DUF2242 - PFAM28P - GREMLIN Contacts

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DUF2242 - Uncharacterized protein conserved in bacteria (DUF2242)

PFAM:	PF10001	Sequences: CEAARRALLSQGYVIDRADADLVTGRKSFQPEPEVHVEIEFRVVCAPDGKGGGGSTVFVNALQDRYALKKSNNSASVGVGALGSVSLPFGSSDDSLVKVASETITDPDFYDRFFALVERYL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (121)
Sequences:	640 (338)
Seq/√Len:	30.8
META:	0.822

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_S	116_L	4.143	1.00
39_I	104_I	2.753	1.00
2_E	5_R	2.732	1.00
26_R	40_E	2.729	1.00
77_V	85_V	2.409	0.99
61_A	65_R	2.308	0.99
20_A	23_V	2.167	0.98
58_F	120_Y	2.138	0.98
32_E	35_V	2.107	0.98
24_T	42_R	2.014	0.97
7_A	10_S	1.992	0.97
42_R	60_N	1.936	0.97
81_A	89_F	1.872	0.96
17_R	20_A	1.871	0.96
53_G	59_V	1.816	0.95
57_V	117_V	1.790	0.95
69_K	112_R	1.776	0.95
29_F	104_I	1.776	0.95
100_A	112_R	1.749	0.94
84_S	88_P	1.748	0.94
18_A	58_F	1.695	0.93
43_V	113_F	1.665	0.92
72_N	90_G	1.635	0.92
28_S	85_V	1.587	0.90
64_D	101_S	1.574	0.90
108_D	118_E	1.563	0.90
4_A	43_V	1.537	0.89
20_A	120_Y	1.534	0.89
29_F	41_F	1.503	0.88
1_C	4_A	1.484	0.87
59_V	107_P	1.449	0.86
49_G	52_G	1.447	0.86
61_A	91_S	1.428	0.85
61_A	109_F	1.411	0.84
102_E	106_D	1.387	0.83
96_L	117_V	1.334	0.81
35_V	67_A	1.333	0.81
115_A	118_E	1.311	0.80
77_V	80_G	1.267	0.77
111_D	119_R	1.263	0.77
8_L	12_G	1.248	0.76
27_K	112_R	1.244	0.76
75_A	94_D	1.211	0.74
62_L	74_S	1.194	0.73
77_V	86_S	1.148	0.70
49_G	57_V	1.130	0.69
19_D	58_F	1.124	0.68
47_P	53_G	1.115	0.67
47_P	51_G	1.098	0.66
65_R	69_K	1.094	0.66
25_G	102_E	1.091	0.66
53_G	108_D	1.090	0.66
62_L	120_Y	1.076	0.65
40_E	56_T	1.074	0.65
47_P	57_V	1.048	0.63
68_L	95_S	1.048	0.63
25_G	32_E	1.042	0.62
2_E	6_R	1.039	0.62
28_S	38_E	1.037	0.62
57_V	82_L	1.028	0.61
38_E	69_K	1.013	0.60
15_I	49_G	0.994	0.58
39_I	60_N	0.992	0.58
70_K	76_S	0.989	0.58
64_D	67_A	0.975	0.57
48_D	54_G	0.961	0.56
71_S	81_A	0.960	0.56
16_D	104_I	0.954	0.55
75_A	83_G	0.953	0.55
29_F	63_Q	0.947	0.55
33_P	56_T	0.946	0.55
39_I	72_N	0.932	0.54
62_L	66_Y	0.911	0.52
75_A	85_V	0.906	0.51
73_N	96_L	0.905	0.51
82_L	99_V	0.903	0.51
37_V	57_V	0.889	0.50
6_R	55_S	0.885	0.50
16_D	41_F	0.880	0.49
25_G	56_T	0.873	0.49
38_E	58_F	0.871	0.49
81_A	106_D	0.846	0.47
14_V	118_E	0.844	0.46
30_Q	61_A	0.839	0.46
11_Q	96_L	0.836	0.46
60_N	92_S	0.835	0.46
41_F	59_V	0.829	0.45
67_A	94_D	0.827	0.45
30_Q	36_H	0.823	0.45
4_A	69_K	0.813	0.44
39_I	106_D	0.811	0.44
17_R	55_S	0.810	0.44
