DUF4860 - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

DUF4860 - Domain of unknown function (DUF4860)

PFAM:	PF16152	Sequences: YDERTALSYIATKVRQNDEAGAVSVGEFDGGDALVLTEEIDGETYETYIYYYDGYLRELFTEAGLEFSPEDGQPILELDSFSFEELEDGLLRITVTDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	98 (95)
Sequences:	1498 (1350)
Seq/√Len:	138.5
META:	0.898

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_R	74_P	3.308	1.00
55_Y	77_E	3.143	1.00
26_G	35_V	3.039	1.00
55_Y	74_P	3.012	1.00
56_L	78_L	2.608	1.00
28_F	33_A	2.222	1.00
35_V	48_Y	2.110	1.00
35_V	46_E	2.038	1.00
11_A	15_R	1.910	1.00
27_E	30_G	1.892	1.00
61_T	65_L	1.864	1.00
50_Y	72_G	1.776	1.00
27_E	32_D	1.758	1.00
10_I	81_F	1.662	1.00
83_F	93_I	1.638	1.00
39_E	42_G	1.629	1.00
14_V	91_L	1.629	1.00
46_E	63_A	1.606	1.00
85_E	89_G	1.603	1.00
24_S	37_T	1.600	1.00
19_E	22_A	1.546	1.00
84_E	92_R	1.535	1.00
85_E	91_L	1.527	1.00
68_S	71_D	1.497	1.00
51_Y	81_F	1.483	1.00
34_L	83_F	1.439	1.00
40_I	60_F	1.437	1.00
12_T	16_Q	1.378	1.00
25_V	83_F	1.356	1.00
44_T	63_A	1.333	1.00
13_K	16_Q	1.307	1.00
26_G	33_A	1.254	1.00
31_G	69_P	1.225	1.00
52_Y	57_R	1.200	1.00
51_Y	80_S	1.174	0.99
6_A	56_L	1.157	0.99
48_Y	61_T	1.121	0.99
37_T	46_E	1.118	0.99
37_T	63_A	1.107	0.99
51_Y	56_L	1.105	0.99
52_Y	69_P	1.103	0.99
78_L	95_V	1.097	0.99
18_D	21_G	1.095	0.99
51_Y	78_L	1.050	0.99
13_K	58_E	1.045	0.99
39_E	44_T	1.045	0.99
9_Y	13_K	1.014	0.99
37_T	44_T	1.013	0.98
33_A	69_P	0.985	0.98
59_L	72_G	0.972	0.98
7_L	11_A	0.967	0.98
82_S	94_T	0.950	0.98
67_F	71_D	0.948	0.98
29_D	69_P	0.938	0.98
10_I	93_I	0.933	0.97
7_L	49_I	0.915	0.97
46_E	64_G	0.906	0.97
43_E	62_E	0.904	0.97
33_A	48_Y	0.868	0.96
17_N	36_L	0.866	0.96
18_D	22_A	0.865	0.96
12_T	76_L	0.862	0.96
39_E	43_E	0.862	0.96
11_A	14_V	0.860	0.96
50_Y	59_L	0.856	0.96
8_S	18_D	0.852	0.96
20_A	39_E	0.840	0.95
13_K	47_T	0.826	0.95
12_T	73_Q	0.821	0.95
4_R	35_V	0.815	0.94
62_E	65_L	0.813	0.94
11_A	16_Q	0.799	0.94
5_T	16_Q	0.791	0.94
40_I	43_E	0.789	0.93
32_D	83_F	0.779	0.93
41_D	44_T	0.767	0.92
36_L	74_P	0.764	0.92
86_L	92_R	0.754	0.92
79_D	96_T	0.749	0.92
66_E	87_E	0.746	0.91
84_E	94_T	0.746	0.91
6_A	16_Q	0.745	0.91
8_S	12_T	0.737	0.91
32_D	82_S	0.735	0.91
82_S	92_R	0.724	0.90
11_A	93_I	0.723	0.90
6_A	75_I	0.720	0.90
5_T	76_L	0.708	0.89
24_S	35_V	0.701	0.89
22_A	36_L	0.699	0.88
83_F	91_L	0.694	0.88
9_Y	58_E	0.693	0.88
22_A	84_E	0.692	0.88
29_D	68_S	0.687	0.88
28_F	31_G	0.673	0.87
18_D	36_L	0.669	0.86
14_V	34_L	0.663	0.86
89_G	92_R	0.660	0.85
57_R	61_T	0.657	0.85
49_I	58_E	0.657	0.85
23_V	64_G	0.651	0.85
87_E	90_L	0.649	0.85
45_Y	60_F	0.639	0.84
5_T	12_T	0.632	0.83
89_G	94_T	0.632	0.83
8_S	25_V	0.631	0.83
28_F	68_S	0.625	0.82
13_K	17_N	0.619	0.82
22_A	86_L	0.617	0.81
7_L	95_V	0.613	0.81
6_A	78_L	0.611	0.81
4_R	78_L	0.608	0.81
17_N	38_E	0.605	0.80
3_E	6_A	0.583	0.78
50_Y	74_P	0.582	0.78
49_I	78_L	0.577	0.77
61_T	67_F	0.570	0.76
40_I	45_Y	0.568	0.76
38_E	41_D	0.568	0.76
12_T	15_R	0.565	0.75
80_S	96_T	0.564	0.75
12_T	51_Y	0.563	0.75
2_D	61_T	0.557	0.74
38_E	43_E	0.557	0.74
14_V	23_V	0.556	0.74
2_D	12_T	0.554	0.74
9_Y	75_I	0.551	0.74
88_D	91_L	0.549	0.73
24_S	46_E	0.546	0.73
59_L	67_F	0.543	0.73
48_Y	59_L	0.528	0.71
16_Q	48_Y	0.527	0.70
17_N	22_A	0.524	0.70
81_F	93_I	0.523	0.70
87_E	91_L	0.519	0.69
36_L	78_L	0.518	0.69
23_V	36_L	0.511	0.68
2_D	56_L	0.508	0.68
28_F	69_P	0.504	0.67
14_V	17_N	0.502	0.67
3_E	11_A	0.500	0.66
12_T	48_Y	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
3u6xS	3	0.5204	10.9	0.902	Contact Map
4ghbA	5	0.9082	7.8	0.908	Contact Map
2cwsA	1	0.8673	5.1	0.916	Contact Map
2wzpR	3	0.3469	4.9	0.917	Contact Map
2p8gA	2	0.6122	4.6	0.918	Contact Map
2qx2A	1	0.4694	3.7	0.922	Contact Map
4pq0A	1	0.3367	3.4	0.923	Contact Map
4hn3A	3	0.5102	3.3	0.923	Contact Map
3v0rA	3	0.3571	3.3	0.924	Contact Map
4w8jA	2	0.8878	3.2	0.924	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.

Page generated in 0.0047 seconds.