DUF367 - PFAM28P - GREMLIN Contacts

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DUF367 - Domain of unknown function (DUF367)

PFAM:	PF04034	Sequences: IVLNPFAEKALSPADRELIEKRGLVALDCSWARAEEVPFKKLKGGIHRALPYLVAANPVNYGKPFKLSTVEALAAALYILGFKEQAEELLSKFKWGHTFLELNKELLEAYAKAKDSEEVVEIQKEYL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (126)
Sequences:	2613 (1511)
Seq/√Len:	134.6
META:	0.776

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_A	69_T	4.055	1.00
98_T	101_E	3.413	1.00
19_I	80_L	3.276	1.00
70_V	93_F	3.199	1.00
4_N	47_H	2.914	1.00
83_K	111_A	2.531	1.00
104_K	108_E	2.324	1.00
109_A	126_Y	2.312	1.00
97_H	101_E	2.274	1.00
74_A	90_L	2.266	1.00
114_K	118_E	2.172	1.00
52_Y	64_P	2.058	1.00
113_A	122_I	1.931	1.00
34_A	38_P	1.908	1.00
83_K	87_E	1.903	1.00
70_V	90_L	1.840	1.00
60_N	66_K	1.832	1.00
78_Y	83_K	1.817	1.00
115_D	118_E	1.747	1.00
49_A	123_Q	1.687	1.00
120_V	123_Q	1.624	1.00
83_K	108_E	1.600	1.00
56_A	102_L	1.577	1.00
20_E	82_F	1.567	1.00
16_R	20_E	1.556	1.00
77_L	85_Q	1.531	1.00
32_A	66_K	1.527	1.00
121_E	125_E	1.489	1.00
10_A	120_V	1.451	1.00
11_L	76_A	1.435	1.00
56_A	98_T	1.427	1.00
10_A	116_S	1.424	1.00
33_R	36_E	1.422	1.00
9_K	14_A	1.396	1.00
52_Y	65_F	1.366	1.00
121_E	124_K	1.336	1.00
70_V	89_L	1.324	1.00
122_I	126_Y	1.318	1.00
70_V	100_L	1.282	1.00
88_E	92_K	1.280	1.00
54_V	62_G	1.273	1.00
108_E	111_A	1.254	1.00
118_E	121_E	1.252	1.00
13_P	16_R	1.242	1.00
70_V	92_K	1.229	1.00
106_L	126_Y	1.214	1.00
116_S	120_V	1.209	1.00
68_S	95_W	1.204	1.00
84_E	87_E	1.201	1.00
61_Y	102_L	1.181	0.99
6_F	34_A	1.175	0.99
53_L	75_A	1.161	0.99
87_E	100_L	1.148	0.99
29_C	34_A	1.145	0.99
11_L	80_L	1.136	0.99
109_A	122_I	1.130	0.99
59_V	62_G	1.117	0.99
15_D	48_R	1.102	0.99
78_Y	107_L	1.098	0.99
10_A	49_A	1.096	0.99
117_E	121_E	1.091	0.99
120_V	124_K	1.082	0.99
54_V	106_L	1.065	0.99
94_K	97_H	1.051	0.99
82_F	85_Q	1.047	0.99
18_L	46_I	1.043	0.99
26_A	73_L	1.022	0.98
60_N	63_K	1.022	0.98
109_A	125_E	1.004	0.98
9_K	116_S	1.002	0.98
17_E	20_E	0.976	0.98
49_A	65_F	0.972	0.98
78_Y	108_E	0.969	0.98
24_L	76_A	0.966	0.98
2_V	45_G	0.965	0.98
85_Q	88_E	0.963	0.98
87_E	97_H	0.937	0.97
12_S	116_S	0.929	0.97
105_E	109_A	0.928	0.97
73_L	89_L	0.923	0.97
16_R	19_I	0.897	0.96
10_A	119_V	0.894	0.96
16_R	82_F	0.889	0.96
26_A	32_A	0.878	0.96
107_L	111_A	0.874	0.96
4_N	27_L	0.873	0.96
112_K	122_I	0.867	0.96
122_I	125_E	0.867	0.96
4_N	7_A	0.854	0.95
101_E	104_K	0.851	0.95
88_E	91_S	0.845	0.95
59_V	68_S	0.838	0.95
10_A	123_Q	0.825	0.94
49_A	52_Y	0.801	0.93
19_I	24_L	0.792	0.93
2_V	44_G	0.782	0.93
