DUF1036 - PFAM28P - GREMLIN Contacts

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DUF1036 - Protein of unknown function (DUF1036)

PFAM:	PF06282	Sequences: ARAGLRVCNRTSYRVGVAIGYDDGGGWVTRGWWRIDPGQCATVLKGPLTARYYYVYAEDVDGGGEWGGDAPFCVRDKKFTIRGAEDCAARGYDRAGFFEVDTGEQKDWTVQLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	113 (110)
Sequences:	4608 (2977)
Seq/√Len:	283.8
META:	0.934

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_C	40_C	5.090	1.00
74_V	95_A	3.029	1.00
73_C	87_C	2.645	1.00
18_A	79_F	2.447	1.00
16_G	34_R	2.425	1.00
28_V	80_T	2.367	1.00
10_R	111_Q	2.365	1.00
7_V	55_V	2.275	1.00
40_C	73_C	2.194	1.00
20_G	72_F	1.988	1.00
71_P	94_R	1.925	1.00
14_R	34_R	1.910	1.00
71_P	96_G	1.831	1.00
7_V	17_V	1.783	1.00
30_R	33_W	1.762	1.00
30_R	80_T	1.692	1.00
8_C	73_C	1.664	1.00
20_G	29_T	1.663	1.00
19_I	33_W	1.536	1.00
14_R	36_D	1.499	1.00
52_Y	99_E	1.473	1.00
86_D	89_A	1.471	1.00
36_D	39_Q	1.460	1.00
55_V	110_V	1.376	1.00
13_Y	59_D	1.369	1.00
15_V	66_W	1.360	1.00
5_L	110_V	1.351	1.00
4_G	42_T	1.346	1.00
48_L	53_Y	1.346	1.00
44_L	48_L	1.343	1.00
59_D	63_G	1.304	1.00
81_I	92_Y	1.292	1.00
21_Y	30_R	1.272	1.00
22_D	27_W	1.268	1.00
29_T	72_F	1.251	1.00
19_I	44_L	1.248	1.00
56_Y	95_A	1.237	1.00
58_E	65_E	1.234	1.00
51_R	101_D	1.231	1.00
27_W	72_F	1.225	1.00
54_Y	99_E	1.200	1.00
6_R	42_T	1.185	1.00
33_W	43_V	1.174	1.00
16_G	58_E	1.171	1.00
52_Y	101_D	1.139	1.00
44_L	53_Y	1.125	1.00
31_G	79_F	1.110	1.00
18_A	97_F	1.096	1.00
26_G	82_R	1.074	1.00
16_G	60_V	1.064	1.00
4_G	107_D	1.058	1.00
35_I	39_Q	1.057	1.00
11_T	73_C	1.055	1.00
70_A	84_A	1.047	1.00
57_A	66_W	1.024	1.00
40_C	87_C	1.023	1.00
55_V	98_F	1.006	1.00
29_T	81_I	0.997	1.00
62_G	65_E	0.989	1.00
71_P	74_V	0.972	1.00
27_W	52_Y	0.963	1.00
33_W	41_A	0.942	1.00
108_W	111_Q	0.931	1.00
12_S	37_P	0.913	1.00
46_G	49_T	0.896	1.00
11_T	37_P	0.889	1.00
72_F	84_A	0.880	1.00
76_D	93_D	0.876	1.00
23_D	26_G	0.867	1.00
103_G	106_K	0.866	1.00
4_G	46_G	0.860	1.00
74_V	97_F	0.857	1.00
75_R	81_I	0.857	1.00
11_T	66_W	0.855	1.00
42_T	45_K	0.852	1.00
74_V	93_D	0.840	1.00
60_V	64_G	0.831	1.00
66_W	95_A	0.824	1.00
7_V	43_V	0.820	1.00
33_W	78_K	0.819	1.00
10_R	38_G	0.817	1.00
15_V	57_A	0.815	0.99
67_G	96_G	0.815	0.99
20_G	27_W	0.813	0.99
59_D	66_W	0.797	0.99
