HalX - PFAM28P - GREMLIN Contacts

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HalX - HalX domain

PFAM:	PF08663	Sequences: TRSEYDEQLQEYFALASKRAVLEAEKSEAELEDSEEYQELEERIEELRAELDETLDELDDDDDFEAAFR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (65)
Sequences:	1496 (1097)
Seq/√Len:	136.1
META:	0.873

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_L	44_I	3.347	1.00
26_K	31_L	3.268	1.00
19_R	44_I	2.860	1.00
16_A	44_I	2.544	1.00
11_E	43_R	2.467	1.00
19_R	41_E	2.151	1.00
19_R	37_Y	2.124	1.00
21_V	25_E	2.037	1.00
16_A	20_A	1.900	1.00
27_S	30_E	1.798	1.00
19_R	23_E	1.592	1.00
8_Q	51_L	1.559	1.00
26_K	30_E	1.534	1.00
31_L	37_Y	1.506	1.00
8_Q	50_E	1.490	1.00
63_D	66_A	1.480	1.00
23_E	37_Y	1.468	1.00
13_F	16_A	1.426	1.00
13_F	20_A	1.407	1.00
12_Y	44_I	1.405	1.00
20_A	24_A	1.374	1.00
12_Y	48_R	1.367	1.00
26_K	34_S	1.308	1.00
17_S	21_V	1.283	1.00
23_E	41_E	1.226	1.00
8_Q	54_T	1.223	1.00
42_E	45_E	1.184	0.99
10_Q	14_A	1.089	0.99
9_L	13_F	1.083	0.99
2_R	10_Q	1.011	0.98
3_S	10_Q	1.009	0.98
2_R	16_A	0.992	0.98
53_E	56_D	0.991	0.98
64_F	67_A	0.969	0.98
37_Y	41_E	0.964	0.98
33_D	38_Q	0.946	0.98
12_Y	55_L	0.922	0.97
30_E	34_S	0.891	0.96
45_E	50_E	0.874	0.96
27_S	34_S	0.874	0.96
5_Y	9_L	0.872	0.96
43_R	47_L	0.854	0.95
60_D	63_D	0.838	0.95
13_F	17_S	0.833	0.95
13_F	55_L	0.813	0.94
16_A	19_R	0.799	0.94
15_L	43_R	0.796	0.93
13_F	54_T	0.770	0.92
12_Y	16_A	0.767	0.92
2_R	17_S	0.761	0.92
23_E	31_L	0.752	0.91
15_L	47_L	0.735	0.90
62_D	65_E	0.735	0.90
34_S	38_Q	0.732	0.90
9_L	12_Y	0.712	0.89
5_Y	57_E	0.702	0.88
28_E	32_E	0.696	0.88
5_Y	21_V	0.687	0.87
38_Q	41_E	0.686	0.87
46_E	49_A	0.676	0.86
21_V	44_I	0.656	0.85
51_L	58_L	0.653	0.84
40_L	58_L	0.652	0.84
10_Q	26_K	0.640	0.83
24_A	27_S	0.630	0.82
40_L	53_E	0.628	0.82
22_L	36_E	0.620	0.81
15_L	19_R	0.615	0.81
9_L	53_E	0.612	0.80
44_I	47_L	0.609	0.80
12_Y	17_S	0.608	0.80
48_R	55_L	0.607	0.80
51_L	66_A	0.600	0.79
53_E	57_E	0.596	0.79
62_D	67_A	0.593	0.78
42_E	46_E	0.588	0.78
14_A	52_D	0.579	0.77
46_E	50_E	0.578	0.76
43_R	46_E	0.577	0.76
16_A	48_R	0.574	0.76
6_D	57_E	0.573	0.76
32_E	49_A	0.565	0.75
7_E	59_D	0.562	0.74
42_E	59_D	0.559	0.74
17_S	48_R	0.557	0.74
55_L	66_A	0.555	0.74
17_S	24_A	0.555	0.74
17_S	20_A	0.536	0.71
33_D	39_E	0.531	0.70
47_L	51_L	0.531	0.70
29_A	67_A	0.524	0.69
58_L	65_E	0.520	0.69
22_L	30_E	0.520	0.69
24_A	51_L	0.515	0.68
39_E	46_E	0.511	0.67
45_E	60_D	0.510	0.67
4_E	66_A	0.503	0.66
3_S	28_E	0.500	0.66

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
4iffA	2	0.7391	10.6	0.837	Contact Map
2cazB	1	0.971	6.8	0.851	Contact Map
1rq0A	3	0.7826	6.2	0.853	Contact Map
4ohfA	3	0.9565	6.2	0.853	Contact Map
4c91A	2	0.9275	5.2	0.859	Contact Map
1go4E	4	0.6377	4.9	0.859	Contact Map
3ghgA	2	0.8551	4.8	0.86	Contact Map
3tnuB	1	1	4.7	0.861	Contact Map
2p22B	2	0.7391	4.7	0.861	Contact Map
2lw1A	1	0.9565	4.5	0.862	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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