DUF2865 - PFAM28P - GREMLIN Contacts

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DUF2865 - Protein of unknown function (DUF2865)

PFAM:	PF11064	Sequences: TYRTVCVRTCDGYYFPISFSTTPSRFASDAQTCQALCPAAETKLYYYRNPGSDIDQAVSLDGQPYSDLPNAFRYRKELVAGCTCNGKGQSWGLALVDAEDDPTLRPGDIVVTEEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	115 (111)
Sequences:	3527 (1677)
Seq/√Len:	159.2
META:	0.92

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_R	77_E	4.468	1.00
10_C	82_C	4.411	1.00
15_F	36_L	3.549	1.00
9_T	68_L	2.941	1.00
64_P	67_D	2.809	1.00
5_V	54_I	2.554	1.00
54_I	57_A	2.550	1.00
37_C	84_C	2.531	1.00
73_R	79_V	2.433	1.00
48_R	52_S	2.396	1.00
43_K	61_D	2.212	1.00
31_Q	34_Q	2.038	1.00
43_K	59_S	1.834	1.00
63_Q	67_D	1.783	1.00
70_N	73_R	1.646	1.00
5_V	47_Y	1.583	1.00
55_D	72_F	1.545	1.00
47_Y	54_I	1.461	1.00
5_V	57_A	1.453	1.00
85_N	88_G	1.430	1.00
46_Y	60_L	1.405	1.00
53_D	56_Q	1.386	1.00
30_A	34_Q	1.384	1.00
72_F	75_R	1.382	1.00
66_S	72_F	1.370	1.00
73_R	76_K	1.336	1.00
101_D	104_L	1.326	1.00
45_Y	59_S	1.311	1.00
25_R	28_S	1.300	1.00
17_I	44_L	1.291	1.00
14_Y	75_R	1.281	1.00
4_T	29_D	1.268	1.00
88_G	91_W	1.263	1.00
13_Y	74_Y	1.221	1.00
104_L	107_G	1.206	1.00
97_D	101_D	1.204	1.00
18_S	29_D	1.188	1.00
2_Y	26_F	1.162	1.00
9_T	43_K	1.157	1.00
21_T	25_R	1.148	1.00
9_T	41_E	1.128	1.00
14_Y	54_I	1.121	1.00
23_P	26_F	1.119	1.00
3_R	19_F	1.113	1.00
55_D	66_S	1.110	1.00
45_Y	70_N	1.109	1.00
91_W	95_L	1.108	1.00
38_P	42_T	1.069	0.99
83_T	86_G	1.064	0.99
92_G	96_V	1.057	0.99
96_V	99_E	1.057	0.99
5_V	14_Y	1.049	0.99
4_T	26_F	1.044	0.99
92_G	95_L	1.037	0.99
29_D	44_L	1.036	0.99
89_Q	93_L	1.001	0.99
104_L	110_V	0.997	0.99
96_V	100_D	0.989	0.99
101_D	105_R	0.985	0.99
86_G	89_Q	0.984	0.99
32_T	36_L	0.976	0.99
59_S	63_Q	0.963	0.99
19_F	50_P	0.955	0.99
98_A	101_D	0.948	0.99
26_F	44_L	0.944	0.99
100_D	109_I	0.938	0.98
47_Y	51_G	0.934	0.98
103_T	107_G	0.925	0.98
8_R	13_Y	0.902	0.98
91_W	94_A	0.902	0.98
83_T	87_K	0.901	0.98
34_Q	42_T	0.882	0.98
97_D	100_D	0.877	0.98
39_A	88_G	0.876	0.98
106_P	112_T	0.872	0.97
26_F	29_D	0.871	0.97
21_T	26_F	0.867	0.97
52_S	56_Q	0.853	0.97
95_L	98_A	0.839	0.97
26_F	30_A	0.839	0.97
22_T	25_R	0.835	0.97
56_Q	66_S	0.834	0.97
71_A	74_Y	0.829	0.97
57_A	72_F	0.805	0.96
2_Y	23_P	0.803	0.96
