.323	1.00
20_V	29_R	1.298	1.00
11_L	15_V	1.281	1.00
63_P	161_T	1.277	1.00
53_A	57_V	1.274	1.00
116_P	128_Q	1.272	1.00
23_L	27_V	1.271	1.00
42_Y	68_A	1.253	1.00
43_A	59_A	1.251	1.00
83_H	93_Y	1.243	1.00
117_T	129_V	1.228	1.00
62_L	86_Y	1.219	1.00
43_A	47_A	1.217	1.00
129_V	156_D	1.215	1.00
135_G	138_A	1.205	1.00
155_S	158_E	1.203	1.00
150_V	163_A	1.202	1.00
82_W	98_Q	1.200	1.00
132_E	136_E	1.199	1.00
79_V	100_D	1.176	1.00
133_G	136_E	1.167	1.00
152_G	159_L	1.158	1.00
46_L	59_A	1.157	1.00
111_L	114_A	1.128	0.99
85_G	93_Y	1.123	0.99
68_A	86_Y	1.121	0.99
98_Q	146_V	1.104	0.99
161_T	165_A	1.097	0.99
58_L	148_V	1.091	0.99
106_L	111_L	1.090	0.99
95_G	151_T	1.090	0.99
122_V	125_R	1.079	0.99
42_Y	82_W	1.072	0.99
18_V	25_L	1.067	0.99
4_Q	8_D	1.059	0.99
68_A	71_A	1.054	0.99
45_A	48_A	1.047	0.99
8_D	16_L	1.047	0.99
42_Y	84_V	1.043	0.99
12_S	16_L	1.043	0.99
101_A	106_L	1.039	0.99
23_L	26_F	1.021	0.99
99_S	106_L	1.015	0.99
54_G	100_D	1.006	0.99
70_S	83_H	1.003	0.99
17_L	21_L	0.988	0.98
61_G	65_G	0.985	0.98
2_G	6_V	0.982	0.98
24_V	27_V	0.973	0.98
134_G	138_A	0.970	0.98
18_V	21_L	0.964	0.98
83_H	95_G	0.963	0.98
22_V	26_F	0.941	0.98
24_V	28_P	0.936	0.98
87_L	93_Y	0.933	0.98
8_D	19_V	0.932	0.98
69_T	85_G	0.925	0.98
116_P	130_Y	0.925	0.98
110_V	149_V	0.923	0.98
120_V	156_D	0.918	0.98
37_V	67_R	0.909	0.97
163_A	166_L	0.893	0.97
17_L	22_V	0.892	0.97
55_F	100_D	0.886	0.97
89_P	158_E	0.860	0.96
60_P	84_V	0.847	0.96
139_L	163_A	0.843	0.96
28_P	106_L	0.838	0.96
3_R	12_S	0.835	0.96
46_L	50_A	0.833	0.96
122_V	131_T	0.822	0.95
81_T	97_E	0.817	0.95
69_T	93_Y	0.815	0.95
3_R	6_V	0.814	0.95
16_L	19_V	0.811	0.95
21_L	24_V	0.803	0.95
106_L	110_V	0.803	0.95
5_T	8_D	0.803	0.95
40_V	71_A	0.790	0.94
94_V	129_V	0.790	0.94
121_T	160_R	0.789	0.94
133_G	139_L	0.788	0.94
69_T	87_L	0.784	0.94
86_Y	96_L	0.784	0.94
132_E	137_T	0.783	0.94
135_G	141_R	0.773	0.94
33_D	37_V	0.770	0.93
75_G	78_G	0.770	0.93
5_T	20_V	0.768	0.93
43_A	86_Y	0.766	0.93
162_L	165_A	0.765	0.93
79_V	106_L	0.758	0.93
156_D	159_L	0.751	0.93
88_T	94_V	0.745	0.92
143_A	148_V	0.745	0.92
8_D	17_L	0.733	0.92
131_T	135_G	0.733	0.92
131_T	134_G	0.730	0.91
27_V	30_P	0.728	0.91
131_T	139_L	0.727	0.91
94_V	159_L	0.724	0.91
50_A	59_A	0.723	0.91
88_T	91_G	0.722	0.91
55_F	80_P	0.718	0.91
135_G	139_L	0.716	0.91
137_T	159_L	0.715	0.91
39_T	65_G	0.701	0.90
131_T	137_T	0.695	0.89
104_A	108_A	0.692	0.89
8_D	27_V	0.691	0.89
34_P	63_P	0.690	0.89
115_A	118_G	0.684	0.89
