DUF1533 - PFAM28P - GREMLIN Contacts

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DUF1533 - Protein of unknown function (DUF1533)

PFAM:	PF07550	Sequences: DAAWRNAITSVTVNGTALAGSVSTAGAYTVNSAGKITIDASLFTTAGDYTIVIKATGYKDATVTQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	65 (59)
Sequences:	1328 (1136)
Seq/√Len:	147.9
META:	0.787

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_K	60_D	3.466	1.00
10_S	54_K	2.627	1.00
10_S	17_A	2.612	1.00
14_N	49_Y	2.558	1.00
8_I	53_I	2.322	1.00
7_A	55_A	2.270	1.00
43_F	49_Y	2.249	1.00
48_D	64_T	2.084	1.00
52_V	60_D	1.963	1.00
14_N	47_G	1.955	1.00
2_A	6_N	1.833	1.00
12_T	17_A	1.827	1.00
50_T	62_T	1.821	1.00
24_T	27_A	1.735	1.00
12_T	54_K	1.481	1.00
32_S	35_K	1.380	1.00
3_A	7_A	1.368	1.00
25_A	28_Y	1.354	1.00
13_V	42_L	1.303	1.00
38_I	42_L	1.280	1.00
12_T	52_V	1.259	1.00
28_Y	31_N	1.211	1.00
13_V	49_Y	1.206	1.00
31_N	34_G	1.203	1.00
2_A	5_R	1.166	1.00
32_S	37_T	1.145	1.00
5_R	34_G	1.142	1.00
4_W	61_A	1.110	0.99
13_V	18_L	1.078	0.99
55_A	58_Y	0.965	0.98
12_T	15_G	0.929	0.98
7_A	56_T	0.915	0.98
9_T	56_T	0.889	0.97
13_V	51_I	0.850	0.96
18_L	49_Y	0.844	0.96
8_I	36_I	0.807	0.95
18_L	38_I	0.785	0.94
4_W	11_V	0.764	0.93
28_Y	36_I	0.733	0.92
24_T	28_Y	0.725	0.92
36_I	53_I	0.720	0.91
26_G	33_A	0.712	0.91
30_V	36_I	0.709	0.91
51_I	65_Q	0.707	0.91
4_W	58_Y	0.698	0.90
24_T	44_T	0.691	0.90
7_A	57_G	0.690	0.89
5_R	18_L	0.687	0.89
25_A	44_T	0.677	0.89
39_D	42_L	0.670	0.88
50_T	64_T	0.662	0.87
5_R	33_A	0.657	0.87
46_A	49_Y	0.654	0.87
16_T	64_T	0.648	0.86
54_K	59_K	0.634	0.85
15_G	52_V	0.626	0.84
3_A	6_N	0.623	0.84
18_L	63_V	0.622	0.84
8_I	30_V	0.622	0.84
27_A	41_S	0.610	0.83
11_V	61_A	0.608	0.83
11_V	64_T	0.604	0.82
8_I	31_N	0.600	0.82
32_S	56_T	0.598	0.82
8_I	12_T	0.596	0.81
38_I	45_T	0.595	0.81
15_G	42_L	0.595	0.81
61_A	65_Q	0.595	0.81
17_A	24_T	0.591	0.81
45_T	49_Y	0.584	0.80
50_T	60_D	0.570	0.78
25_A	35_K	0.564	0.78
26_G	30_V	0.559	0.77
37_T	40_A	0.553	0.76
38_I	41_S	0.552	0.76
41_S	44_T	0.548	0.76
48_D	52_V	0.545	0.75
11_V	55_A	0.526	0.73
11_V	36_I	0.526	0.73
40_A	49_Y	0.519	0.72
41_S	61_A	0.513	0.71
44_T	49_Y	0.512	0.71
25_A	48_D	0.509	0.70
27_A	42_L	0.505	0.70
11_V	54_K	0.502	0.69
9_T	16_T	0.502	0.69
29_T	39_D	0.501	0.69
29_T	32_S	0.500	0.69

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
1o75A	2	0.9231	22.5	0.79	Contact Map
4l3aA	1	0.7692	20.3	0.794	Contact Map
1cvrA	1	0.8923	20	0.795	Contact Map
2nsmA	1	0.9385	9.8	0.821	Contact Map
3nqhA	2	0.8923	8.8	0.825	Contact Map
3kcpA	1	0.8308	8.4	0.827	Contact Map
4d6gA	1	0.9385	8	0.828	Contact Map
2vzsA	1	0	7.9	0.829	Contact Map
1uwyA	1	0.9231	7.5	0.83	Contact Map
1h8lA	1	0.9385	7.4	0.83	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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