GYD - PFAM28P - GREMLIN Contacts

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GYD - GYD domain

PFAM:	PF08734	Sequences: YLLLASYTDEGIKGLKDGPERRRAAVKAAVEKLGGKLEAFYFTFGEYDVVVIVEAPDDETAAAVSLALGASGNVRTETLRAFTPEEFDKAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (89)
Sequences:	32912 (19161)
Seq/√Len:	2031.0
META:	0.982

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_D	80_R	3.222	1.00
46_E	77_E	3.106	1.00
57_D	60_T	3.058	1.00
5_A	49_V	2.924	1.00
35_G	55_A	2.341	1.00
43_T	50_V	2.243	1.00
4_L	77_E	2.080	1.00
10_E	13_K	2.078	1.00
4_L	47_Y	2.014	1.00
27_K	31_E	1.925	1.00
38_E	54_E	1.875	1.00
36_K	54_E	1.809	1.00
24_A	27_K	1.802	1.00
23_R	27_K	1.802	1.00
9_D	13_K	1.732	1.00
3_L	53_V	1.713	1.00
6_S	75_R	1.674	1.00
43_T	81_A	1.592	1.00
6_S	47_Y	1.578	1.00
4_L	79_L	1.535	1.00
2_L	50_V	1.526	1.00
59_E	86_E	1.520	1.00
83_T	86_E	1.449	1.00
14_G	17_D	1.417	1.00
39_A	52_I	1.387	1.00
55_A	61_A	1.299	1.00
35_G	64_V	1.252	1.00
31_E	36_K	1.250	1.00
28_A	32_K	1.246	1.00
59_E	89_K	1.221	1.00
29_A	35_G	1.179	1.00
2_L	81_A	1.160	1.00
41_Y	52_I	1.147	1.00
26_V	84_P	1.128	1.00
42_F	87_F	1.088	1.00
23_R	84_P	1.074	1.00
29_A	64_V	1.071	1.00
17_D	21_R	1.060	1.00
25_A	64_V	1.060	1.00
86_E	89_K	1.035	1.00
1_Y	58_D	1.007	1.00
20_E	24_A	1.002	1.00
24_A	28_A	0.998	1.00
56_P	60_T	0.982	1.00
84_P	88_D	0.972	1.00
55_A	64_V	0.969	1.00
33_L	64_V	0.963	1.00
53_V	61_A	0.935	1.00
22_R	26_V	0.929	1.00
17_D	20_E	0.922	1.00
3_L	65_S	0.916	1.00
82_F	90_A	0.914	1.00
12_I	75_R	0.913	1.00
40_F	51_V	0.910	1.00
16_K	70_A	0.905	1.00
85_E	88_D	0.902	1.00
62_A	82_F	0.896	1.00
42_F	84_P	0.893	1.00
23_R	88_D	0.876	1.00
4_L	50_V	0.873	1.00
7_Y	49_V	0.867	1.00
9_D	75_R	0.864	1.00
10_E	14_G	0.864	1.00
47_Y	77_E	0.856	1.00
6_S	77_E	0.846	1.00
43_T	79_L	0.843	1.00
55_A	60_T	0.837	1.00
62_A	66_L	0.829	1.00
21_R	24_A	0.828	1.00
25_A	29_A	0.818	1.00
44_F	82_F	0.800	1.00
44_F	80_R	0.793	1.00
85_E	89_K	0.780	1.00
45_G	48_D	0.780	1.00
7_Y	15_L	0.778	1.00
47_Y	50_V	0.777	1.00
50_V	79_L	0.770	1.00
23_R	26_V	0.766	1.00
44_F	58_D	0.759	1.00
8_T	11_G	0.758	1.00
40_F	49_V	0.751	1.00
11_G	15_L	0.746	1.00
22_R	40_F	0.727	1.00
44_F	62_A	0.726	1.00
28_A	33_L	0.714	1.00
16_K	19_P	0.704	1.00
80_R	86_E	0.697	1.00
63_A	67_A	0.695	1.00
38_E	41_Y	0.689	1.00
33_L	63_A	0.688	1.00
67_A	71_S	0.683	1.00
18_G	21_R	0.669	1.00
32_K	67_A	0.664	1.00
65_S	69_G	0.661	1.00
6_S	76_T	0.661	1.00
10_E	73_N	0.650	1.00
20_E	88_D	0.640	1.00
5_A	74_V	0.638	1.00
68_L	74_V	0.631	1.00
19_P	88_D	0.626	1.00
61_A	78_T	0.623	1.00
23_R	85_E	0.619	1.00
12_I	69_G	0.614	1.00
21_R	26_V	0.603	1.00
2_L	41_Y	0.586	1.00
46_E	79_L	0.585	1.00
42_F	49_V	0.584	1.00
23_R	40_F	0.581	1.00
2_L	43_T	0.571	1.00
61_A	65_S	0.570	1.00
26_V	29_A	0.564	1.00
67_A	70_A	0.563	1.00
22_R	88_D	0.562	1.00
58_D	62_A	0.561	1.00
27_K	32_K	0.558	1.00
25_A	68_L	0.553	1.00
19_P	87_F	0.553	1.00
19_P	22_R	0.545	1.00
4_L	46_E	0.545	1.00
12_I	66_L	0.544	1.00
65_S	78_T	0.541	1.00
44_F	78_T	0.537	1.00
14_G	18_G	0.536	1.00
63_A	90_A	0.532	1.00
40_F	84_P	0.528	1.00
33_L	67_A	0.527	1.00
16_K	21_R	0.526	1.00
35_G	53_V	0.520	1.00
37_L	40_F	0.515	1.00
3_L	76_T	0.514	1.00
38_E	52_I	0.513	1.00
6_S	46_E	0.504	1.00
71_S	74_V	0.500	1.00
69_G	78_T	0.500	1.00

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
1mliA	5	0.978	73.1	0.799	Contact Map
4un1A	1	0.956	70.4	0.803	Contact Map
2jsxA	1	0.9341	65.6	0.81	Contact Map
2cviA	2	0.8571	57.6	0.819	Contact Map
2djwA	6	0.8242	56.7	0.819	Contact Map
2zbcA	6	0.8352	56.2	0.82	Contact Map
4ch7A	1	0.9341	56.1	0.82	Contact Map
3znuA	5	0.9231	53.3	0.823	Contact Map
2w25A	6	0.978	49.1	0.827	Contact Map
4oi3A	2	0.8242	47.7	0.829	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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