11_T	14_R	0.793	0.99
105_Q	108_W	0.790	0.99
5_L	100_V	0.787	0.99
11_T	59_D	0.785	0.99
12_S	38_G	0.784	0.99
90_R	94_R	0.775	0.99
66_W	96_G	0.768	0.99
55_V	100_V	0.761	0.99
98_F	104_E	0.760	0.99
75_R	78_K	0.753	0.99
13_Y	61_D	0.752	0.99
22_D	26_G	0.749	0.99
47_P	106_K	0.748	0.99
21_Y	28_V	0.743	0.99
60_V	65_E	0.742	0.99
14_R	37_P	0.737	0.99
27_W	99_E	0.733	0.99
35_I	41_A	0.730	0.99
102_T	108_W	0.721	0.99
7_V	15_V	0.720	0.99
11_T	20_G	0.719	0.99
58_E	76_D	0.718	0.99
44_L	54_Y	0.717	0.99
5_L	53_Y	0.710	0.99
42_T	107_D	0.708	0.99
29_T	83_G	0.688	0.98
14_R	60_V	0.687	0.98
59_D	62_G	0.686	0.98
45_K	53_Y	0.686	0.98
8_C	87_C	0.681	0.98
23_D	82_R	0.677	0.98
3_A	107_D	0.671	0.98
43_V	58_E	0.671	0.98
5_L	19_I	0.670	0.98
13_Y	62_G	0.664	0.98
61_D	64_G	0.662	0.98
5_L	48_L	0.655	0.98
19_I	30_R	0.652	0.98
60_V	67_G	0.648	0.97
105_Q	111_Q	0.645	0.97
59_D	64_G	0.635	0.97
81_I	90_R	0.632	0.97
69_D	98_F	0.629	0.97
86_D	90_R	0.626	0.97
21_Y	80_T	0.624	0.97
69_D	96_G	0.622	0.97
88_A	91_G	0.615	0.97
75_R	92_Y	0.613	0.96
89_A	93_D	0.610	0.96
15_V	68_G	0.610	0.96
104_E	107_D	0.602	0.96
45_K	48_L	0.600	0.96
44_L	47_P	0.598	0.96
74_V	79_F	0.591	0.96
68_G	96_G	0.591	0.96
29_T	40_C	0.591	0.96
2_R	15_V	0.589	0.96
70_A	99_E	0.589	0.96
85_E	88_A	0.581	0.95
54_Y	72_F	0.569	0.95
48_L	102_T	0.564	0.94
12_S	36_D	0.562	0.94
58_E	62_G	0.558	0.94
29_T	84_A	0.551	0.94
60_V	63_G	0.544	0.93
83_G	90_R	0.541	0.93
19_I	43_V	0.534	0.93
20_G	53_Y	0.532	0.93
104_E	108_W	0.526	0.92
22_D	25_G	0.522	0.92
52_Y	55_V	0.521	0.92
45_K	82_R	0.518	0.92
78_K	88_A	0.517	0.92
21_Y	29_T	0.511	0.91
71_P	77_K	0.510	0.91
43_V	107_D	0.509	0.91
16_G	59_D	0.507	0.91
57_A	68_G	0.502	0.90
9_N	20_G	0.501	0.90
13_Y	68_G	0.500	0.90

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
2ahnA	1	0.9292	45.7	0.871	Contact Map
2vhkA	1	0.8938	35.1	0.879	Contact Map
4bctA	1	0.8496	25.9	0.887	Contact Map
1du5A	2	0.8584	24.2	0.888	Contact Map
3g7mA	2	0.9027	23.3	0.889	Contact Map
1aunA	1	0.8673	18.6	0.894	Contact Map
3qisA	1	0.8673	6.2	0.914	Contact Map
3qbtB	1	0.7965	5	0.918	Contact Map
4gioA	1	0.5133	2.7	0.928	Contact Map
2huhA	2	0.8673	2.7	0.928	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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