DUF1427 - PFAM28P - GREMLIN Contacts

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DUF1427 - Protein of unknown function (DUF1427)

PFAM:	PF07235	Sequences: KPYLLSLGAGLLVGVIYSLLNVRSPAPPVIALVGLLGILVGEQIVPLAKRLLAGEPLAAAWLRSQCAPHVFGELPGRHAAAAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	83 (80)
Sequences:	1187 (684)
Seq/√Len:	76.5
META:	0.775

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_P	30_I	4.389	1.00
33_V	38_I	4.274	1.00
9_A	20_L	4.268	1.00
40_V	70_V	2.597	1.00
4_L	8_G	2.518	1.00
9_A	16_I	2.395	1.00
45_V	48_A	2.392	1.00
5_L	9_A	1.937	1.00
69_H	74_L	1.927	1.00
61_W	68_P	1.852	1.00
13_V	23_R	1.688	1.00
5_L	20_L	1.590	0.99
73_E	76_G	1.532	0.99
47_L	57_L	1.491	0.99
5_L	8_G	1.474	0.99
5_L	18_S	1.466	0.99
39_L	43_Q	1.444	0.99
71_F	74_L	1.442	0.99
52_L	55_E	1.380	0.99
15_V	44_I	1.363	0.98
12_L	16_I	1.349	0.98
49_K	53_A	1.320	0.98
18_S	45_V	1.315	0.98
66_C	70_V	1.253	0.97
56_P	78_H	1.206	0.97
48_A	57_L	1.187	0.96
61_W	71_F	1.183	0.96
3_Y	23_R	1.175	0.96
23_R	39_L	1.140	0.95
62_L	65_Q	1.134	0.95
6_S	15_V	1.128	0.95
70_V	73_E	1.124	0.95
50_R	58_A	1.119	0.95
50_R	66_C	1.098	0.94
29_V	71_F	1.096	0.94
27_P	41_G	1.064	0.93
63_R	67_A	1.019	0.92
54_G	64_S	1.002	0.91
76_G	79_A	0.991	0.90
70_V	77_R	0.980	0.90
61_W	66_C	0.971	0.90
51_L	54_G	0.963	0.89
9_A	22_V	0.961	0.89
19_L	49_K	0.958	0.89
53_A	59_A	0.943	0.88
8_G	15_V	0.935	0.88
2_P	6_S	0.932	0.88
28_P	31_A	0.895	0.85
57_L	66_C	0.894	0.85
6_S	9_A	0.874	0.84
40_V	44_I	0.871	0.84
59_A	63_R	0.818	0.80
2_P	5_L	0.811	0.79
39_L	72_G	0.800	0.78
34_G	41_G	0.796	0.78
36_L	76_G	0.793	0.78
44_I	68_P	0.789	0.77
55_E	67_A	0.777	0.76
28_P	35_L	0.769	0.75
47_L	52_L	0.769	0.75
60_A	76_G	0.768	0.75
57_L	62_L	0.766	0.75
53_A	57_L	0.759	0.74
74_L	77_R	0.758	0.74
11_L	44_I	0.753	0.74
45_V	66_C	0.746	0.73
22_V	33_V	0.743	0.73
21_N	49_K	0.724	0.71
43_Q	72_G	0.719	0.70
23_R	43_Q	0.705	0.69
16_I	46_P	0.699	0.68
16_I	20_L	0.688	0.67
2_P	9_A	0.687	0.67
24_S	41_G	0.676	0.66
19_L	36_L	0.674	0.65
2_P	8_G	0.672	0.65
63_R	70_V	0.672	0.65
63_R	71_F	0.656	0.63
4_L	68_P	0.649	0.63
1_K	71_F	0.636	0.61
30_I	73_E	0.625	0.60
69_H	73_E	0.623	0.59
57_L	67_A	0.622	0.59
51_L	78_H	0.621	0.59
66_C	72_G	0.613	0.58
62_L	68_P	0.609	0.58
26_A	32_L	0.606	0.57
21_N	65_Q	0.601	0.57
27_P	34_G	0.596	0.56
9_A	12_L	0.594	0.56
7_L	10_G	0.590	0.55
50_R	53_A	0.587	0.55
53_A	79_A	0.584	0.55
4_L	48_A	0.583	0.54
68_P	77_R	0.576	0.54
29_V	38_I	0.562	0.52
73_E	77_R	0.558	0.51
11_L	40_V	0.556	0.51
48_A	51_L	0.553	0.51
56_P	63_R	0.552	0.50
28_P	41_G	0.541	0.49
11_L	20_L	0.540	0.49
26_A	31_A	0.540	0.49
28_P	32_L	0.539	0.49
8_G	13_V	0.539	0.49
57_L	61_W	0.538	0.49
17_Y	24_S	0.533	0.48
73_E	78_H	0.532	0.48
65_Q	68_P	0.531	0.48
1_K	21_N	0.522	0.47
32_L	41_G	0.519	0.46
68_P	76_G	0.509	0.45
38_I	69_H	0.509	0.45
26_A	41_G	0.508	0.45
69_H	75_P	0.506	0.45
15_V	79_A	0.505	0.45
31_A	35_L	0.504	0.44
47_L	66_C	0.503	0.44
21_N	52_L	0.501	0.44
59_A	64_S	0.500	0.44

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
2xq2A	2	0.5904	5.8	0.927	Contact Map
1ciiA	1	0.6145	5.5	0.928	Contact Map
3j61O	1	0.3976	4.3	0.932	Contact Map
4njnA	4	0.5904	3.8	0.933	Contact Map
4dx5A	3	0.5301	3.3	0.935	Contact Map
1rh1A	1	0.6386	2.8	0.938	Contact Map
3s0xA	1	0.3133	2.7	0.938	Contact Map
3kxsF	2	0.3373	2.6	0.939	Contact Map
3t33A	2	0.4096	2.6	0.939	Contact Map
2lk9A	1	0.2289	2.6	0.939	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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