NVEALA - PFAM28P - GREMLIN Contacts

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NVEALA - NVEALA protein

PFAM:	PF14055	Sequences: KKILKIIFVAAIAAAAGYNVVNSSQKNVNLSDLALANVEALAQGEGDCGGGGGYTCYGSGSVDC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (59)
Sequences:	1508 (1411)
Seq/√Len:	183.7
META:	0.853

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_L	34_A	3.515	1.00
54_Y	57_Y	2.413	1.00
2_K	5_K	2.367	1.00
22_N	25_Q	2.102	1.00
21_V	24_S	2.047	1.00
5_K	8_F	1.872	1.00
54_Y	58_G	1.796	1.00
52_G	55_T	1.679	1.00
53_G	57_Y	1.621	1.00
50_G	53_G	1.619	1.00
18_Y	23_S	1.593	1.00
55_T	58_G	1.563	1.00
46_G	49_G	1.559	1.00
48_C	53_G	1.539	1.00
51_G	55_T	1.418	1.00
38_V	49_G	1.412	1.00
8_F	12_I	1.342	1.00
46_G	50_G	1.326	1.00
4_L	7_I	1.293	1.00
54_Y	59_S	1.272	1.00
48_C	51_G	1.270	1.00
6_I	10_A	1.210	1.00
3_I	7_I	1.204	1.00
50_G	56_C	1.177	1.00
31_S	34_A	1.151	1.00
52_G	57_Y	1.140	1.00
50_G	54_Y	1.107	1.00
5_K	12_I	1.090	1.00
44_G	52_G	1.080	1.00
46_G	52_G	1.057	1.00
46_G	55_T	1.039	1.00
49_G	53_G	1.020	1.00
30_L	35_L	1.000	0.99
55_T	59_S	0.948	0.99
1_K	4_L	0.943	0.99
48_C	52_G	0.942	0.99
47_D	52_G	0.941	0.99
40_A	44_G	0.930	0.99
32_D	42_A	0.919	0.99
51_G	58_G	0.918	0.99
18_Y	25_Q	0.904	0.99
26_K	29_N	0.883	0.99
16_A	19_N	0.863	0.98
12_I	16_A	0.854	0.98
11_A	16_A	0.837	0.98
18_Y	22_N	0.834	0.98
8_F	13_A	0.809	0.97
26_K	36_A	0.791	0.97
49_G	54_Y	0.768	0.97
6_I	9_V	0.766	0.96
51_G	54_Y	0.760	0.96
15_A	18_Y	0.751	0.96
52_G	58_G	0.744	0.96
33_L	42_A	0.720	0.95
30_L	36_A	0.713	0.95
48_C	54_Y	0.712	0.95
31_S	36_A	0.712	0.95
7_I	11_A	0.688	0.94
34_A	38_V	0.684	0.94
44_G	49_G	0.679	0.93
6_I	14_A	0.673	0.93
15_A	19_N	0.667	0.93
22_N	28_V	0.649	0.92
3_I	8_F	0.648	0.92
12_I	18_Y	0.642	0.91
27_N	30_L	0.625	0.90
46_G	51_G	0.621	0.90
50_G	58_G	0.616	0.89
7_I	12_I	0.607	0.89
48_C	55_T	0.602	0.88
49_G	52_G	0.602	0.88
51_G	59_S	0.590	0.87
19_N	34_A	0.580	0.86
21_V	25_Q	0.570	0.85
47_D	53_G	0.564	0.85
13_A	17_G	0.560	0.84
17_G	25_Q	0.552	0.84
18_Y	24_S	0.537	0.82
52_G	59_S	0.536	0.82
30_L	42_A	0.529	0.81
14_A	19_N	0.526	0.81
38_V	41_L	0.524	0.80
35_L	38_V	0.522	0.80
36_A	43_Q	0.518	0.80
43_Q	59_S	0.518	0.80
43_Q	50_G	0.513	0.79
46_G	53_G	0.502	0.78
50_G	57_Y	0.500	0.77

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
1z1nX	1	0.5781	4.3	0.863	Contact Map
3ne5B	3	0	4.2	0.863	Contact Map
2cvcA	1	0.5938	4.1	0.864	Contact Map
2kogA	1	0.3594	3.7	0.867	Contact Map
1xjtA	1	0.7656	3.2	0.87	Contact Map
2a3mA	1	0.5469	3.2	0.871	Contact Map
2qzuA	2	0.6719	3.1	0.872	Contact Map
4wl1A	3	0	3	0.873	Contact Map
3wbhA	2	0.6406	2.6	0.877	Contact Map
2m8rA	1	0.3906	2.5	0.878	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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