NDUF_B12 - PFAM28P - GREMLIN Contacts

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NDUF_B12 - NADH-ubiquinone oxidoreductase B12 subunit family

PFAM:	PF08122	Sequences: RDPWARNEAWRYHGPFSRWNRFKGAFFPGFGIGFVAFAVYVAYEYLFLKDKHHHGH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (54)
Sequences:	541 (402)
Seq/√Len:	54.7
META:	0.392

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_F	34_F	3.702	1.00
2_D	8_E	2.855	1.00
35_V	39_V	2.584	1.00
41_V	45_Y	2.065	1.00
43_Y	47_F	1.972	1.00
34_F	37_F	1.834	0.99
33_G	38_A	1.802	0.99
28_P	40_Y	1.709	0.99
38_A	42_A	1.699	0.99
32_I	36_A	1.689	0.99
43_Y	48_L	1.632	0.99
33_G	37_F	1.611	0.98
8_E	11_R	1.505	0.97
17_S	21_R	1.453	0.97
34_F	38_A	1.438	0.97
41_V	44_E	1.435	0.97
31_G	35_V	1.420	0.96
37_F	44_E	1.378	0.96
44_E	47_F	1.360	0.95
52_H	55_G	1.332	0.95
48_L	51_K	1.283	0.94
51_K	55_G	1.280	0.94
23_K	26_F	1.223	0.92
42_A	47_F	1.163	0.90
8_E	13_H	1.128	0.88
19_W	23_K	1.082	0.86
29_G	33_G	1.022	0.83
38_A	41_V	0.995	0.81
12_Y	32_I	0.987	0.81
9_A	16_F	0.949	0.78
39_V	44_E	0.941	0.77
28_P	37_F	0.935	0.77
49_K	52_H	0.927	0.76
18_R	22_F	0.885	0.73
16_F	22_F	0.803	0.65
51_K	54_H	0.782	0.63
28_P	35_V	0.771	0.62
6_R	12_Y	0.768	0.62
37_F	40_Y	0.758	0.61
50_D	55_G	0.757	0.61
7_N	40_Y	0.748	0.60
15_P	18_R	0.739	0.59
20_N	25_A	0.736	0.59
16_F	30_F	0.722	0.57
20_N	23_K	0.716	0.56
7_N	28_P	0.713	0.56
4_W	7_N	0.705	0.55
5_A	53_H	0.702	0.55
8_E	12_Y	0.701	0.55
40_Y	44_E	0.699	0.55
13_H	55_G	0.687	0.53
47_F	50_D	0.676	0.52
17_S	20_N	0.672	0.52
39_V	42_A	0.663	0.51
26_F	51_K	0.652	0.50
1_R	6_R	0.649	0.49
21_R	25_A	0.629	0.47
18_R	21_R	0.622	0.46
25_A	51_K	0.622	0.46
50_D	54_H	0.600	0.44
18_R	48_L	0.597	0.44
50_D	53_H	0.575	0.42
32_I	35_V	0.573	0.41
6_R	24_G	0.570	0.41
46_L	49_K	0.566	0.41
37_F	41_V	0.559	0.40
28_P	34_F	0.557	0.40
30_F	33_G	0.554	0.39
1_R	7_N	0.552	0.39
12_Y	21_R	0.550	0.39
5_A	25_A	0.547	0.39
31_G	52_H	0.545	0.38
20_N	55_G	0.541	0.38
5_A	37_F	0.536	0.38
21_R	24_G	0.528	0.37
14_G	26_F	0.527	0.37
17_S	23_K	0.520	0.36
1_R	18_R	0.512	0.35
18_R	24_G	0.511	0.35
2_D	29_G	0.509	0.35
20_N	46_L	0.500	0.34

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
3okzA	1	0.9643	33.6	0.843	Contact Map
4k6mA	2	0.375	24.5	0.853	Contact Map
1pc2A	1	0.9464	23.6	0.854	Contact Map
3e2vA	1	0.8393	19.8	0.859	Contact Map
2kxtA	1	0.8036	17.6	0.863	Contact Map
4tnwA	3	0.6786	17.2	0.863	Contact Map
3dh4A	3	0.6786	14.2	0.868	Contact Map
2jneA	1	0	13.6	0.869	Contact Map
3mi9A	1	0.6071	12.7	0.871	Contact Map
3tlkA	1	0.875	12.4	0.872	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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