127_W	150_V	0.684	0.89
138_A	141_R	0.684	0.89
112_G	135_G	0.683	0.89
67_R	87_L	0.679	0.88
61_G	64_E	0.678	0.88
62_L	68_A	0.673	0.88
4_Q	7_R	0.670	0.88
17_L	24_V	0.665	0.87
48_A	52_A	0.664	0.87
20_V	26_F	0.661	0.87
117_T	156_D	0.660	0.87
51_R	57_V	0.658	0.87
141_R	144_G	0.654	0.86
120_V	124_G	0.652	0.86
41_D	44_A	0.651	0.86
24_V	29_R	0.651	0.86
37_V	70_S	0.648	0.86
59_A	86_Y	0.642	0.85
94_V	150_V	0.640	0.85
20_V	27_V	0.639	0.85
55_F	146_V	0.639	0.85
2_G	5_T	0.638	0.85
14_A	18_V	0.635	0.85
132_E	139_L	0.629	0.84
9_M	16_L	0.629	0.84
53_A	73_F	0.625	0.84
37_V	87_L	0.625	0.84
12_S	15_V	0.623	0.84
119_T	122_V	0.622	0.83
13_L	20_V	0.619	0.83
143_A	146_V	0.618	0.83
74_D	81_T	0.618	0.83
20_V	24_V	0.614	0.83
8_D	101_A	0.610	0.82
68_A	84_V	0.609	0.82
53_A	80_P	0.604	0.82
16_L	28_P	0.600	0.81
134_G	137_T	0.598	0.81
3_R	7_R	0.597	0.81
46_L	98_Q	0.595	0.81
96_L	162_L	0.586	0.80
65_G	88_T	0.586	0.80
27_V	33_D	0.585	0.80
5_T	9_M	0.582	0.79
96_L	150_V	0.582	0.79
121_T	125_R	0.579	0.79
75_G	80_P	0.579	0.79
159_L	163_A	0.577	0.79
7_R	13_L	0.575	0.78
133_G	153_T	0.575	0.78
136_E	139_L	0.571	0.78
73_F	79_V	0.570	0.78
29_R	32_F	0.568	0.78
44_A	48_A	0.567	0.77
52_A	73_F	0.566	0.77
119_T	128_Q	0.563	0.77
4_Q	12_S	0.562	0.77
49_A	71_A	0.562	0.77
62_L	65_G	0.561	0.77
15_V	24_V	0.556	0.76
99_S	102_A	0.554	0.76
103_A	128_Q	0.554	0.76
132_E	150_V	0.553	0.76
30_P	33_D	0.549	0.75
74_D	113_G	0.548	0.75
27_V	31_S	0.548	0.75
54_G	75_G	0.548	0.75
119_T	129_V	0.545	0.75
49_A	82_W	0.545	0.75
15_V	19_V	0.544	0.74
50_A	54_G	0.540	0.74
158_E	162_L	0.539	0.74
101_A	114_A	0.537	0.74
25_L	30_P	0.535	0.73
131_T	136_E	0.535	0.73
23_L	33_D	0.534	0.73
121_T	161_T	0.532	0.73
45_A	91_G	0.526	0.72
70_S	84_V	0.523	0.72
67_R	141_R	0.520	0.71
6_V	17_L	0.515	0.70
86_Y	163_A	0.514	0.70
133_G	150_V	0.511	0.70
142_T	145_G	0.508	0.69
3_R	9_M	0.504	0.69
114_A	120_V	0.504	0.69
79_V	101_A	0.503	0.69
146_V	150_V	0.502	0.69
83_H	110_V	0.500	0.68

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
3lydA	2	0.747	33.6	0.921	Contact Map
4ps6A	1	0.5361	13	0.935	Contact Map
2ls2A	1	0.1506	7.5	0.942	Contact Map
3m4wA	2	0.7831	6.3	0.944	Contact Map
3vxvA	1	0.3855	5.7	0.945	Contact Map
2llzA	1	0.4518	4.7	0.947	Contact Map
3cp0A	1	0.3434	4.7	0.947	Contact Map
3wu2X	1	0.2229	4.2	0.948	Contact Map
3bz1X	1	0.2169	3.4	0.95	Contact Map
3q2bA	1	0.3012	3.1	0.952	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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