YcxB - PFAM28P - GREMLIN Contacts

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YcxB - YcxB-like protein

PFAM:	PF14317	Sequences: FSEEGITVETEGGESELPWSAISKVVETKDFFLLYLSKRSAFIIPKRAFSEEELEEFRELLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (61)
Sequences:	15404 (13073)
Seq/√Len:	1673.8
META:	0.936

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_G	16_E	2.614	1.00
7_T	16_E	2.595	1.00
7_T	14_E	2.313	1.00
46_K	54_L	2.267	1.00
9_E	14_E	2.211	1.00
27_E	46_K	2.115	1.00
27_E	58_R	1.904	1.00
32_F	54_L	1.778	1.00
36_L	42_F	1.754	1.00
31_F	43_I	1.729	1.00
54_L	58_R	1.621	1.00
10_T	13_G	1.566	1.00
32_F	58_R	1.483	1.00
28_T	31_F	1.441	1.00
26_V	35_Y	1.429	1.00
2_S	5_G	1.416	1.00
36_L	40_S	1.349	1.00
50_S	53_E	1.329	1.00
33_L	41_A	1.314	1.00
12_G	21_A	1.301	1.00
32_F	46_K	1.292	1.00
24_K	35_Y	1.260	1.00
53_E	56_E	1.244	1.00
49_F	57_F	1.183	1.00
35_Y	41_A	1.164	1.00
51_E	55_E	1.130	1.00
56_E	59_E	1.119	1.00
22_I	34_L	1.119	1.00
45_P	48_A	1.114	1.00
52_E	55_E	1.089	1.00
51_E	54_L	1.046	1.00
22_I	42_F	1.042	1.00
1_F	19_W	1.033	1.00
27_E	32_F	1.032	1.00
37_S	40_S	1.024	1.00
57_F	61_L	1.015	1.00
25_V	61_L	0.979	1.00
23_S	38_K	0.976	1.00
17_L	42_F	0.973	1.00
18_P	21_A	0.970	1.00
5_G	18_P	0.963	1.00
17_L	21_A	0.910	1.00
55_E	59_E	0.909	1.00
23_S	37_S	0.885	1.00
17_L	22_I	0.857	1.00
19_W	61_L	0.841	1.00
55_E	58_R	0.836	1.00
56_E	60_L	0.822	1.00
4_E	16_E	0.817	1.00
6_I	22_I	0.815	1.00
35_Y	39_R	0.812	1.00
34_L	44_I	0.811	1.00
57_F	60_L	0.806	1.00
2_S	7_T	0.802	1.00
28_T	33_L	0.801	1.00
30_D	46_K	0.782	1.00
52_E	56_E	0.756	1.00
1_F	57_F	0.738	1.00
31_F	46_K	0.735	1.00
8_V	15_S	0.730	1.00
34_L	61_L	0.683	1.00
6_I	42_F	0.669	1.00
12_G	18_P	0.657	1.00
49_F	54_L	0.644	1.00
27_E	54_L	0.634	1.00
5_G	19_W	0.632	1.00
17_L	36_L	0.630	1.00
8_V	13_G	0.606	1.00
49_F	53_E	0.598	1.00
20_S	23_S	0.595	1.00
12_G	20_S	0.592	1.00
25_V	34_L	0.592	1.00
2_S	19_W	0.590	1.00
36_L	41_A	0.564	1.00
8_V	17_L	0.561	1.00
6_I	34_L	0.557	1.00
34_L	43_I	0.556	1.00
23_S	26_V	0.554	1.00
23_S	36_L	0.548	1.00
25_V	32_F	0.542	1.00
15_S	36_L	0.540	1.00
19_W	22_I	0.531	1.00
35_Y	38_K	0.528	1.00
46_K	51_E	0.527	1.00
36_L	39_R	0.524	1.00
15_S	21_A	0.523	1.00
4_E	18_P	0.519	1.00
1_F	60_L	0.518	1.00
10_T	15_S	0.516	1.00
1_F	6_I	0.508	1.00
26_V	33_L	0.501	1.00
23_S	35_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
2i1jA	3	0.9516	46.6	0.728	Contact Map
1h4rA	2	0.9516	45.2	0.73	Contact Map
4yl8A	1	0.9516	40.6	0.738	Contact Map
1mixA	1	0.9516	38.3	0.742	Contact Map
2cs7A	1	0.8065	33.8	0.749	Contact Map
3ivfA	1	0.9516	28.9	0.758	Contact Map
4c9yA	1	0.9677	24	0.767	Contact Map
3qijA	1	0.9355	21.7	0.772	Contact Map
3au4A	1	0.9032	21.4	0.773	Contact Map
4f7gA	1	0.9355	21.2	0.773	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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