Plasmid_RAQPRD - PFAM28P - GREMLIN Contacts

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Plasmid_RAQPRD - Plasmid protein of unknown function (Plasmid_RAQPRD)

PFAM:	PF09686	Sequences: ADAAEREQLARILRQLDALERLIERAEAQADPDPGARYRFDYDRLRQDLERIRQGIQDYLSPPRAQPRDPPPLRGDY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (75)
Sequences:	927 (596)
Seq/√Len:	68.8
META:	0.676

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_L	49_L	3.937	1.00
5_E	42_Y	3.358	1.00
40_F	56_I	3.250	1.00
41_D	44_R	3.159	1.00
27_E	46_R	2.791	1.00
20_E	53_R	2.563	1.00
13_L	53_R	2.287	1.00
12_I	19_L	2.241	1.00
48_D	55_G	2.086	1.00
20_E	46_R	1.977	1.00
23_I	45_L	1.970	1.00
2_D	6_R	1.900	1.00
9_L	56_I	1.647	0.99
59_Y	63_P	1.549	0.99
11_R	15_Q	1.543	0.99
12_I	22_L	1.462	0.99
31_D	36_A	1.410	0.98
38_Y	66_Q	1.401	0.98
24_E	46_R	1.297	0.97
32_P	52_I	1.256	0.96
22_L	45_L	1.232	0.96
13_L	17_D	1.217	0.96
6_R	49_L	1.175	0.95
59_Y	62_P	1.173	0.95
55_G	75_G	1.168	0.94
5_E	9_L	1.157	0.94
55_G	64_R	1.129	0.93
8_Q	11_R	1.121	0.93
35_G	49_L	1.058	0.91
4_A	8_Q	1.041	0.90
51_R	69_D	1.025	0.89
26_A	30_A	1.023	0.89
17_D	53_R	1.023	0.89
8_Q	25_R	0.989	0.88
13_L	60_L	0.984	0.87
44_R	62_P	0.978	0.87
27_E	57_Q	0.972	0.87
62_P	65_A	0.933	0.85
51_R	58_D	0.919	0.84
4_A	29_Q	0.899	0.82
42_Y	49_L	0.896	0.82
30_A	42_Y	0.883	0.81
41_D	62_P	0.861	0.79
24_E	32_P	0.857	0.79
15_Q	59_Y	0.857	0.79
45_L	52_I	0.834	0.77
10_A	36_A	0.833	0.77
40_F	59_Y	0.832	0.77
63_P	73_L	0.831	0.77
36_A	73_L	0.820	0.76
44_R	70_P	0.818	0.76
8_Q	22_L	0.811	0.75
7_E	10_A	0.788	0.73
19_L	45_L	0.785	0.73
13_L	73_L	0.781	0.72
15_Q	65_A	0.765	0.71
70_P	74_R	0.764	0.71
38_Y	44_R	0.756	0.70
13_L	57_Q	0.754	0.70
19_L	28_A	0.752	0.70
18_A	56_I	0.751	0.69
4_A	7_E	0.736	0.68
11_R	19_L	0.736	0.68
5_E	30_A	0.710	0.65
50_E	54_Q	0.710	0.65
15_Q	19_L	0.709	0.65
26_A	35_G	0.708	0.65
43_D	47_Q	0.705	0.65
44_R	75_G	0.690	0.63
41_D	64_R	0.683	0.62
5_E	12_I	0.670	0.61
47_Q	60_L	0.670	0.61
5_E	26_A	0.669	0.61
23_I	27_E	0.667	0.60
25_R	32_P	0.662	0.60
25_R	28_A	0.655	0.59
14_R	17_D	0.637	0.57
38_Y	41_D	0.619	0.55
15_Q	53_R	0.613	0.54
23_I	43_D	0.598	0.52
32_P	35_G	0.598	0.52
27_E	31_D	0.597	0.52
7_E	63_P	0.596	0.52
24_E	28_A	0.594	0.52
58_D	68_R	0.593	0.52
4_A	33_D	0.593	0.52
7_E	41_D	0.587	0.51
32_P	46_R	0.585	0.51
39_R	47_Q	0.584	0.50
3_A	38_Y	0.583	0.50
39_R	74_R	0.582	0.50
15_Q	39_R	0.581	0.50
22_L	25_R	0.567	0.48
12_I	30_A	0.562	0.48
56_I	76_D	0.561	0.48
14_R	36_A	0.559	0.47
47_Q	51_R	0.557	0.47
17_D	70_P	0.553	0.47
60_L	67_P	0.552	0.47
39_R	51_R	0.546	0.46
33_D	36_A	0.544	0.46
42_Y	63_P	0.543	0.46
59_Y	73_L	0.540	0.45
38_Y	64_R	0.530	0.44
55_G	59_Y	0.529	0.44
71_P	74_R	0.526	0.44
23_I	46_R	0.520	0.43
13_L	29_Q	0.519	0.43
16_L	55_G	0.517	0.42
60_L	64_R	0.514	0.42
14_R	47_Q	0.513	0.42
29_Q	35_G	0.500	0.41

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
1dd5A	1	0.5584	6.3	0.883	Contact Map
1is1A	1	0.5714	6.1	0.884	Contact Map
1iseA	1	0.5584	5.5	0.886	Contact Map
4kddA	1	0.5714	5.2	0.888	Contact Map
1t92A	2	0.5584	5.1	0.888	Contact Map
2kepA	1	0.5714	4.7	0.89	Contact Map
4jkvA	2	1	4.6	0.89	Contact Map
4qinA	2	1	4.5	0.891	Contact Map
1ge9A	1	0.6104	4.5	0.891	Contact Map
1eh1A	1	0.5844	4.4	0.891	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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