YqjK - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YqjK - YqjK-like protein

PFAM:	PF13997	Sequences: LLARAAAQRADLAAQAAPLRAPLALADRGLAAVRWLRRHPLLVAGAVALLAVLRPRRALRWARRGWGLWRLWR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (73)
Sequences:	2324 (1780)
Seq/√Len:	208.3
META:	0.896

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_A	8_Q	5.430	1.00
62_A	65_G	4.126	1.00
2_L	5_A	2.389	1.00
61_W	64_R	2.265	1.00
19_L	22_P	2.047	1.00
63_R	67_G	2.004	1.00
29_G	32_A	1.897	1.00
68_L	71_L	1.842	1.00
28_R	31_A	1.828	1.00
45_G	49_L	1.796	1.00
11_D	15_Q	1.795	1.00
15_Q	18_P	1.657	1.00
49_L	53_L	1.655	1.00
1_L	4_R	1.602	1.00
7_A	10_A	1.564	1.00
30_L	34_R	1.551	1.00
55_P	58_A	1.542	1.00
32_A	35_W	1.517	1.00
6_A	10_A	1.484	1.00
11_D	14_A	1.404	1.00
68_L	72_W	1.313	1.00
12_L	15_Q	1.298	1.00
53_L	61_W	1.254	1.00
10_A	14_A	1.242	1.00
30_L	33_V	1.226	1.00
13_A	29_G	1.213	1.00
65_G	68_L	1.169	1.00
54_R	57_R	1.117	1.00
26_A	29_G	1.114	1.00
64_R	68_L	1.107	1.00
63_R	66_W	1.087	1.00
5_A	16_A	1.066	1.00
31_A	34_R	1.049	1.00
48_A	52_V	0.977	1.00
44_A	48_A	0.973	1.00
47_V	51_A	0.971	1.00
34_R	37_R	0.949	0.99
17_A	21_A	0.943	0.99
45_G	48_A	0.942	0.99
19_L	23_L	0.899	0.99
64_R	67_G	0.898	0.99
3_A	46_A	0.891	0.99
31_A	35_W	0.878	0.99
12_L	58_A	0.871	0.99
8_Q	67_G	0.859	0.99
42_L	45_G	0.856	0.99
36_L	40_P	0.851	0.99
7_A	11_D	0.829	0.99
18_P	21_A	0.822	0.98
17_A	20_R	0.818	0.98
13_A	17_A	0.811	0.98
22_P	25_L	0.810	0.98
35_W	39_H	0.795	0.98
23_L	30_L	0.778	0.98
43_V	46_A	0.775	0.98
3_A	10_A	0.755	0.97
18_P	22_P	0.754	0.97
69_W	72_W	0.746	0.97
7_A	42_L	0.738	0.97
3_A	6_A	0.725	0.97
35_W	53_L	0.725	0.97
25_L	29_G	0.725	0.97
19_L	27_D	0.724	0.97
62_A	66_W	0.723	0.97
27_D	30_L	0.723	0.97
23_L	27_D	0.719	0.97
39_H	42_L	0.716	0.96
41_L	48_A	0.709	0.96
66_W	72_W	0.706	0.96
65_G	73_R	0.695	0.96
41_L	45_G	0.689	0.96
41_L	57_R	0.684	0.95
46_A	49_L	0.683	0.95
53_L	57_R	0.659	0.94
7_A	24_A	0.652	0.94
63_R	70_R	0.643	0.94
46_A	52_V	0.636	0.93
1_L	9_R	0.623	0.93
21_A	25_L	0.621	0.92
47_V	55_P	0.614	0.92
16_A	30_L	0.612	0.92
22_P	35_W	0.604	0.91
63_R	69_W	0.602	0.91
56_R	69_W	0.600	0.91
50_L	54_R	0.597	0.91
2_L	6_A	0.595	0.91
6_A	14_A	0.594	0.91
32_A	36_L	0.594	0.91
30_L	37_R	0.588	0.90
43_V	47_V	0.583	0.90
41_L	44_A	0.583	0.90
53_L	67_G	0.582	0.90
4_R	8_Q	0.566	0.88
23_L	60_R	0.566	0.88
60_R	71_L	0.564	0.88
50_L	53_L	0.561	0.88
36_L	43_V	0.556	0.88
16_A	23_L	0.551	0.87
8_Q	11_D	0.548	0.87
41_L	46_A	0.542	0.86
25_L	28_R	0.534	0.85
16_A	19_L	0.533	0.85
3_A	7_A	0.529	0.85
38_R	66_W	0.526	0.85
34_R	50_L	0.519	0.84
52_V	55_P	0.515	0.83
8_Q	15_Q	0.514	0.83
33_V	71_L	0.511	0.83
52_V	67_G	0.504	0.82
23_L	26_A	0.500	0.82

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
3m6cA	1	0.4521	4.3	0.869	Contact Map
2lonA	1	0.8356	3.8	0.871	Contact Map
4rh7A	1	0.8904	3.3	0.875	Contact Map
2mi2A	1	0.5479	2.9	0.879	Contact Map
1r8dA	2	0.4658	2.7	0.882	Contact Map
2vz4A	2	0.411	2.4	0.885	Contact Map
2l16A	1	0.5616	2.4	0.885	Contact Map
3vz6A	1	0.411	2.3	0.885	Contact Map
4fm3A	3	0.3699	1.8	0.892	Contact Map
1t7sA	3	0.2329	1.6	0.895	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.

Page generated in 0.0039 seconds.