Complex1_LYR - PFAM28P - GREMLIN Contacts

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Complex1_LYR - Complex 1 protein (LYR family)

PFAM:	PF05347	Sequences: QRVLSLYRRLLRAARKFPDYNFREYFRRRIREEFRKNRNVTDPEKIEELLRKGEKELEM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (57)
Sequences:	4541 (3311)
Seq/√Len:	438.6
META:	0.407

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_R	38_R	2.658	1.00
40_V	45_K	2.644	1.00
40_V	49_L	2.435	1.00
6_L	53_G	2.204	1.00
31_R	35_R	2.197	1.00
10_L	30_I	2.182	1.00
33_E	36_K	2.070	1.00
29_R	33_E	1.715	1.00
5_S	9_R	1.663	1.00
52_K	56_E	1.620	1.00
37_N	49_L	1.568	1.00
27_R	31_R	1.523	1.00
18_P	21_N	1.291	1.00
9_R	54_E	1.290	1.00
45_K	48_E	1.285	1.00
29_R	32_E	1.270	1.00
17_F	21_N	1.253	1.00
42_D	45_K	1.249	1.00
8_R	12_R	1.238	1.00
51_R	55_K	1.234	1.00
43_P	47_E	1.171	1.00
11_L	30_I	1.151	1.00
25_Y	29_R	1.141	1.00
2_R	54_E	1.135	1.00
50_L	54_E	1.100	1.00
13_A	16_K	1.090	1.00
37_N	40_V	1.072	1.00
3_V	50_L	1.065	1.00
48_E	51_R	1.050	1.00
14_A	26_F	1.046	1.00
48_E	52_K	1.044	1.00
11_L	27_R	1.024	1.00
46_I	50_L	1.014	1.00
50_L	53_G	1.011	1.00
14_A	30_I	0.965	1.00
32_E	36_K	0.964	1.00
26_F	29_R	0.920	1.00
7_Y	31_R	0.912	1.00
28_R	32_E	0.911	1.00
47_E	51_R	0.904	1.00
40_V	43_P	0.870	1.00
25_Y	28_R	0.870	1.00
33_E	52_K	0.863	1.00
17_F	26_F	0.853	1.00
13_A	57_L	0.830	1.00
23_R	26_F	0.818	1.00
24_E	28_R	0.816	1.00
22_F	25_Y	0.808	1.00
49_L	53_G	0.792	1.00
3_V	34_F	0.791	1.00
16_K	20_Y	0.782	1.00
6_L	10_L	0.779	1.00
53_G	56_E	0.775	1.00
23_R	27_R	0.756	1.00
14_A	27_R	0.755	1.00
22_F	26_F	0.745	1.00
28_R	35_R	0.706	1.00
49_L	52_K	0.703	1.00
30_I	56_E	0.684	1.00
19_D	22_F	0.679	1.00
52_K	55_K	0.671	1.00
17_F	22_F	0.665	1.00
17_F	25_Y	0.663	1.00
45_K	49_L	0.650	0.99
15_R	27_R	0.639	0.99
10_L	14_A	0.639	0.99
33_E	56_E	0.633	0.99
8_R	15_R	0.632	0.99
44_E	48_E	0.631	0.99
42_D	47_E	0.623	0.99
9_R	13_A	0.590	0.99
34_F	50_L	0.589	0.99
51_R	54_E	0.573	0.99
43_P	46_I	0.573	0.99
14_A	19_D	0.564	0.99
41_T	46_I	0.561	0.98
17_F	20_Y	0.539	0.98
42_D	46_I	0.535	0.98
44_E	47_E	0.532	0.98
54_E	58_E	0.513	0.97
6_L	34_F	0.511	0.97
2_R	5_S	0.508	0.97
11_L	14_A	0.506	0.97
10_L	56_E	0.504	0.97
19_D	23_R	0.502	0.97
13_A	17_F	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
2ld7A	1	0.9492	9.5	0.814	Contact Map
2qr4A	2	0.8305	8	0.82	Contact Map
3fvbA	6	0.9492	5.1	0.836	Contact Map
3ce2A	1	0.8305	5	0.837	Contact Map
1s94A	1	0.5763	5	0.837	Contact Map
4cvrA	2	0.9492	4.4	0.84	Contact Map
4ynvA	1	0.6441	4.3	0.841	Contact Map
2cqnA	1	0.9831	4.2	0.842	Contact Map
4tofA	6	0.9492	4.2	0.842	Contact Map
3gvyA	5	0.9492	4	0.844	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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