DUF3748 - PFAM28P - GREMLIN Contacts

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DUF3748 - Protein of unknown function (DUF3748)

PFAM:	PF12566	Sequences: HCGVVTFSPVEPNRVVFIHGPENPTPDWQYGFHHRQGVIVDADRPGVAINLDARDITPPFTPGALRGGSHVHVFSPDGQWVSFTYNDHVLAQLDTGHDLNLRNVGVSVPGRPVRVPKDHPRNH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	123 (121)
Sequences:	851 (556)
Seq/√Len:	50.5
META:	0.814

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_E	14_R	5.779	1.00
55_D	61_T	4.228	1.00
86_N	100_N	4.068	1.00
83_F	105_G	3.617	1.00
73_V	82_S	3.332	1.00
60_F	89_V	2.734	1.00
93_L	97_H	2.584	1.00
34_H	88_H	2.334	1.00
21_P	24_P	2.204	1.00
29_Q	34_H	2.156	1.00
75_S	79_Q	2.139	1.00
7_F	42_A	2.053	1.00
8_S	74_F	1.980	1.00
71_V	82_S	1.916	0.99
36_Q	50_N	1.896	0.99
8_S	11_E	1.751	0.99
33_H	91_A	1.749	0.99
19_H	36_Q	1.738	0.99
88_H	92_Q	1.682	0.98
24_P	28_W	1.656	0.98
13_N	43_D	1.571	0.97
80_W	109_P	1.553	0.97
13_N	42_A	1.552	0.97
2_C	19_H	1.551	0.97
8_S	14_R	1.547	0.97
101_L	105_G	1.467	0.96
88_H	103_N	1.458	0.96
37_G	72_H	1.415	0.95
94_D	97_H	1.402	0.95
10_V	75_S	1.388	0.95
74_F	77_D	1.378	0.95
6_T	73_V	1.369	0.94
40_V	48_A	1.345	0.94
83_F	107_S	1.299	0.93
33_H	88_H	1.292	0.92
33_H	100_N	1.287	0.92
22_E	28_W	1.267	0.92
15_V	40_V	1.218	0.90
93_L	99_L	1.207	0.90
86_N	90_L	1.197	0.89
32_F	54_R	1.184	0.89
80_W	103_N	1.158	0.88
93_L	101_L	1.154	0.87
40_V	45_P	1.143	0.87
38_V	50_N	1.142	0.87
32_F	86_N	1.081	0.84
91_A	100_N	1.080	0.84
51_L	81_V	1.074	0.83
88_H	91_A	1.062	0.83
7_F	13_N	1.050	0.82
69_S	83_F	1.046	0.82
8_S	79_Q	1.045	0.82
93_L	96_G	1.040	0.81
98_D	101_L	0.999	0.79
56_I	88_H	0.998	0.79
17_F	20_G	0.997	0.78
39_I	51_L	0.991	0.78
90_L	100_N	0.986	0.78
14_R	39_I	0.975	0.77
7_F	11_E	0.972	0.77
44_R	47_V	0.972	0.77
55_D	116_P	0.967	0.76
22_E	50_N	0.944	0.75
21_P	28_W	0.940	0.74
21_P	29_Q	0.929	0.73
115_V	118_D	0.918	0.72
25_T	30_Y	0.915	0.72
41_D	44_R	0.914	0.72
94_D	104_V	0.908	0.72
28_W	34_H	0.902	0.71
92_Q	97_H	0.866	0.68
54_R	61_T	0.861	0.68
72_H	105_G	0.852	0.67
57_T	118_D	0.850	0.67
86_N	91_A	0.839	0.66
29_Q	33_H	0.831	0.65
33_H	86_N	0.830	0.65
74_F	101_L	0.814	0.63
52_D	62_P	0.805	0.62
60_F	104_V	0.801	0.62
83_F	101_L	0.794	0.61
27_D	30_Y	0.792	0.61
92_Q	95_T	0.785	0.60
57_T	116_P	0.783	0.60
74_F	92_Q	0.783	0.60
32_F	90_L	0.781	0.60
40_V	49_I	0.777	0.60
32_F	56_I	0.774	0.59
16_V	51_L	0.766	0.58
2_C	25_T	0.765	0.58
76_P	94_D	0.761	0.58
64_A	80_W	0.759	0.58
82_S	108_V	0.756	0.57
