DUF441 - PFAM28P - GREMLIN Contacts

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DUF441 - Protein of unknown function (DUF441)

PFAM:	PF04284	Sequences: LFLLILLALGLIGKNNSVAIAAAVLLLLKLLGLDRYFPLLEKRGLNIGLIILTIAVLVPIASGKIGFKDLLESFKSWKGLLAIAGGILVAYLNGRGVTLLKSDPEIVVGLVIGTIIGVAFFKGVPVGPLIAAGIAALLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	139 (139)
Sequences:	1013 (590)
Seq/√Len:	50.1
META:	0.494

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_L	23_A	3.374	1.00
3_L	61_A	3.208	1.00
15_N	90_A	2.958	1.00
93_N	130_I	2.895	1.00
47_I	51_I	2.505	1.00
11_L	14_K	2.478	1.00
116_I	121_F	2.114	1.00
39_L	47_I	2.076	1.00
74_F	132_A	2.038	1.00
49_L	93_N	2.011	1.00
13_G	18_V	1.996	1.00
83_I	112_I	1.929	0.99
126_V	129_L	1.875	0.99
97_V	137_L	1.806	0.99
40_L	58_V	1.796	0.99
85_G	93_N	1.740	0.99
76_S	79_G	1.731	0.99
81_L	138_L	1.696	0.98
33_L	38_P	1.692	0.98
114_T	118_V	1.683	0.98
69_D	72_E	1.675	0.98
56_V	111_V	1.671	0.98
18_V	53_T	1.658	0.98
7_L	26_L	1.590	0.98
116_I	120_F	1.571	0.97
85_G	135_A	1.520	0.97
89_V	118_V	1.514	0.97
24_V	54_I	1.482	0.96
58_V	62_S	1.480	0.96
22_A	57_L	1.411	0.95
43_R	46_N	1.409	0.95
12_I	138_L	1.407	0.95
117_G	131_A	1.390	0.95
119_A	124_V	1.372	0.94
11_L	16_N	1.345	0.94
26_L	60_I	1.331	0.93
27_L	75_K	1.320	0.93
56_V	129_L	1.306	0.93
85_G	89_V	1.303	0.93
10_G	18_V	1.288	0.92
81_L	135_A	1.285	0.92
95_R	136_A	1.281	0.92
60_I	108_V	1.270	0.92
28_L	37_F	1.261	0.91
130_I	135_A	1.260	0.91
28_L	40_L	1.257	0.91
43_R	49_L	1.252	0.91
66_G	69_D	1.244	0.91
15_N	118_V	1.234	0.90
40_L	54_I	1.233	0.90
49_L	85_G	1.224	0.90
57_L	111_V	1.218	0.90
124_V	130_I	1.218	0.90
60_I	120_F	1.206	0.89
4_L	26_L	1.205	0.89
20_I	100_L	1.197	0.89
6_L	25_L	1.197	0.89
81_L	84_A	1.189	0.89
4_L	8_A	1.188	0.89
1_L	5_I	1.171	0.88
49_L	97_V	1.156	0.87
5_I	75_K	1.145	0.87
43_R	85_G	1.104	0.85
30_L	61_A	1.093	0.84
31_L	87_I	1.083	0.84
13_G	139_L	1.076	0.83
18_V	129_L	1.065	0.83
5_I	74_F	1.060	0.82
17_S	60_I	1.058	0.82
115_I	119_A	1.054	0.82
67_F	70_L	1.052	0.82
92_L	101_K	1.047	0.81
56_V	66_G	1.044	0.81
2_F	8_A	1.035	0.81
136_A	139_L	1.034	0.81
66_G	80_L	1.032	0.81
13_G	30_L	1.030	0.80
34_D	83_I	1.021	0.80
28_L	58_V	1.017	0.80
14_K	27_L	0.997	0.78
111_V	126_V	0.993	0.78
67_F	71_L	0.970	0.76
114_T	130_I	0.970	0.76
19_A	22_A	0.967	0.76
118_V	130_I	0.949	0.75
83_I	117_G	0.947	0.74
23_A	54_I	0.945	0.74
75_K	139_L	0.938	0.74
84_A	88_L	0.938	0.74
66_G	115_I	0.937	0.74
6_L	132_A	0.930	0.73
11_L	23_A	0.923	0.73
19_A	23_A	0.915	0.72
86_G	104_P	0.904	0.71
78_K	139_L	0.897	0.70
89_V	93_N	0.893	0.70
57_L	76_S	0.888	0.70
89_V	130_I	0.879	0.69
49_L	130_I	0.877	0.69
1_L	12_I	0.855	0.67
52_L	107_V	0.854	0.67
15_N	93_N	0.852	0.66
25_L	29_K	0.846	0.66
123_G	127_G	0.833	0.65
20_I	31_L	0.831	0.64
