DUF883 - PFAM28P - GREMLIN Contacts

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DUF883 - Bacterial protein of unknown function (DUF883)

PFAM:	PF05957	Sequences: EKLAADLKALVADAEELLKATADQAGEKAAEARERAEEALEDAKERLAEAADAARERAREAAKATDDYVRENPWQAVGIAAGVGLLLGLLLRRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (90)
Sequences:	19556 (13466)
Seq/√Len:	1419.5
META:	0.893

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_N	75_Q	3.462	1.00
55_R	59_R	2.147	1.00
66_D	70_R	2.141	1.00
65_T	68_Y	2.037	1.00
54_A	58_A	2.004	1.00
51_A	55_R	1.917	1.00
66_D	74_W	1.892	1.00
69_V	76_A	1.872	1.00
53_A	57_R	1.701	1.00
89_L	92_R	1.652	1.00
57_R	60_E	1.601	1.00
50_A	53_A	1.600	1.00
79_I	82_G	1.595	1.00
81_A	85_L	1.584	1.00
50_A	54_A	1.561	1.00
25_A	29_A	1.512	1.00
61_A	64_A	1.511	1.00
76_A	79_I	1.492	1.00
58_A	62_A	1.478	1.00
78_G	81_A	1.477	1.00
46_R	49_E	1.459	1.00
35_R	39_A	1.437	1.00
47_L	51_A	1.432	1.00
43_A	47_L	1.394	1.00
39_A	43_A	1.392	1.00
6_D	9_A	1.389	1.00
80_A	84_G	1.388	1.00
85_L	89_L	1.368	1.00
82_G	86_L	1.355	1.00
39_A	42_D	1.343	1.00
62_A	65_T	1.337	1.00
79_I	83_V	1.268	1.00
42_D	46_R	1.267	1.00
28_K	31_E	1.217	1.00
64_A	67_D	1.211	1.00
64_A	68_Y	1.200	1.00
74_W	78_G	1.193	1.00
81_A	84_G	1.182	1.00
46_R	50_A	1.169	1.00
28_K	32_A	1.164	1.00
44_K	48_A	1.149	1.00
33_R	37_E	1.143	1.00
24_Q	28_K	1.128	1.00
85_L	88_G	1.113	1.00
62_A	66_D	1.097	1.00
77_V	81_A	1.092	1.00
21_T	25_A	1.087	1.00
48_A	51_A	1.073	1.00
16_E	20_A	1.070	1.00
75_Q	79_I	1.069	1.00
9_A	13_D	1.054	1.00
35_R	38_E	1.052	1.00
59_R	62_A	1.046	1.00
69_V	77_V	1.043	1.00
5_A	8_K	1.014	1.00
37_E	41_E	1.011	1.00
4_A	8_K	0.997	1.00
55_R	58_A	0.985	1.00
59_R	63_K	0.982	1.00
75_Q	78_G	0.979	1.00
78_G	82_G	0.978	1.00
11_V	15_E	0.974	1.00
63_K	66_D	0.972	1.00
68_Y	75_Q	0.952	1.00
32_A	36_A	0.945	1.00
68_Y	74_W	0.942	1.00
68_Y	72_N	0.896	1.00
61_A	65_T	0.859	1.00
24_Q	27_E	0.852	1.00
31_E	35_R	0.837	1.00
14_A	18_L	0.811	1.00
42_D	45_E	0.807	1.00
74_W	77_V	0.803	1.00
41_E	45_E	0.790	1.00
58_A	61_A	0.789	1.00
15_E	18_L	0.789	1.00
28_K	36_A	0.788	1.00
6_D	13_D	0.786	1.00
87_L	91_L	0.782	1.00
60_E	64_A	0.780	1.00
51_A	54_A	0.776	1.00
20_A	24_Q	0.776	1.00
10_L	17_L	0.770	1.00
57_R	61_A	0.759	1.00
56_E	59_R	0.753	1.00
47_L	50_A	0.750	1.00
13_D	16_E	0.744	1.00
52_D	56_E	0.731	1.00
48_A	52_D	0.723	1.00
17_L	24_Q	0.706	1.00
69_V	74_W	0.701	1.00
11_V	14_A	0.687	1.00
17_L	20_A	0.683	1.00
54_A	57_R	0.680	1.00
19_K	22_A	0.670	1.00
81_A	88_G	0.666	1.00
36_A	39_A	0.659	1.00
26_G	30_A	0.650	1.00
15_E	19_K	0.650	1.00
76_A	80_A	0.648	1.00
23_D	26_G	0.646	1.00
65_T	69_V	0.641	1.00
66_D	69_V	0.634	1.00
12_A	16_E	0.630	1.00
43_A	46_R	0.628	1.00
86_L	89_L	0.628	1.00
40_L	44_K	0.623	1.00
41_E	44_K	0.622	1.00
22_A	26_G	0.607	1.00
11_V	21_T	0.605	1.00
8_K	12_A	0.604	1.00
45_E	49_E	0.601	1.00
82_G	85_L	0.588	1.00
5_A	9_A	0.586	1.00
85_L	91_L	0.585	1.00
70_R	74_W	0.583	1.00
30_A	34_E	0.581	1.00
8_K	11_V	0.574	1.00
38_E	42_D	0.569	1.00
29_A	32_A	0.567	1.00
6_D	10_L	0.566	1.00
12_A	15_E	0.560	1.00
62_A	74_W	0.557	1.00
77_V	80_A	0.552	1.00
40_L	43_A	0.548	1.00
4_A	14_A	0.546	1.00
13_D	17_L	0.539	1.00
80_A	83_V	0.537	1.00
67_D	71_E	0.537	1.00
52_D	55_R	0.519	1.00
49_E	53_A	0.516	1.00
63_K	67_D	0.514	1.00
21_T	26_G	0.503	1.00
21_T	29_A	0.503	1.00
56_E	60_E	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
2a01A	1	0.766	85.3	0.743	Contact Map
3r2pA	2	0.8191	79.1	0.76	Contact Map
1nfnA	1	0.6702	75.3	0.768	Contact Map
1gs9A	1	0.7979	74.4	0.769	Contact Map
2lemA	1	0.8191	70.1	0.777	Contact Map
2l7bA	1	0.8617	66.7	0.782	Contact Map
3s84A	2	0.5319	58.9	0.792	Contact Map
1rykA	1	0.734	46.8	0.807	Contact Map
1eq1A	1	0.766	31.6	0.824	Contact Map
2m8rA	1	0.9149	30.1	0.826	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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