DUF61 - PFAM28P - GREMLIN Contacts

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DUF61 - Protein of unknown function DUF61

PFAM:	PF01886	Sequences: DRWLRKELRRLNAHLPRERKSLSELLEEEKPHVVTRDGSTHRFDREELEYLASLLPEEEQDRLRLPILIEIDPDLGEGAYRVRGKVEAKVVSKILGMEREREGRLRIYRPQLAELRRKLPTTTQYVF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (126)
Sequences:	932 (663)
Seq/√Len:	59.0
META:	0.897

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_K	28_E	5.959	1.00
26_L	48_L	2.900	1.00
50_Y	118_K	2.713	1.00
56_P	59_E	2.712	1.00
23_S	61_D	2.685	1.00
91_V	115_L	2.668	1.00
25_L	28_E	2.318	1.00
56_P	60_Q	2.251	1.00
119_L	122_T	2.181	1.00
6_K	9_R	2.156	1.00
47_E	121_T	2.152	1.00
43_F	65_L	2.103	1.00
25_L	31_P	2.101	1.00
28_E	31_P	2.052	1.00
16_P	47_E	1.998	1.00
31_P	48_L	1.944	1.00
33_V	41_H	1.941	1.00
17_R	34_V	1.906	1.00
32_H	40_T	1.866	1.00
45_R	49_E	1.858	1.00
7_E	10_R	1.797	0.99
114_E	118_K	1.654	0.99
63_L	90_V	1.605	0.99
79_A	106_R	1.593	0.99
20_K	25_L	1.553	0.98
52_A	60_Q	1.543	0.98
49_E	53_S	1.504	0.98
50_Y	53_S	1.462	0.98
84_G	87_E	1.454	0.98
116_R	123_T	1.454	0.98
34_V	40_T	1.384	0.97
43_F	122_T	1.367	0.96
18_E	34_V	1.361	0.96
71_I	80_Y	1.332	0.96
21_S	64_R	1.330	0.96
33_V	43_F	1.318	0.96
50_Y	119_L	1.315	0.96
59_E	89_K	1.309	0.95
63_L	86_V	1.309	0.95
4_L	10_R	1.303	0.95
97_M	111_Q	1.300	0.95
116_R	119_L	1.300	0.95
119_L	123_T	1.288	0.95
57_E	60_Q	1.262	0.94
115_L	123_T	1.247	0.94
51_L	110_P	1.190	0.92
21_S	24_E	1.182	0.92
68_L	126_V	1.168	0.92
50_Y	94_I	1.168	0.92
23_S	27_E	1.153	0.91
51_L	90_V	1.146	0.91
19_R	44_D	1.142	0.91
35_T	41_H	1.139	0.91
46_E	49_E	1.132	0.90
69_I	80_Y	1.120	0.90
116_R	122_T	1.117	0.90
69_I	82_V	1.110	0.90
75_L	78_G	1.101	0.89
116_R	121_T	1.091	0.89
26_L	52_A	1.082	0.88
88_A	92_S	1.081	0.88
47_E	116_R	1.070	0.88
37_D	107_I	1.066	0.88
110_P	114_E	1.059	0.87
17_R	21_S	1.024	0.85
8_L	20_K	1.017	0.85
67_I	82_V	1.004	0.84
25_L	29_E	0.959	0.81
22_L	48_L	0.937	0.80
16_P	124_Q	0.918	0.78
12_N	15_L	0.911	0.78
84_G	91_V	0.910	0.78
71_I	125_Y	0.895	0.77
74_D	126_V	0.888	0.76
43_F	107_I	0.883	0.76
54_L	93_K	0.872	0.75
26_L	31_P	0.870	0.75
14_H	76_G	0.846	0.72
5_R	73_P	0.843	0.72
92_S	97_M	0.839	0.72
19_R	67_I	0.833	0.71
108_Y	111_Q	0.822	0.70
115_L	119_L	0.810	0.69
15_L	19_R	0.806	0.69
70_E	83_R	0.806	0.69
57_E	67_I	0.795	0.68
29_E	32_H	0.794	0.68
74_D	110_P	0.793	0.68
11_L	14_H	0.788	0.67
56_P	89_K	0.781	0.66
3_W	7_E	0.760	0.64
69_I	91_V	0.753	0.64
11_L	68_L	0.750	0.63
20_K	26_L	0.742	0.62
84_G	97_M	0.741	0.62
46_E	52_A	0.741	0.62
