DUF651 - PFAM28P - GREMLIN Contacts

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DUF651 - Archaeal protein of unknown function (DUF651)

PFAM:	PF04895	Sequences: EGYRGRKTYASIGGGYYAARLAVLEYLEKIKRQAGVLVLREITPEYWAPLGVWVVRENVRKALKQKPLKFDSLEEALEYISKRLKIPLSRWLKKSKLLKELLTQKRLTDF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	110 (110)
Sequences:	3798 (2573)
Seq/√Len:	245.3
META:	0.943

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_K	109_D	3.797	1.00
26_Y	30_I	3.599	1.00
70_F	79_Y	2.807	1.00
10_A	17_Y	2.800	1.00
68_L	79_Y	2.735	1.00
71_D	75_E	2.510	1.00
72_S	75_E	2.506	1.00
19_A	55_V	2.506	1.00
26_Y	29_K	2.218	1.00
27_L	34_A	2.206	1.00
54_V	58_N	2.182	1.00
23_V	36_V	2.117	1.00
25_E	60_R	2.111	1.00
61_K	64_K	2.059	1.00
50_L	54_V	1.989	1.00
6_R	10_A	1.958	1.00
19_A	38_V	1.949	1.00
74_E	78_E	1.920	1.00
18_A	55_V	1.919	1.00
22_A	60_R	1.898	1.00
23_V	63_L	1.788	1.00
99_K	103_T	1.765	1.00
52_V	55_V	1.593	1.00
79_Y	82_K	1.503	1.00
12_I	15_G	1.501	1.00
81_S	88_L	1.494	1.00
19_A	59_V	1.491	1.00
61_K	65_Q	1.470	1.00
73_L	76_A	1.460	1.00
90_R	93_K	1.302	1.00
46_Y	54_V	1.298	1.00
15_G	55_V	1.288	1.00
8_T	11_S	1.284	1.00
58_N	61_K	1.266	1.00
78_E	81_S	1.219	1.00
55_V	59_V	1.201	1.00
86_I	91_W	1.175	1.00
1_E	4_R	1.171	1.00
27_L	36_V	1.137	1.00
18_A	52_V	1.078	1.00
2_G	16_Y	1.074	1.00
23_V	38_V	1.073	1.00
52_V	56_R	1.050	1.00
15_G	54_V	1.041	1.00
81_S	87_P	1.035	1.00
79_Y	83_R	1.030	1.00
10_A	13_G	1.030	1.00
24_L	28_E	1.021	1.00
96_K	99_K	1.017	1.00
40_R	46_Y	1.004	1.00
46_Y	50_L	1.000	1.00
42_I	49_P	0.991	1.00
96_K	100_E	0.976	1.00
18_A	22_A	0.975	1.00
92_L	102_L	0.974	1.00
74_E	102_L	0.971	1.00
43_T	85_K	0.970	1.00
78_E	82_K	0.967	1.00
90_R	94_K	0.964	1.00
81_S	89_S	0.961	1.00
87_P	90_R	0.953	1.00
26_Y	63_L	0.950	1.00
37_L	97_L	0.942	1.00
22_A	25_E	0.901	1.00
89_S	93_K	0.895	1.00
15_G	22_A	0.888	1.00
75_E	78_E	0.886	1.00
66_K	69_K	0.874	0.99
105_K	108_T	0.872	0.99
38_V	62_A	0.870	0.99
15_G	21_L	0.869	0.99
39_L	76_A	0.866	0.99
3_Y	33_Q	0.859	0.99
4_R	7_K	0.851	0.99
57_E	64_K	0.835	0.99
106_R	109_D	0.832	0.99
84_L	87_P	0.829	0.99
29_K	64_K	0.813	0.99
105_K	110_F	0.807	0.99
39_L	91_W	0.798	0.99
22_A	59_V	0.796	0.99
40_R	54_V	0.789	0.99
38_V	59_V	0.776	0.99
21_L	60_R	0.771	0.99
