DUF2095 - PFAM28P - GREMLIN Contacts

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DUF2095 - Uncharacterized protein conserved in archaea (DUF2095)

PFAM:	PF09868	Sequences: KKKKRPVDDFAWQEIDKEEFKKMFPNLAKELEEENKVSIDSVRTDEEEAVEEEEKAASDKFRGYNPDVIDFIRRCDTEEQAEEIIDYLEKRGEITKEYAEELRKQLKEKGVRSFGPKKEEGYYFKHGRH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	129 (113)
Sequences:	545 (395)
Seq/√Len:	37.2
META:	0.945

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
105_Q	113_S	4.258	1.00
81_A	111_V	4.028	1.00
73_R	118_K	3.263	1.00
26_N	29_K	3.147	1.00
89_E	103_R	3.127	1.00
85_I	102_L	3.088	1.00
76_D	80_Q	3.050	1.00
68_V	88_L	2.880	1.00
65_N	71_F	2.817	1.00
72_I	81_A	2.548	1.00
104_K	108_E	2.520	1.00
82_E	86_D	2.509	1.00
61_F	64_Y	2.328	1.00
105_Q	109_K	2.267	0.99
17_K	32_E	1.958	0.98
121_G	124_F	1.808	0.97
89_E	96_K	1.766	0.97
19_E	23_M	1.681	0.96
120_E	124_F	1.616	0.95
112_R	117_K	1.614	0.95
64_Y	68_V	1.604	0.94
86_D	103_R	1.562	0.94
71_F	84_I	1.517	0.93
118_K	123_Y	1.488	0.92
52_E	55_K	1.403	0.89
76_D	117_K	1.392	0.89
26_N	31_L	1.321	0.86
121_G	125_K	1.298	0.85
29_K	35_N	1.271	0.84
78_E	111_V	1.265	0.84
82_E	103_R	1.252	0.83
30_E	110_G	1.230	0.82
94_I	98_Y	1.221	0.81
71_F	124_F	1.166	0.78
31_L	126_H	1.159	0.78
95_T	98_Y	1.150	0.77
59_D	62_R	1.135	0.76
29_K	33_E	1.126	0.76
69_I	118_K	1.115	0.75
119_E	125_K	1.095	0.74
80_Q	120_E	1.081	0.73
78_E	92_G	1.077	0.72
99_A	103_R	1.055	0.71
96_K	100_E	1.046	0.70
67_D	70_D	1.004	0.67
19_E	22_K	1.000	0.67
72_I	85_I	0.997	0.66
95_T	101_E	0.991	0.66
45_D	48_E	0.986	0.66
46_E	80_Q	0.968	0.64
72_I	102_L	0.949	0.63
69_I	72_I	0.948	0.63
19_E	72_I	0.948	0.63
76_D	84_I	0.946	0.62
65_N	87_Y	0.932	0.61
14_E	20_F	0.918	0.60
20_F	31_L	0.915	0.60
84_I	117_K	0.902	0.59
20_F	28_A	0.900	0.58
79_E	121_G	0.896	0.58
82_E	107_K	0.887	0.57
69_I	73_R	0.877	0.56
97_E	111_V	0.875	0.56
18_E	103_R	0.864	0.55
91_R	97_E	0.850	0.54
60_K	80_Q	0.846	0.54
22_K	77_T	0.841	0.53
38_S	121_G	0.840	0.53
64_Y	70_D	0.835	0.53
40_D	58_S	0.830	0.52
76_D	112_R	0.821	0.52
72_I	111_V	0.818	0.51
59_D	124_F	0.816	0.51
83_E	106_L	0.815	0.51
34_E	108_E	0.809	0.51
88_L	94_I	0.807	0.50
36_K	82_E	0.807	0.50
89_E	99_A	0.791	0.49
83_E	94_I	0.787	0.49
69_I	102_L	0.785	0.48
80_Q	112_R	0.777	0.48
63_G	124_F	0.773	0.47
33_E	65_N	0.771	0.47
26_N	62_R	0.762	0.46
108_E	121_G	0.751	0.45
35_N	38_S	0.743	0.45