108_E	112_K	0.778	0.92
25_V	69_T	0.772	0.92
98_T	102_L	0.761	0.92
113_A	118_E	0.758	0.91
102_L	106_L	0.755	0.91
16_R	80_L	0.737	0.90
61_Y	98_T	0.722	0.89
5_P	28_D	0.712	0.89
49_A	69_T	0.709	0.88
63_K	66_K	0.708	0.88
70_V	96_G	0.702	0.88
24_L	77_L	0.700	0.88
63_K	68_S	0.700	0.88
53_L	107_L	0.698	0.88
13_P	115_D	0.696	0.88
118_E	122_I	0.694	0.87
117_E	120_V	0.679	0.86
4_N	25_V	0.677	0.86
7_A	11_L	0.668	0.85
104_K	121_E	0.654	0.84
55_A	65_F	0.654	0.84
29_C	37_V	0.653	0.84
13_P	114_K	0.652	0.84
56_A	97_H	0.652	0.84
10_A	65_F	0.645	0.83
39_F	42_L	0.637	0.83
69_T	73_L	0.635	0.82
86_A	100_L	0.633	0.82
91_S	94_K	0.633	0.82
58_P	95_W	0.616	0.80
58_P	94_K	0.616	0.80
77_L	89_L	0.615	0.80
26_A	68_S	0.606	0.79
27_L	61_Y	0.603	0.79
27_L	42_L	0.600	0.79
32_A	63_K	0.600	0.79
24_L	73_L	0.598	0.78
14_A	116_S	0.598	0.78
41_K	45_G	0.596	0.78
54_V	81_G	0.593	0.78
12_S	15_D	0.592	0.78
74_A	89_L	0.592	0.78
92_K	95_W	0.589	0.77
101_E	106_L	0.584	0.77
58_P	70_V	0.580	0.76
29_C	38_P	0.580	0.76
56_A	100_L	0.575	0.76
74_A	96_G	0.572	0.75
116_S	119_V	0.571	0.75
59_V	66_K	0.570	0.75
52_Y	55_A	0.569	0.75
21_K	125_E	0.565	0.74
60_N	95_W	0.563	0.74
65_F	123_Q	0.561	0.74
35_E	83_K	0.560	0.74
19_I	82_F	0.560	0.74
29_C	33_R	0.557	0.73
27_L	37_V	0.556	0.73
27_L	38_P	0.554	0.73
11_L	19_I	0.554	0.73
55_A	63_K	0.551	0.73
88_E	115_D	0.550	0.72
13_P	81_G	0.547	0.72
116_S	123_Q	0.547	0.72
107_L	110_Y	0.544	0.72
38_P	41_K	0.542	0.71
10_A	52_Y	0.542	0.71
10_A	14_A	0.540	0.71
59_V	106_L	0.540	0.71
52_Y	123_Q	0.540	0.71
14_A	115_D	0.534	0.70
109_A	113_A	0.530	0.70
79_I	119_V	0.530	0.70
30_S	68_S	0.530	0.70
90_L	93_F	0.530	0.70
28_D	120_V	0.528	0.69
100_L	104_K	0.528	0.69
68_S	94_K	0.525	0.69
28_D	94_K	0.525	0.69
1_I	15_D	0.520	0.68
106_L	125_E	0.519	0.68
78_Y	100_L	0.518	0.68
12_S	119_V	0.518	0.68
7_A	47_H	0.515	0.68
25_V	38_P	0.512	0.67
78_Y	86_A	0.512	0.67
56_A	62_G	0.508	0.66
12_S	64_P	0.504	0.66
4_N	38_P	0.504	0.66
6_F	35_E	0.502	0.66
117_E	125_E	0.502	0.66
3_L	28_D	0.501	0.65
108_E	126_Y	0.500	0.65

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
2raaA	1	0.8504	45.6	0.933	Contact Map
3on3A	2	0.8346	29.2	0.94	Contact Map
1yt5A	4	0.7559	25.7	0.941	Contact Map
1y9jA	1	0.7795	20.1	0.944	Contact Map
2c42A	2	0.9528	18.8	0.945	Contact Map
3oqcA	1	0.3701	17.6	0.945	Contact Map
3bdnA	2	0.5433	9.7	0.951	Contact Map
4ccaA	1	0.7717	7	0.955	Contact Map
2f02A	2	0.7795	6.2	0.955	Contact Map
3g2eA	4	0.8661	6	0.956	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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