DUF2061 - PFAM28P - GREMLIN Contacts

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DUF2061 - Predicted membrane protein (DUF2061)

PFAM:	PF09834	Sequences: IAKTISWRIIGTLDTFLISYLITGSLKLALSIGLIEVVTKTVLYYLHERAWN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (52)
Sequences:	14354 (8092)
Seq/√Len:	1122.1
META:	0.951

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_F	33_G	3.154	1.00
6_S	47_H	3.056	1.00
19_S	32_I	2.788	1.00
4_T	41_T	2.124	1.00
27_K	31_S	1.953	1.00
30_L	33_G	1.933	1.00
36_E	40_K	1.851	1.00
14_D	43_L	1.677	1.00
20_Y	29_A	1.644	1.00
14_D	39_T	1.595	1.00
17_L	21_L	1.547	1.00
20_Y	26_L	1.500	1.00
12_T	37_V	1.479	1.00
46_L	50_A	1.377	1.00
34_L	37_V	1.342	1.00
11_G	40_K	1.335	1.00
44_Y	47_H	1.326	1.00
27_K	30_L	1.311	1.00
28_L	31_S	1.257	1.00
7_W	11_G	1.203	1.00
34_L	38_V	1.160	1.00
8_R	12_T	1.108	1.00
25_S	28_L	1.106	1.00
38_V	42_V	1.092	1.00
28_L	36_E	1.036	1.00
22_I	28_L	0.992	1.00
5_I	9_I	0.954	1.00
7_W	44_Y	0.906	1.00
12_T	33_G	0.887	1.00
15_T	36_E	0.882	1.00
23_T	32_I	0.879	1.00
11_G	14_D	0.873	1.00
42_V	46_L	0.871	1.00
9_I	13_L	0.862	1.00
8_R	41_T	0.849	1.00
12_T	16_F	0.847	1.00
23_T	29_A	0.838	1.00
15_T	40_K	0.823	1.00
4_T	44_Y	0.815	1.00
16_F	29_A	0.813	1.00
39_T	43_L	0.810	1.00
11_G	36_E	0.810	1.00
45_Y	49_R	0.797	1.00
23_T	28_L	0.757	1.00
3_K	48_E	0.740	1.00
7_W	47_H	0.720	1.00
20_Y	23_T	0.711	1.00
2_A	5_I	0.699	1.00
13_L	17_L	0.692	1.00
16_F	30_L	0.689	1.00
10_I	43_L	0.688	1.00
20_Y	24_G	0.686	1.00
6_S	10_I	0.672	1.00
14_D	21_L	0.671	1.00
15_T	32_I	0.652	1.00
31_S	34_L	0.646	1.00
30_L	34_L	0.644	1.00
7_W	37_V	0.639	1.00
7_W	41_T	0.632	1.00
47_H	51_W	0.626	1.00
46_L	49_R	0.621	1.00
18_I	35_I	0.617	1.00
29_A	33_G	0.604	1.00
49_R	52_N	0.593	1.00
25_S	31_S	0.585	1.00
4_T	52_N	0.577	1.00
22_I	35_I	0.568	1.00
10_I	13_L	0.568	1.00
21_L	24_G	0.564	1.00
14_D	17_L	0.563	1.00
25_S	29_A	0.545	1.00
31_S	35_I	0.527	1.00
15_T	19_S	0.522	1.00
5_I	8_R	0.510	1.00
19_S	23_T	0.509	1.00
2_A	49_R	0.505	1.00
44_Y	48_E	0.500	1.00
41_T	45_Y	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
1ciiA	1	0.9808	3.9	0.841	Contact Map
5a63B	1	1	2.3	0.859	Contact Map
2qtsA	4	0.8269	1.9	0.864	Contact Map
4kf7A	1	0.4423	1.7	0.867	Contact Map
4wd8A	3	0.9423	1.6	0.87	Contact Map
4rdqA	5	0.9808	1.5	0.873	Contact Map
2k1oA	2	0.3462	1.3	0.877	Contact Map
2i88A	1	0.9231	1.3	0.878	Contact Map
1colA	1	0.9808	0.9	0.888	Contact Map
3fewX	1	0.9808	0.9	0.888	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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