24_P	29_Q	0.754	0.57
25_T	28_W	0.748	0.57
43_D	112_P	0.747	0.57
7_F	74_F	0.747	0.57
5_V	54_R	0.744	0.56
88_H	109_P	0.721	0.54
91_A	103_N	0.720	0.54
94_D	99_L	0.714	0.53
76_P	80_W	0.712	0.53
89_V	105_G	0.711	0.53
26_P	114_R	0.708	0.53
29_Q	92_Q	0.708	0.53
69_S	104_V	0.699	0.52
31_G	86_N	0.689	0.51
47_V	112_P	0.689	0.51
69_S	76_P	0.686	0.50
31_G	34_H	0.673	0.49
54_R	69_S	0.671	0.49
13_N	16_V	0.667	0.48
5_V	18_I	0.661	0.48
6_T	16_V	0.659	0.48
4_V	71_V	0.658	0.47
23_N	80_W	0.657	0.47
81_V	107_S	0.655	0.47
96_G	106_V	0.652	0.47
16_V	71_V	0.647	0.46
7_F	19_H	0.647	0.46
62_P	116_P	0.642	0.46
5_V	32_F	0.641	0.46
86_N	103_N	0.638	0.45
4_V	21_P	0.637	0.45
46_G	51_L	0.637	0.45
114_R	118_D	0.636	0.45
70_H	84_T	0.621	0.44
38_V	48_A	0.618	0.43
32_F	123_H	0.618	0.43
11_E	41_D	0.608	0.42
74_F	94_D	0.606	0.42
78_G	103_N	0.606	0.42
26_P	41_D	0.599	0.41
51_L	107_S	0.599	0.41
10_V	13_N	0.597	0.41
47_V	106_V	0.597	0.41
60_F	64_A	0.596	0.41
44_R	49_I	0.595	0.41
38_V	51_L	0.592	0.41
73_V	103_N	0.588	0.40
41_D	49_I	0.584	0.40
50_N	57_T	0.581	0.40
14_R	49_I	0.580	0.40
74_F	103_N	0.574	0.39
74_F	109_P	0.572	0.39
21_P	25_T	0.572	0.39
43_D	77_D	0.569	0.38
54_R	123_H	0.569	0.38
32_F	100_N	0.566	0.38
95_T	118_D	0.565	0.38
16_V	81_V	0.563	0.38
53_A	76_P	0.557	0.37
5_V	13_N	0.557	0.37
96_G	99_L	0.556	0.37
79_Q	111_R	0.552	0.37
10_V	77_D	0.551	0.37
29_Q	49_I	0.550	0.37
33_H	38_V	0.548	0.36
74_F	79_Q	0.546	0.36
93_L	98_D	0.543	0.36
7_F	83_F	0.542	0.36
10_V	79_Q	0.541	0.36
117_K	120_P	0.540	0.36
21_P	30_Y	0.539	0.36
53_A	65_L	0.536	0.35
4_V	18_I	0.533	0.35
34_H	91_A	0.532	0.35
8_S	13_N	0.531	0.35
44_R	118_D	0.522	0.34
95_T	98_D	0.519	0.34
92_Q	98_D	0.519	0.34
7_F	14_R	0.519	0.34
43_D	114_R	0.516	0.33
71_V	100_N	0.515	0.33
50_N	89_V	0.513	0.33
13_N	95_T	0.512	0.33
60_F	65_L	0.510	0.33
44_R	96_G	0.509	0.33
57_T	61_T	0.506	0.33
21_P	36_Q	0.504	0.32
95_T	99_L	0.502	0.32
15_V	123_H	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
4wjlA	2	0.878	59.8	0.933	Contact Map
1xfdA	2	0.8374	44.1	0.939	Contact Map
2z3zA	2	0.7886	36.3	0.942	Contact Map
1z68A	2	0.8618	27.3	0.945	Contact Map
4bp8A	1	0.7886	25	0.946	Contact Map
4cj0B	1	0.2764	22.7	0.947	Contact Map
4a5sA	2	0.8211	22.1	0.948	Contact Map
2ecfA	2	0.7886	21.9	0.948	Contact Map
3c5mA	1	0.6829	19.7	0.949	Contact Map
2xe4A	1	0.8211	19.1	0.949	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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