NapE - PFAM28P - GREMLIN Contacts

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NapE - Periplasmic nitrate reductase protein NapE

PFAM:	PF06796	Sequences: QNDTDDPPRRRRRELRAFLFLTVVLAPVLAVAVVGGYGFLVWMYQLIAGPPGP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (50)
Sequences:	1754 (1013)
Seq/√Len:	143.3
META:	0.856

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_Y	48_A	4.186	1.00
39_F	43_M	3.762	1.00
32_A	35_G	3.058	1.00
43_M	46_L	2.677	1.00
21_L	26_A	2.011	1.00
37_Y	41_V	1.859	1.00
10_R	13_R	1.551	1.00
36_G	40_L	1.458	1.00
31_V	35_G	1.435	1.00
35_G	39_F	1.394	1.00
12_R	16_R	1.350	1.00
13_R	16_R	1.329	1.00
31_V	34_V	1.264	1.00
18_F	22_T	1.239	1.00
17_A	25_L	1.213	1.00
9_R	13_R	1.171	1.00
40_L	44_Y	1.162	1.00
43_M	47_I	1.129	0.99
26_A	29_L	1.081	0.99
16_R	20_F	1.067	0.99
20_F	24_V	1.046	0.99
26_A	30_A	1.039	0.99
19_L	24_V	1.037	0.99
30_A	33_V	1.033	0.99
17_A	53_P	0.994	0.98
29_L	33_V	0.991	0.98
41_V	45_Q	0.905	0.97
36_G	39_F	0.887	0.97
32_A	36_G	0.880	0.97
16_R	23_V	0.880	0.97
16_R	25_L	0.878	0.97
22_T	26_A	0.842	0.96
37_Y	40_L	0.836	0.96
17_A	26_A	0.832	0.95
30_A	34_V	0.823	0.95
4_T	8_P	0.805	0.95
4_T	7_P	0.789	0.94
36_G	43_M	0.788	0.94
9_R	12_R	0.784	0.94
20_F	47_I	0.774	0.93
6_D	10_R	0.770	0.93
23_V	26_A	0.765	0.93
7_P	53_P	0.748	0.92
15_L	26_A	0.726	0.91
24_V	28_V	0.723	0.91
5_D	8_P	0.720	0.91
10_R	40_L	0.714	0.90
8_P	12_R	0.709	0.90
19_L	22_T	0.702	0.90
31_V	41_V	0.697	0.89
6_D	9_R	0.691	0.89
18_F	53_P	0.687	0.89
50_P	53_P	0.659	0.86
15_L	21_L	0.655	0.86
4_T	9_R	0.630	0.84
37_Y	44_Y	0.629	0.84
9_R	17_A	0.623	0.83
33_V	41_V	0.598	0.81
17_A	24_V	0.585	0.79
37_Y	45_Q	0.584	0.79
6_D	12_R	0.582	0.79
19_L	23_V	0.582	0.79
24_V	37_Y	0.576	0.78
5_D	9_R	0.568	0.77
28_V	45_Q	0.564	0.77
16_R	32_A	0.550	0.75
31_V	36_G	0.550	0.75
42_W	45_Q	0.543	0.74
33_V	36_G	0.540	0.74
5_D	47_I	0.533	0.73
17_A	23_V	0.532	0.72
46_L	50_P	0.523	0.71
40_L	43_M	0.504	0.68
7_P	36_G	0.501	0.68
7_P	10_R	0.500	0.68

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
3pe5A	1	0	14.5	0.868	Contact Map
3owqA	1	0.0189	10.5	0.876	Contact Map
2m8rA	1	0.6981	5.4	0.891	Contact Map
1a91A	1	0.8491	4.8	0.894	Contact Map
4bbjA	1	0.9057	4.3	0.897	Contact Map
3fymA	1	0	4	0.898	Contact Map
4aq5A	1	0.8679	3.7	0.9	Contact Map
3wvfA	1	0	3.6	0.9	Contact Map
2xndJ	3	0.7925	3.6	0.9	Contact Map
3vmtA	1	0.5283	3.6	0.9	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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