DUF2335 - PFAM28P - GREMLIN Contacts

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DUF2335 - Predicted membrane protein (DUF2335)

PFAM:	PF10097	Sequences: PPPEILAEYEEILPGAAERILAMAEKQQAHRHELEKKVLEANIRRSRRGQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	50 (49)
Sequences:	3473 (3086)
Seq/√Len:	440.8
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
7_A	11_E	2.440	1.00
28_Q	32_H	2.180	1.00
13_L	16_A	2.148	1.00
2_P	5_I	2.129	1.00
26_K	29_A	2.128	1.00
16_A	21_L	2.124	1.00
33_E	36_K	2.112	1.00
10_E	15_G	1.948	1.00
19_R	25_E	1.839	1.00
18_E	22_A	1.791	1.00
10_E	17_A	1.788	1.00
27_Q	31_R	1.661	1.00
22_A	26_K	1.563	1.00
37_K	40_E	1.449	1.00
30_H	35_E	1.433	1.00
44_R	47_R	1.357	1.00
4_E	8_E	1.335	1.00
26_K	32_H	1.192	1.00
27_Q	32_H	1.188	1.00
8_E	11_E	1.142	1.00
30_H	34_L	1.099	1.00
23_M	28_Q	1.079	1.00
5_I	8_E	1.059	1.00
7_A	12_I	1.055	1.00
13_L	18_E	1.035	1.00
22_A	25_E	1.005	1.00
42_N	45_R	0.959	1.00
38_V	42_N	0.931	1.00
10_E	13_L	0.912	1.00
31_R	35_E	0.906	1.00
44_R	48_R	0.886	1.00
29_A	33_E	0.863	1.00
13_L	21_L	0.843	1.00
6_L	17_A	0.836	1.00
24_A	28_Q	0.806	1.00
42_N	46_S	0.802	1.00
34_L	39_L	0.791	1.00
33_E	37_K	0.780	1.00
15_G	18_E	0.761	1.00
43_I	47_R	0.753	1.00
34_L	38_V	0.748	1.00
36_K	40_E	0.729	1.00
27_Q	35_E	0.719	1.00
43_I	46_S	0.715	1.00
41_A	45_R	0.712	1.00
23_M	32_H	0.689	1.00
22_A	29_A	0.685	1.00
29_A	32_H	0.680	1.00
6_L	12_I	0.677	1.00
13_L	17_A	0.668	1.00
41_A	47_R	0.667	1.00
33_E	40_E	0.662	1.00
40_E	44_R	0.627	0.99
16_A	20_I	0.625	0.99
6_L	21_L	0.622	0.99
12_I	17_A	0.619	0.99
19_R	23_M	0.615	0.99
37_K	43_I	0.614	0.99
3_P	9_Y	0.610	0.99
3_P	8_E	0.606	0.99
20_I	24_A	0.599	0.99
12_I	20_I	0.596	0.99
10_E	16_A	0.584	0.99
37_K	41_A	0.573	0.99
10_E	14_P	0.572	0.99
4_E	7_A	0.548	0.98
46_S	49_G	0.548	0.98
39_L	42_N	0.533	0.98
41_A	44_R	0.525	0.98
19_R	24_A	0.511	0.97
7_A	10_E	0.507	0.97
32_H	36_K	0.504	0.97
15_G	21_L	0.501	0.97
9_Y	20_I	0.500	0.97

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
3lhoA	1	0.28	6.9	0.836	Contact Map
3erxA	3	0.58	4.8	0.847	Contact Map
4gfjA	1	0	4.2	0.852	Contact Map
1h3oA	1	0.52	4.1	0.853	Contact Map
3u1wA	3	0.96	4.1	0.853	Contact Map
1gqiA	2	0.44	3.8	0.855	Contact Map
3j7yq	1	0.98	3.5	0.857	Contact Map
4g09A	2	1	3.5	0.858	Contact Map
1kaeA	2	1	3.4	0.859	Contact Map
1pazA	1	0.52	3.1	0.861	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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