DUF4134 - PFAM28P - GREMLIN Contacts

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DUF4134 - Domain of unknown function (DUF4134)

PFAM:	PF13572	Sequences: MMLLLLLLLAALSAFAQDGGNAGINEATTMVRSYFDPGTNLMYAIGAVVGLIGAVKVYQKWNSGDPDTGKVAAAWFGSCIFLVVVATVLKSFF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	93 (91)
Sequences:	1650 (768)
Seq/√Len:	80.5
META:	0.849

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_T	32_R	4.886	1.00
21_N	37_P	3.862	1.00
26_E	30_M	3.112	1.00
60_K	67_D	2.853	1.00
46_G	82_L	2.771	1.00
65_D	70_K	2.569	1.00
62_N	78_S	2.429	1.00
7_L	10_A	2.017	1.00
49_V	59_Q	1.915	1.00
12_L	15_F	1.914	1.00
41_L	45_I	1.875	1.00
60_K	71_V	1.693	1.00
60_K	65_D	1.687	1.00
25_N	37_P	1.587	1.00
24_I	41_L	1.576	1.00
58_Y	62_N	1.515	0.99
63_S	66_P	1.495	0.99
21_N	33_S	1.365	0.99
61_W	68_T	1.364	0.99
3_L	7_L	1.360	0.99
4_L	12_L	1.326	0.98
5_L	15_F	1.304	0.98
26_E	29_T	1.304	0.98
20_G	34_Y	1.293	0.98
57_V	68_T	1.253	0.98
68_T	72_A	1.245	0.98
8_L	14_A	1.202	0.97
42_M	51_L	1.187	0.97
6_L	10_A	1.151	0.96
81_F	85_V	1.150	0.96
40_N	44_A	1.141	0.96
5_L	8_L	1.128	0.96
68_T	71_V	1.097	0.95
4_L	7_L	1.094	0.95
18_D	30_M	1.092	0.95
7_L	11_A	1.082	0.95
86_A	89_L	1.071	0.94
43_Y	87_T	1.064	0.94
79_C	83_V	1.055	0.94
25_N	40_N	1.054	0.94
36_D	90_K	1.047	0.94
10_A	13_S	1.030	0.93
25_N	33_S	1.011	0.92
62_N	70_K	0.988	0.91
5_L	12_L	0.968	0.91
42_M	54_A	0.968	0.91
83_V	92_F	0.967	0.91
59_Q	73_A	0.962	0.90
46_G	79_C	0.954	0.90
23_G	27_A	0.937	0.89
39_T	86_A	0.929	0.89
29_T	32_R	0.927	0.89
6_L	13_S	0.924	0.88
9_L	14_A	0.923	0.88
6_L	15_F	0.917	0.88
61_W	74_A	0.912	0.88
45_I	49_V	0.911	0.88
10_A	15_F	0.908	0.88
25_N	36_D	0.898	0.87
45_I	52_I	0.887	0.86
56_K	71_V	0.882	0.86
84_V	87_T	0.875	0.86
87_T	91_S	0.873	0.85
67_D	70_K	0.864	0.85
4_L	10_A	0.862	0.85
37_P	48_V	0.849	0.84
9_L	13_S	0.840	0.83
41_L	47_A	0.832	0.83
30_M	42_M	0.830	0.82
65_D	71_V	0.812	0.81
35_F	73_A	0.808	0.81
5_L	10_A	0.807	0.81
53_G	75_W	0.778	0.78
79_C	89_L	0.773	0.78
3_L	11_A	0.756	0.76
4_L	13_S	0.755	0.76
25_N	28_T	0.754	0.76
57_V	72_A	0.751	0.76
7_L	12_L	0.745	0.75
69_G	73_A	0.735	0.74
60_K	70_K	0.734	0.74
67_D	71_V	0.722	0.73
28_T	40_N	0.716	0.72
68_T	74_A	0.715	0.72
6_L	9_L	0.715	0.72
21_N	25_N	0.706	0.71
36_D	40_N	0.704	0.71
3_L	10_A	0.699	0.70
39_T	90_K	0.688	0.69
22_A	56_K	0.682	0.68
59_Q	62_N	0.677	0.68
51_L	69_G	0.672	0.67
79_C	86_A	0.671	0.67
35_F	38_G	0.662	0.66
43_Y	86_A	0.661	0.66
20_G	23_G	0.651	0.65
19_G	40_N	0.643	0.64
49_V	82_L	0.642	0.64
8_L	13_S	0.638	0.63
39_T	43_Y	0.633	0.63
7_L	14_A	0.627	0.62
73_A	76_F	0.623	0.61
63_S	70_K	0.613	0.60
4_L	8_L	0.613	0.60
18_D	22_A	0.595	0.58
9_L	12_L	0.594	0.58
6_L	12_L	0.589	0.57
54_A	85_V	0.586	0.57
79_C	92_F	0.585	0.57
21_N	36_D	0.584	0.57
18_D	21_N	0.579	0.56
3_L	6_L	0.576	0.55
33_S	44_A	0.573	0.55
58_Y	64_G	0.573	0.55
6_L	11_A	0.562	0.54
50_G	69_G	0.561	0.54
8_L	12_L	0.558	0.53
29_T	40_N	0.558	0.53
46_G	50_G	0.557	0.53
29_T	33_S	0.553	0.53
7_L	13_S	0.552	0.52
80_I	84_V	0.551	0.52
84_V	89_L	0.544	0.51
7_L	15_F	0.540	0.51
5_L	13_S	0.536	0.50
27_A	31_V	0.535	0.50
24_I	27_A	0.533	0.50
78_S	85_V	0.532	0.50
58_Y	78_S	0.526	0.49
25_N	29_T	0.522	0.48
28_T	44_A	0.514	0.47
79_C	82_L	0.513	0.47
20_G	79_C	0.510	0.47
53_G	67_D	0.510	0.47
19_G	33_S	0.504	0.46
27_A	53_G	0.500	0.46

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
2wswA	3	0.9677	16.6	0.882	Contact Map
4k1cA	4	0.8495	13	0.888	Contact Map
4c7rA	3	0.9677	12.2	0.889	Contact Map
3bz1X	1	0.3978	9.6	0.895	Contact Map
2zy9A	2	0.9032	7.5	0.899	Contact Map
2yevB	1	0.8065	6.6	0.902	Contact Map
3j01A	1	0.3871	5.7	0.905	Contact Map
4lz6A	1	0.9462	5.6	0.905	Contact Map
4humA	1	0.9785	5.6	0.905	Contact Map
3mktA	1	0.9462	5.2	0.907	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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