39_I	43_R	0.743	0.45
69_I	75_C	0.741	0.45
75_C	88_L	0.739	0.44
98_Y	102_L	0.736	0.44
80_Q	124_F	0.734	0.44
50_V	54_E	0.728	0.43
106_L	114_F	0.728	0.43
75_C	84_I	0.727	0.43
23_M	126_H	0.722	0.43
47_E	72_I	0.716	0.42
65_N	101_E	0.702	0.41
18_E	78_E	0.697	0.41
41_S	122_Y	0.696	0.41
42_V	87_Y	0.696	0.41
84_I	91_R	0.695	0.41
88_L	123_Y	0.695	0.41
39_I	105_Q	0.695	0.41
42_V	122_Y	0.691	0.40
100_E	108_E	0.689	0.40
20_F	87_Y	0.681	0.39
36_K	69_I	0.676	0.39
49_A	97_E	0.671	0.39
36_K	40_D	0.671	0.39
38_S	41_S	0.666	0.38
72_I	91_R	0.665	0.38
19_E	67_D	0.662	0.38
51_E	79_E	0.655	0.37
23_M	82_E	0.653	0.37
94_I	109_K	0.642	0.36
31_L	67_D	0.638	0.36
35_N	65_N	0.625	0.35
99_A	113_S	0.625	0.35
63_G	71_F	0.614	0.34
86_D	116_P	0.614	0.34
85_I	99_A	0.610	0.34
85_I	105_Q	0.610	0.34
35_N	72_I	0.609	0.33
16_D	37_V	0.605	0.33
87_Y	119_E	0.604	0.33
50_V	86_D	0.603	0.33
100_E	126_H	0.603	0.33
29_K	111_V	0.601	0.33
100_E	107_K	0.600	0.33
78_E	107_K	0.599	0.33
37_V	69_I	0.596	0.32
27_L	74_R	0.595	0.32
28_A	67_D	0.592	0.32
79_E	97_E	0.586	0.32
70_D	88_L	0.582	0.31
107_K	122_Y	0.581	0.31
40_D	70_D	0.581	0.31
19_E	28_A	0.580	0.31
20_F	114_F	0.577	0.31
88_L	92_G	0.567	0.30
16_D	19_E	0.566	0.30
103_R	125_K	0.566	0.30
82_E	120_E	0.564	0.30
28_A	32_E	0.561	0.30
61_F	84_I	0.560	0.30
73_R	81_A	0.559	0.30
40_D	63_G	0.553	0.29
119_E	124_F	0.552	0.29
88_L	93_E	0.551	0.29
44_T	80_Q	0.551	0.29
78_E	104_K	0.548	0.29
17_K	22_K	0.546	0.29
36_K	108_E	0.545	0.29
15_I	28_A	0.544	0.29
94_I	126_H	0.543	0.28
43_R	73_R	0.541	0.28
99_A	114_F	0.537	0.28
101_E	105_Q	0.536	0.28
21_K	39_I	0.536	0.28
27_L	118_K	0.533	0.28
18_E	38_S	0.530	0.28
77_T	80_Q	0.521	0.27
76_D	107_K	0.519	0.27
58_S	95_T	0.513	0.26
79_E	96_K	0.511	0.26
38_S	92_G	0.510	0.26
98_Y	122_Y	0.509	0.26
60_K	84_I	0.505	0.26
53_E	57_A	0.501	0.26
53_E	95_T	0.500	0.25

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
3qweA	2	0.5814	15.7	0.941	Contact Map
4jupA	2	0.5504	10.7	0.945	Contact Map
2xvsA	1	0.3953	8.1	0.948	Contact Map
1ng7A	2	0.4419	8	0.949	Contact Map
4edgA	1	0.5814	7.7	0.949	Contact Map
4rhwE	1	0.5194	7.5	0.949	Contact Map
2wujA	2	0.3798	6.8	0.95	Contact Map
3ml6A	1	0.6279	6.1	0.951	Contact Map
2yy0A	6	0.3488	6.1	0.951	Contact Map
2choA	1	0.8527	5.7	0.952	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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