67_A	112_R	0.801	0.43
43_V	80_G	0.798	0.43
70_K	94_D	0.792	0.42
27_K	63_Q	0.786	0.42
18_A	23_V	0.784	0.42
28_S	96_L	0.784	0.42
25_G	118_E	0.771	0.41
13_Y	45_C	0.769	0.41
1_C	8_L	0.769	0.41
57_V	105_T	0.768	0.40
74_S	86_S	0.768	0.40
2_E	20_A	0.765	0.40
23_V	62_L	0.762	0.40
75_A	92_S	0.757	0.40
77_V	87_L	0.751	0.39
95_S	98_K	0.750	0.39
100_A	105_T	0.746	0.39
28_S	61_A	0.746	0.39
39_I	65_R	0.741	0.38
15_I	50_K	0.735	0.38
2_E	97_V	0.727	0.37
32_E	52_G	0.726	0.37
15_I	18_A	0.725	0.37
73_N	91_S	0.718	0.37
24_T	60_N	0.716	0.36
57_V	116_L	0.716	0.36
69_K	85_V	0.715	0.36
21_D	63_Q	0.715	0.36
63_Q	90_G	0.710	0.36
49_G	54_G	0.708	0.36
60_N	107_P	0.707	0.36
64_D	78_G	0.702	0.35
23_V	90_G	0.699	0.35
88_P	96_L	0.690	0.35
26_R	58_F	0.674	0.33
23_V	58_F	0.669	0.33
5_R	14_V	0.659	0.32
24_T	54_G	0.651	0.32
72_N	85_V	0.651	0.32
54_G	59_V	0.650	0.32
94_D	97_V	0.649	0.32
43_V	70_K	0.645	0.31
40_E	55_S	0.645	0.31
11_Q	99_V	0.644	0.31
31_P	35_V	0.644	0.31
1_C	6_R	0.639	0.31
57_V	112_R	0.637	0.31
44_V	99_V	0.629	0.30
96_L	99_V	0.625	0.30
25_G	46_A	0.623	0.30
9_L	12_G	0.621	0.30
15_I	65_R	0.621	0.30
25_G	49_G	0.620	0.30
15_I	73_N	0.619	0.30
10_S	30_Q	0.618	0.30
55_S	107_P	0.612	0.29
71_S	74_S	0.601	0.28
30_Q	101_S	0.601	0.28
64_D	74_S	0.592	0.28
14_V	91_S	0.586	0.27
32_E	38_E	0.585	0.27
77_V	98_K	0.581	0.27
29_F	79_V	0.581	0.27
1_C	5_R	0.579	0.27
33_P	50_K	0.571	0.26
36_H	101_S	0.563	0.26
1_C	12_G	0.556	0.26
6_R	86_S	0.552	0.25
38_E	86_S	0.552	0.25
64_D	83_G	0.551	0.25
37_V	80_G	0.547	0.25
24_T	46_A	0.544	0.25
75_A	86_S	0.542	0.25
22_L	58_F	0.535	0.24
52_G	107_P	0.535	0.24
33_P	107_P	0.531	0.24
27_K	45_C	0.529	0.24
38_E	77_V	0.527	0.24
7_A	11_Q	0.525	0.24
63_Q	111_D	0.523	0.24
42_R	104_I	0.522	0.24
2_E	23_V	0.518	0.23
17_R	49_G	0.512	0.23
87_L	108_D	0.511	0.23
91_S	109_F	0.507	0.23
92_S	95_S	0.507	0.23
87_L	97_V	0.504	0.23
70_K	95_S	0.500	0.22
37_V	85_V	0.500	0.22
68_L	99_V	0.500	0.22

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
2ab1A	1	0.3719	13.3	0.944	Contact Map
3qneA	2	0.0661	9.7	0.947	Contact Map
4e18B	1	0.1488	8	0.949	Contact Map
3nrkA	3	0.2479	7.6	0.95	Contact Map
3p9yA	1	0.5785	6.8	0.95	Contact Map
4ywtA	1	0.8264	6.1	0.951	Contact Map
2dulA	2	0.3223	5.9	0.952	Contact Map
5a21G	1	0.3802	4.8	0.954	Contact Map
4ixjA	1	0.7355	4.6	0.954	Contact Map
1mk4A	2	0.3471	4.5	0.954	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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