69_I	117_R	0.738	0.62
13_A	37_D	0.732	0.61
89_K	93_K	0.729	0.61
16_P	19_R	0.728	0.61
30_K	42_R	0.717	0.60
20_K	52_A	0.717	0.60
17_R	36_R	0.716	0.60
73_P	80_Y	0.715	0.59
11_L	46_E	0.712	0.59
59_E	62_R	0.711	0.59
72_D	126_V	0.710	0.59
67_I	78_G	0.707	0.59
88_A	98_E	0.706	0.59
81_R	84_G	0.703	0.58
109_R	112_L	0.703	0.58
20_K	24_E	0.701	0.58
27_E	53_S	0.697	0.58
9_R	36_R	0.696	0.57
35_T	39_S	0.691	0.57
14_H	37_D	0.685	0.56
72_D	80_Y	0.682	0.56
24_E	32_H	0.679	0.56
31_P	121_T	0.676	0.55
24_E	64_R	0.672	0.55
85_K	103_G	0.666	0.54
18_E	24_E	0.664	0.54
50_Y	54_L	0.660	0.53
69_I	107_I	0.660	0.53
46_E	50_Y	0.654	0.53
46_E	53_S	0.652	0.53
7_E	35_T	0.651	0.52
113_A	120_P	0.651	0.52
9_R	35_T	0.645	0.52
27_E	102_E	0.644	0.52
48_L	52_A	0.641	0.51
91_V	112_L	0.635	0.51
60_Q	106_R	0.633	0.50
11_L	30_K	0.630	0.50
30_K	34_V	0.627	0.50
8_L	108_Y	0.623	0.49
85_K	115_L	0.622	0.49
6_K	10_R	0.621	0.49
89_K	96_G	0.619	0.49
47_E	119_L	0.618	0.49
120_P	123_T	0.614	0.48
28_E	32_H	0.613	0.48
8_L	15_L	0.612	0.48
33_V	48_L	0.606	0.47
12_N	65_L	0.602	0.47
75_L	79_A	0.599	0.47
33_V	39_S	0.598	0.47
19_R	114_E	0.594	0.46
7_E	11_L	0.592	0.46
8_L	14_H	0.579	0.44
47_E	95_L	0.579	0.44
20_K	65_L	0.578	0.44
80_Y	125_Y	0.577	0.44
61_D	93_K	0.574	0.44
8_L	13_A	0.572	0.44
112_L	119_L	0.567	0.43
93_K	96_G	0.566	0.43
92_S	99_R	0.565	0.43
50_Y	96_G	0.564	0.43
24_E	72_D	0.560	0.42
11_L	44_D	0.555	0.42
54_L	119_L	0.555	0.42
55_L	90_V	0.551	0.41
16_P	95_L	0.551	0.41
108_Y	112_L	0.550	0.41
51_L	122_T	0.549	0.41
87_E	90_V	0.549	0.41
88_A	91_V	0.548	0.41
20_K	31_P	0.545	0.41
16_P	68_L	0.540	0.40
79_A	108_Y	0.534	0.40
72_D	77_E	0.534	0.40
44_D	114_E	0.529	0.39
44_D	127_F	0.529	0.39
88_A	120_P	0.528	0.39
40_T	79_A	0.523	0.38
95_L	101_R	0.522	0.38
14_H	78_G	0.521	0.38
94_I	115_L	0.520	0.38
84_G	105_L	0.516	0.38
24_E	118_K	0.514	0.37
14_H	21_S	0.508	0.37
9_R	48_L	0.506	0.37
96_G	117_R	0.505	0.37
74_D	96_G	0.504	0.36
37_D	116_R	0.503	0.36
2_R	34_V	0.501	0.36
37_D	68_L	0.501	0.36
109_R	120_P	0.500	0.36

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
2egzA	1	0.8504	15.3	0.921	Contact Map
1mukA	1	0.8425	14.1	0.922	Contact Map
3t0pA	2	0.7008	8.9	0.929	Contact Map
4k3lA	2	0.6457	7.5	0.931	Contact Map
4j2nA	4	0.4094	7.1	0.932	Contact Map
2oczA	2	0.8976	7	0.932	Contact Map
2o7sA	2	0.9291	6.9	0.932	Contact Map
3l9cA	1	0.8583	6.9	0.932	Contact Map
1sflA	2	0.8976	6.5	0.933	Contact Map
1rypF	1	0.4094	6.2	0.934	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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