DUF1599 - PFAM28P - GREMLIN Contacts

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DUF1599 - Domain of Unknown Function (DUF1599)

PFAM:	PF07659	Sequences: KNHDYGEAWRIMRLSSLTDQILIKAQRIRSIEEKGKTKVSEGIEDEFIDIINYAIMALIQL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (61)
Sequences:	7401 (2592)
Seq/√Len:	331.8
META:	0.952

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_N	7_E	2.914	1.00
31_I	37_T	2.459	1.00
42_G	45_D	2.448	1.00
44_E	48_I	2.384	1.00
20_Q	23_I	2.208	1.00
51_I	55_I	2.044	1.00
37_T	40_S	2.042	1.00
52_N	56_M	1.894	1.00
16_S	19_D	1.837	1.00
47_F	57_A	1.756	1.00
28_I	46_E	1.745	1.00
13_R	57_A	1.699	1.00
13_R	32_E	1.609	1.00
28_I	43_I	1.578	1.00
42_G	46_E	1.498	1.00
41_E	45_D	1.442	1.00
45_D	49_D	1.416	1.00
21_I	50_I	1.365	1.00
34_K	37_T	1.356	1.00
32_E	47_F	1.328	1.00
30_S	34_K	1.297	1.00
17_L	57_A	1.283	1.00
29_R	33_E	1.260	1.00
2_N	56_M	1.238	1.00
4_D	39_V	1.214	1.00
19_D	23_I	1.178	1.00
51_I	54_A	1.175	1.00
15_S	18_T	1.166	1.00
18_T	26_Q	1.138	1.00
22_L	26_Q	1.107	1.00
44_E	58_L	1.064	1.00
54_A	57_A	1.024	1.00
11_I	18_T	0.984	1.00
26_Q	29_R	0.980	1.00
9_W	57_A	0.960	1.00
37_T	41_E	0.949	1.00
15_S	33_E	0.917	1.00
25_A	50_I	0.914	1.00
17_L	50_I	0.886	1.00
10_R	60_Q	0.853	1.00
24_K	27_R	0.839	1.00
32_E	43_I	0.832	1.00
50_I	54_A	0.819	1.00
9_W	56_M	0.807	1.00
1_K	5_Y	0.796	1.00
18_T	25_A	0.786	1.00
3_H	7_E	0.783	1.00
46_E	49_D	0.774	1.00
31_I	35_G	0.773	1.00
48_I	58_L	0.771	1.00
34_K	38_K	0.736	0.99
28_I	32_E	0.726	0.99
17_L	25_A	0.717	0.99
12_M	15_S	0.699	0.99
18_T	29_R	0.684	0.99
41_E	49_D	0.681	0.99
16_S	24_K	0.673	0.99
12_M	16_S	0.672	0.99
8_A	26_Q	0.671	0.99
14_L	28_I	0.670	0.99
20_Q	24_K	0.668	0.99
41_E	46_E	0.667	0.99
31_I	43_I	0.653	0.99
13_R	16_S	0.643	0.98
29_R	32_E	0.640	0.98
43_I	47_F	0.637	0.98
3_H	38_K	0.634	0.98
11_I	14_L	0.625	0.98
25_A	29_R	0.623	0.98
14_L	18_T	0.614	0.98
25_A	28_I	0.611	0.98
16_S	20_Q	0.608	0.98
6_G	9_W	0.600	0.98
4_D	37_T	0.596	0.97
11_I	29_R	0.591	0.97
6_G	20_Q	0.572	0.97
16_S	21_I	0.563	0.96
19_D	22_L	0.559	0.96
34_K	39_V	0.558	0.96
13_R	18_T	0.553	0.96
13_R	17_L	0.552	0.96
10_R	13_R	0.543	0.96
47_F	51_I	0.540	0.95
49_D	56_M	0.533	0.95
52_N	59_I	0.530	0.95
24_K	45_D	0.520	0.94
27_R	31_I	0.515	0.94
14_L	61_L	0.514	0.94
11_I	33_E	0.509	0.94
47_F	54_A	0.506	0.94
7_E	56_M	0.504	0.93
12_M	57_A	0.500	0.93

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
2p06A	4	0.9508	55.1	0.808	Contact Map
4wsrA	5	1	8.3	0.873	Contact Map
4rvqA	1	0.9672	7.3	0.876	Contact Map
4mc5A	3	1	5.4	0.883	Contact Map
2wr1A	3	1	5.4	0.883	Contact Map
2yp5A	3	1	5	0.885	Contact Map
4o5nB	3	1	4.3	0.889	Contact Map
4f23A	3	0.9672	4	0.891	Contact Map
4bsgB	3	1	3.9	0.891	Contact Map
4lvhA	3	0.2295	3.6	0.893	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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