7_L	22_A	0.830	0.64
18_V	29_K	0.829	0.64
86_G	99_L	0.829	0.64
45_L	104_P	0.819	0.63
89_V	114_T	0.813	0.63
127_G	133_G	0.811	0.63
15_N	130_I	0.803	0.62
50_I	55_A	0.802	0.62
15_N	119_A	0.802	0.62
126_V	133_G	0.801	0.62
20_I	24_V	0.799	0.61
33_L	36_Y	0.797	0.61
114_T	122_K	0.794	0.61
7_L	106_I	0.791	0.61
114_T	117_G	0.788	0.60
114_T	125_P	0.782	0.60
35_R	121_F	0.771	0.59
49_L	89_V	0.770	0.59
37_F	82_A	0.761	0.58
25_L	129_L	0.751	0.57
90_A	114_T	0.742	0.56
72_E	75_K	0.734	0.55
28_L	34_D	0.731	0.55
94_G	103_D	0.728	0.54
72_E	105_E	0.723	0.54
90_A	93_N	0.722	0.54
57_L	79_G	0.719	0.53
25_L	125_P	0.717	0.53
72_E	98_T	0.715	0.53
46_N	50_I	0.712	0.53
6_L	21_A	0.707	0.52
4_L	7_L	0.707	0.52
62_S	80_L	0.699	0.51
41_E	64_K	0.699	0.51
46_N	136_A	0.698	0.51
90_A	119_A	0.697	0.51
5_I	8_A	0.689	0.50
106_I	122_K	0.689	0.50
46_N	89_V	0.687	0.50
4_L	121_F	0.684	0.50
1_L	120_F	0.681	0.49
49_L	55_A	0.680	0.49
109_G	125_P	0.676	0.49
11_L	63_G	0.673	0.49
53_T	90_A	0.670	0.48
6_L	31_L	0.666	0.48
75_K	107_V	0.665	0.48
2_F	106_I	0.661	0.47
16_N	40_L	0.658	0.47
109_G	136_A	0.652	0.47
46_N	121_F	0.647	0.46
35_R	42_K	0.646	0.46
88_L	92_L	0.641	0.45
23_A	27_L	0.640	0.45
130_I	133_G	0.637	0.45
74_F	92_L	0.625	0.44
15_N	114_T	0.623	0.44
41_E	117_G	0.623	0.44
13_G	120_F	0.612	0.42
63_G	66_G	0.611	0.42
57_L	115_I	0.609	0.42
21_A	74_F	0.608	0.42
9_L	18_V	0.595	0.41
83_I	87_I	0.592	0.40
64_K	81_L	0.591	0.40
56_V	104_P	0.588	0.40
37_F	58_V	0.586	0.40
100_L	111_V	0.583	0.40
2_F	112_I	0.582	0.39
85_G	91_Y	0.581	0.39
126_V	134_I	0.576	0.39
45_L	55_A	0.571	0.38
90_A	97_V	0.571	0.38
33_L	66_G	0.571	0.38
31_L	39_L	0.569	0.38
52_L	126_V	0.566	0.38
16_N	122_K	0.566	0.38
68_K	72_E	0.566	0.38
13_G	100_L	0.563	0.38
9_L	67_F	0.551	0.36
82_A	106_I	0.551	0.36
8_A	12_I	0.546	0.36
69_D	111_V	0.543	0.36
92_L	106_I	0.543	0.36
91_Y	136_A	0.542	0.36
53_T	101_K	0.541	0.36
61_A	98_T	0.540	0.35
71_L	84_A	0.537	0.35
108_V	135_A	0.536	0.35
16_N	19_A	0.536	0.35
13_G	79_G	0.533	0.35
25_L	56_V	0.525	0.34
5_I	84_A	0.524	0.34
95_R	124_V	0.523	0.34
10_G	84_A	0.521	0.34
17_S	130_I	0.520	0.34
93_N	129_L	0.519	0.33
93_N	126_V	0.514	0.33
112_I	120_F	0.510	0.33
5_I	14_K	0.506	0.32
87_I	121_F	0.505	0.32
91_Y	94_G	0.501	0.32
80_L	84_A	0.500	0.32

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
2qi9A	2	0.7842	12.8	0.937	Contact Map
1i5pA	1	0.5612	5	0.948	Contact Map
4o93B	1	0.8417	4.8	0.948	Contact Map
4o9uB	2	0.8201	4.3	0.949	Contact Map
1gntA	1	0.5971	3.1	0.952	Contact Map
2nq2A	2	0.705	2.7	0.954	Contact Map
1gnlA	1	0.5755	2.7	0.954	Contact Map
2zy9A	2	0.9065	2.3	0.956	Contact Map
2l9uA	2	0.1151	2.3	0.956	Contact Map
3wajA	1	0.8633	1.8	0.958	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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