46_Y	58_V	0.800	0.96
95_L	99_E	0.796	0.96
103_T	108_D	0.781	0.95
78_L	91_W	0.779	0.95
60_L	63_Q	0.779	0.95
18_S	21_T	0.778	0.95
89_Q	95_L	0.746	0.94
103_T	110_V	0.740	0.94
21_T	29_D	0.735	0.93
32_T	35_A	0.713	0.92
40_A	83_T	0.701	0.92
40_A	82_C	0.699	0.92
34_Q	41_E	0.697	0.92
106_P	113_E	0.696	0.91
43_K	46_Y	0.677	0.90
16_P	74_Y	0.674	0.90
66_S	69_P	0.670	0.90
54_I	72_F	0.668	0.90
43_K	63_Q	0.664	0.89
104_L	108_D	0.660	0.89
94_A	97_D	0.651	0.89
45_Y	68_L	0.650	0.88
91_W	98_A	0.648	0.88
8_R	11_D	0.645	0.88
20_S	29_D	0.636	0.87
102_P	106_P	0.636	0.87
56_Q	77_E	0.632	0.87
93_L	96_V	0.630	0.87
38_P	83_T	0.627	0.87
3_R	47_Y	0.625	0.86
85_N	89_Q	0.624	0.86
41_E	69_P	0.623	0.86
3_R	17_I	0.621	0.86
38_P	89_Q	0.617	0.86
4_T	18_S	0.609	0.85
10_C	40_A	0.607	0.85
33_C	37_C	0.603	0.84
4_T	44_L	0.601	0.84
101_D	106_P	0.600	0.84
35_A	92_G	0.600	0.84
7_V	11_D	0.593	0.83
109_I	113_E	0.591	0.83
42_T	82_C	0.591	0.83
24_S	48_R	0.590	0.83
37_C	68_L	0.588	0.83
42_T	47_Y	0.584	0.83
29_D	32_T	0.582	0.82
98_A	102_P	0.579	0.82
39_A	86_G	0.578	0.82
91_W	99_E	0.575	0.82
31_Q	35_A	0.575	0.82
3_R	29_D	0.572	0.81
101_D	110_V	0.566	0.81
6_C	11_D	0.565	0.80
76_K	85_N	0.563	0.80
8_R	12_G	0.559	0.80
102_P	105_R	0.557	0.80
47_Y	52_S	0.555	0.79
39_A	79_V	0.554	0.79
66_S	87_K	0.554	0.79
57_A	65_Y	0.553	0.79
94_A	98_A	0.548	0.78
101_D	107_G	0.547	0.78
30_A	44_L	0.546	0.78
30_A	41_E	0.546	0.78
105_R	108_D	0.541	0.78
79_V	83_T	0.535	0.77
7_V	12_G	0.531	0.76
6_C	12_G	0.529	0.76
85_N	91_W	0.528	0.76
103_T	106_P	0.526	0.76
68_L	84_C	0.522	0.75
4_T	17_I	0.522	0.75
61_D	66_S	0.516	0.74
19_F	29_D	0.514	0.74
105_R	109_I	0.511	0.73
39_A	42_T	0.508	0.73
31_Q	43_K	0.507	0.73
21_T	44_L	0.502	0.72
24_S	62_G	0.501	0.72
19_F	47_Y	0.500	0.72

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
2pbiA	1	0.8435	10.5	0.937	Contact Map
3wvqA	2	0.3652	4.1	0.948	Contact Map
2gmhA	1	0.4609	4	0.948	Contact Map
1j3gA	1	0.4522	3.7	0.949	Contact Map
1bgkA	1	0.113	2.4	0.953	Contact Map
4didB	1	0.6609	2.1	0.955	Contact Map
4gdiA	4	0.3304	1.6	0.958	Contact Map
2eknA	5	0.4261	1.5	0.959	Contact Map
2ohdA	5	0.4261	1.5	0.959	Contact Map
1byyA	1	0.0783	1.4	0.959	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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