Cmc1 - PFAM28P - GREMLIN Contacts

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Cmc1 - Cytochrome c oxidase biogenesis protein Cmc1 like

PFAM:	PF08583	Sequences: MHPDLKEKAHEKCAEEIKALAECHKERGLKVVGACNDEKRALNKCLRKERTDERFKNREKAEYLRERLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (68)
Sequences:	1045 (784)
Seq/√Len:	95.0
META:	0.33

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_K	22_E	2.717	1.00
30_K	33_G	2.501	1.00
22_E	26_E	2.175	1.00
27_R	30_K	1.994	1.00
21_A	24_H	1.941	1.00
37_D	41_A	1.938	1.00
6_K	10_H	1.769	1.00
57_N	60_K	1.761	1.00
64_L	67_R	1.722	1.00
15_E	19_A	1.693	1.00
59_E	62_E	1.692	1.00
41_A	44_K	1.629	1.00
56_K	59_E	1.617	1.00
58_R	62_E	1.607	1.00
63_Y	66_E	1.549	1.00
59_E	63_Y	1.545	1.00
19_A	41_A	1.521	1.00
40_R	44_K	1.443	1.00
14_A	18_K	1.393	0.99
22_E	25_K	1.375	0.99
60_K	63_Y	1.370	0.99
20_L	24_H	1.277	0.99
43_N	50_R	1.263	0.99
39_K	43_N	1.237	0.99
2_H	5_L	1.233	0.99
1_M	4_D	1.231	0.99
61_A	65_R	1.230	0.99
56_K	60_K	1.199	0.98
57_N	61_A	1.176	0.98
4_D	8_K	1.176	0.98
54_R	58_R	1.172	0.98
27_R	34_A	1.162	0.98
29_L	32_V	1.085	0.97
24_H	36_N	1.082	0.97
53_E	56_K	1.062	0.96
65_R	68_L	1.051	0.96
26_E	30_K	1.048	0.96
6_K	9_A	1.035	0.96
24_H	39_K	1.034	0.96
53_E	57_N	1.033	0.96
10_H	49_E	1.027	0.95
3_P	7_E	1.012	0.95
1_M	5_L	1.005	0.95
58_R	61_A	0.983	0.94
18_K	21_A	0.953	0.93
47_R	54_R	0.948	0.93
20_L	39_K	0.931	0.92
12_K	49_E	0.910	0.92
46_L	50_R	0.883	0.90
63_Y	67_R	0.869	0.90
16_E	38_E	0.865	0.89
27_R	33_G	0.861	0.89
51_T	55_F	0.839	0.88
43_N	46_L	0.819	0.87
36_N	39_K	0.813	0.86
55_F	59_E	0.807	0.86
34_A	41_A	0.789	0.85
61_A	64_L	0.785	0.84
28_G	32_V	0.777	0.84
47_R	50_R	0.773	0.83
38_E	41_A	0.754	0.82
60_K	67_R	0.738	0.80
24_H	33_G	0.724	0.79
60_K	64_L	0.715	0.78
36_N	46_L	0.714	0.78
23_C	45_C	0.714	0.78
13_C	23_C	0.713	0.78
44_K	48_K	0.707	0.77
23_C	35_C	0.699	0.77
33_G	36_N	0.691	0.76
25_K	51_T	0.659	0.72
52_D	55_F	0.651	0.71
52_D	56_K	0.651	0.71
28_G	33_G	0.646	0.71
15_E	25_K	0.646	0.71
35_C	45_C	0.639	0.70
13_C	35_C	0.631	0.69
13_C	45_C	0.625	0.68
17_I	42_L	0.624	0.68
22_E	29_L	0.623	0.68
20_L	42_L	0.609	0.66
16_E	19_A	0.602	0.66
17_I	32_V	0.596	0.65
64_L	68_L	0.588	0.64
15_E	18_K	0.582	0.63
20_L	50_R	0.581	0.63
41_A	48_K	0.572	0.62
37_D	44_K	0.560	0.60
26_E	32_V	0.548	0.58
12_K	62_E	0.546	0.58
24_H	31_V	0.538	0.57
32_V	39_K	0.534	0.56
11_E	14_A	0.533	0.56
12_K	52_D	0.529	0.56
60_K	66_E	0.529	0.56
5_L	46_L	0.523	0.55
17_I	47_R	0.523	0.55
33_G	39_K	0.522	0.55
26_E	34_A	0.518	0.54
21_A	65_R	0.511	0.53
44_K	47_R	0.507	0.53
17_I	24_H	0.500	0.52

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
5aj3m	1	0.9565	32.3	0.794	Contact Map
4xhrN	1	0.9275	26.7	0.802	Contact Map
2l0yB	1	0.3043	18.3	0.817	Contact Map
1ei0A	1	0.5507	17.4	0.818	Contact Map
2lqtA	1	0.8406	7.3	0.847	Contact Map
4xizM	1	0.913	7.3	0.847	Contact Map
3cx5F	1	0.8551	6.3	0.852	Contact Map
1u96A	1	0.5072	5.6	0.855	Contact Map
2lqlA	1	0.7681	5	0.858	Contact Map
4d6tH	1	0.8551	3.7	0.867	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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