YCAR - ECOLI - GREMLIN Contacts

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YCAR - UPF0434 protein YcaR

UniProt:	P0AAZ7	Sequences: MDHRLLEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRDGIPVLLETEARVLTADESKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14287
Length:	60 (54)
Sequences:	709 (329)
Seq/√Len:	44.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_E	51_R	4.290	1.00
29_C	32_D	4.018	1.00
14_C	32_D	3.315	1.00
14_C	29_C	2.991	1.00
39_R	49_E	2.315	1.00
21_N	24_K	2.118	1.00
19_W	30_K	2.105	1.00
16_G	31_L	2.044	0.99
8_I	48_T	1.985	0.99
9_I	45_L	1.533	0.96
20_Y	38_L	1.514	0.95
13_V	47_E	1.284	0.90
21_N	28_I	1.281	0.90
5_L	8_I	1.245	0.88
25_Q	38_L	1.214	0.87
46_L	49_E	1.152	0.84
13_V	34_L	1.116	0.82
5_L	15_N	1.098	0.81
28_I	53_L	1.075	0.79
8_I	15_N	1.052	0.78
10_A	16_G	1.035	0.77
2_D	7_E	1.028	0.76
16_G	29_C	1.024	0.76
32_D	36_F	1.022	0.76
14_C	31_L	1.004	0.74
52_V	55_A	0.922	0.68
16_G	40_D	0.898	0.66
13_V	32_D	0.897	0.66
3_H	7_E	0.897	0.66
15_N	42_I	0.897	0.66
24_K	42_I	0.885	0.65
13_V	54_T	0.872	0.64
4_R	15_N	0.820	0.59
41_G	55_A	0.797	0.57
21_N	53_L	0.793	0.56
35_A	51_R	0.786	0.56
26_E	35_A	0.783	0.55
16_G	32_D	0.779	0.55
15_N	33_N	0.772	0.54
20_Y	25_Q	0.754	0.53
26_E	45_L	0.751	0.52
3_H	22_Q	0.733	0.50
36_F	43_P	0.708	0.48
10_A	44_V	0.701	0.47
22_Q	42_I	0.684	0.46
30_K	33_N	0.683	0.46
36_F	45_L	0.669	0.44
40_D	46_L	0.668	0.44
47_E	52_V	0.664	0.44
49_E	52_V	0.662	0.44
18_L	34_L	0.658	0.43
34_L	47_E	0.650	0.42
5_L	44_V	0.645	0.42
4_R	53_L	0.626	0.40
2_D	42_I	0.625	0.40
4_R	7_E	0.624	0.40
38_L	55_A	0.619	0.40
13_V	40_D	0.616	0.39
18_L	45_L	0.597	0.38
22_Q	30_K	0.592	0.37
21_N	25_Q	0.590	0.37
9_I	37_P	0.590	0.37
30_K	52_V	0.582	0.36
5_L	25_Q	0.566	0.35
8_I	46_L	0.565	0.35
37_P	51_R	0.565	0.35
36_F	47_E	0.563	0.35
30_K	54_T	0.552	0.34
10_A	45_L	0.550	0.33
45_L	49_E	0.544	0.33
23_E	46_L	0.542	0.33
31_L	38_L	0.541	0.33
17_K	20_Y	0.535	0.32
19_W	28_I	0.531	0.32
33_N	55_A	0.531	0.32
9_I	39_R	0.530	0.32
16_G	33_N	0.519	0.31
14_C	33_N	0.509	0.30
22_Q	28_I	0.505	0.30
23_E	28_I	0.501	0.29
21_N	36_F	0.500	0.29

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
2jr6A	1	1	99.9	0.248	Contact Map
2js4A	1	1	99.9	0.25	Contact Map
2hf1A	2	0.9833	99.9	0.25	Contact Map
2pk7A	2	0.9667	99.9	0.255	Contact Map
2jnyA	1	0.9833	99.9	0.27	Contact Map
2k5rA	1	0.9833	99.8	0.32	Contact Map
2kpiA	1	0.8667	99.8	0.344	Contact Map
3q87A	1	0.8	99	0.579	Contact Map
1dl6A	1	0.9	98.9	0.603	Contact Map
2j6aA	1	0.8167	98.8	0.618	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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