DUF2129 - PFAM28P - GREMLIN Contacts

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DUF2129 - Uncharacterized protein conserved in bacteria (DUF2129)

PFAM:	PF09902	Sequences: RQGLIVWLYSLKQAKQLRKYGNVHYVSKKMKYVVLYVNQDDVEETIKKLKKLPFVKKVEPSYRPEIKTEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (70)
Sequences:	885 (592)
Seq/√Len:	70.8
META:	0.429

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_Q	39_Q	3.439	1.00
38_N	41_D	3.332	1.00
23_V	33_V	3.229	1.00
7_W	59_E	3.055	1.00
41_D	44_E	3.038	1.00
62_Y	65_E	2.630	1.00
46_I	60_P	2.381	1.00
5_I	34_V	2.281	1.00
8_L	33_V	2.115	1.00
67_K	70_F	2.084	1.00
46_I	50_K	2.041	1.00
42_V	46_I	1.881	1.00
27_S	30_M	1.785	1.00
20_Y	52_L	1.502	0.99
2_Q	64_P	1.453	0.99
37_V	45_T	1.423	0.98
9_Y	56_K	1.390	0.98
8_L	14_A	1.371	0.98
11_L	33_V	1.290	0.97
13_Q	16_Q	1.255	0.97
39_Q	65_E	1.213	0.96
44_E	47_K	1.170	0.95
8_L	13_Q	1.165	0.95
4_L	46_I	1.126	0.94
37_V	42_V	1.124	0.94
40_D	43_E	1.115	0.93
4_L	37_V	1.114	0.93
10_S	18_R	1.064	0.92
4_L	42_V	1.054	0.91
34_V	38_N	1.015	0.90
7_W	22_N	0.999	0.89
44_E	50_K	0.973	0.88
2_Q	65_E	0.962	0.87
63_R	68_T	0.957	0.87
3_G	24_H	0.949	0.86
61_S	66_I	0.940	0.86
3_G	62_Y	0.933	0.85
10_S	13_Q	0.890	0.83
4_L	58_V	0.862	0.81
2_Q	5_I	0.849	0.80
14_A	26_V	0.846	0.79
8_L	26_V	0.835	0.78
18_R	23_V	0.833	0.78
25_Y	31_K	0.821	0.77
20_Y	44_E	0.813	0.77
45_T	49_L	0.803	0.76
42_V	45_T	0.800	0.75
4_L	35_L	0.796	0.75
11_L	26_V	0.784	0.74
12_K	26_V	0.783	0.74
15_K	52_L	0.782	0.74
12_K	21_G	0.750	0.71
46_I	49_L	0.750	0.71
28_K	43_E	0.748	0.70
16_Q	20_Y	0.725	0.68
9_Y	70_F	0.714	0.67
25_Y	39_Q	0.707	0.66
10_S	51_K	0.701	0.65
46_I	69_E	0.692	0.64
31_K	49_L	0.686	0.64
3_G	34_V	0.671	0.62
64_P	68_T	0.670	0.62
33_V	63_R	0.663	0.61
12_K	15_K	0.650	0.60
25_Y	30_M	0.649	0.59
28_K	61_S	0.649	0.59
15_K	31_K	0.641	0.58
14_A	18_R	0.639	0.58
39_Q	48_K	0.632	0.57
6_V	58_V	0.625	0.57
20_Y	45_T	0.624	0.56
44_E	48_K	0.621	0.56
6_V	35_L	0.619	0.56
39_Q	42_V	0.615	0.55
7_W	53_P	0.605	0.54
5_I	52_L	0.600	0.54
18_R	56_K	0.597	0.53
16_Q	54_F	0.594	0.53
20_Y	48_K	0.590	0.52
66_I	70_F	0.588	0.52
40_D	55_V	0.588	0.52
2_Q	42_V	0.582	0.51
27_S	54_F	0.573	0.50
1_R	6_V	0.569	0.50
26_V	29_K	0.568	0.50
47_K	50_K	0.565	0.49
48_K	51_K	0.565	0.49
39_Q	64_P	0.564	0.49
11_L	53_P	0.563	0.49
18_R	64_P	0.561	0.49
10_S	31_K	0.558	0.48
15_K	59_E	0.557	0.48
21_G	52_L	0.556	0.48
23_V	50_K	0.547	0.47
9_Y	67_K	0.544	0.47
22_N	37_V	0.539	0.46
59_E	62_Y	0.537	0.46
43_E	58_V	0.534	0.45
11_L	14_A	0.522	0.44
19_K	25_Y	0.518	0.44
49_L	52_L	0.515	0.43
4_L	21_G	0.509	0.42
53_P	66_I	0.503	0.42
6_V	47_K	0.503	0.42
4_L	48_K	0.500	0.41

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
3wiuA	2	0.9429	22.8	0.875	Contact Map
3whiA	2	0.9429	16.6	0.882	Contact Map
2x4jA	3	0.5429	16.1	0.883	Contact Map
1r6vA	1	1	14.8	0.885	Contact Map
3afgA	1	1	14.8	0.885	Contact Map
1u0sA	1	0.9	12.4	0.888	Contact Map
1q5yA	4	0.9571	8.3	0.897	Contact Map
4n8nA	1	0.6286	8.1	0.898	Contact Map
2c5sA	2	0.9429	7.5	0.899	Contact Map
2hzaA	3	0.9286	6.3	0.902	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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