65_Q	68_L	0.758	0.99
1_E	5_G	0.745	0.98
15_G	42_I	0.741	0.98
46_Y	62_A	0.736	0.98
44_P	85_K	0.730	0.98
13_G	55_V	0.724	0.98
43_T	84_L	0.720	0.98
53_W	91_W	0.709	0.98
93_K	99_K	0.704	0.98
2_G	100_E	0.702	0.98
12_I	19_A	0.702	0.98
40_R	55_V	0.700	0.98
97_L	100_E	0.695	0.97
24_L	53_W	0.687	0.97
70_F	76_A	0.686	0.97
70_F	77_L	0.685	0.97
88_L	92_L	0.679	0.97
43_T	48_A	0.667	0.97
44_P	47_W	0.665	0.97
35_G	97_L	0.665	0.97
42_I	58_N	0.660	0.96
9_Y	17_Y	0.660	0.96
13_G	52_V	0.658	0.96
77_L	80_I	0.651	0.96
100_E	106_R	0.650	0.96
76_A	80_I	0.649	0.96
84_L	88_L	0.646	0.96
39_L	84_L	0.646	0.96
5_G	8_T	0.639	0.96
57_E	60_R	0.636	0.96
55_V	58_N	0.635	0.96
12_I	91_W	0.634	0.96
17_Y	52_V	0.628	0.95
41_E	91_W	0.628	0.95
73_L	101_L	0.625	0.95
15_G	18_A	0.623	0.95
77_L	98_L	0.618	0.95
77_L	92_L	0.618	0.95
25_E	29_K	0.614	0.95
30_I	36_V	0.610	0.95
73_L	98_L	0.604	0.94
6_R	11_S	0.603	0.94
75_E	79_Y	0.591	0.94
68_L	82_K	0.591	0.94
37_L	95_S	0.591	0.94
38_V	55_V	0.581	0.93
9_Y	16_Y	0.579	0.93
2_G	7_K	0.575	0.93
41_E	85_K	0.566	0.92
47_W	53_W	0.565	0.92
42_I	50_L	0.561	0.92
35_G	54_V	0.561	0.92
6_R	9_Y	0.560	0.92
15_G	19_A	0.558	0.92
19_A	53_W	0.552	0.91
5_G	11_S	0.551	0.91
69_K	82_K	0.550	0.91
95_S	98_L	0.548	0.91
16_Y	52_V	0.546	0.91
9_Y	20_R	0.543	0.90
37_L	98_L	0.542	0.90
15_G	43_T	0.539	0.90
91_W	94_K	0.536	0.90
8_T	13_G	0.535	0.90
23_V	27_L	0.525	0.89
71_D	90_R	0.524	0.89
22_A	56_R	0.524	0.89
31_K	70_F	0.523	0.89
28_E	31_K	0.523	0.89
18_A	42_I	0.521	0.89
68_L	75_E	0.518	0.88
1_E	9_Y	0.518	0.88
2_G	35_G	0.511	0.88
43_T	54_V	0.507	0.87
22_A	55_V	0.506	0.87
38_V	58_N	0.504	0.87
96_K	107_L	0.504	0.87
6_R	16_Y	0.504	0.87
83_R	87_P	0.504	0.87
4_R	8_T	0.503	0.87
30_I	63_L	0.500	0.86

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
2gfqA	3	0.7545	12.2	0.934	Contact Map
3ugoA	1	0.2909	6.7	0.941	Contact Map
1rxwA	1	0.6545	6.5	0.941	Contact Map
1io7A	1	0.7	6	0.942	Contact Map
2ahmE	5	0.5636	5.3	0.944	Contact Map
2hx6A	1	0.5545	5.3	0.944	Contact Map
1t35A	5	0.7636	5.2	0.944	Contact Map
1qhkA	1	0.3909	5.2	0.944	Contact Map
3ub0A	1	0.5909	5.2	0.944	Contact Map
2yy0A	6	0.3364	5.1	0.944	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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