DUF3000 - PFAM28P - GREMLIN Contacts

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DUF3000 - Protein of unknown function (DUF3000)

PFAM:	PF11452	Sequences: TPAEFRAAVASLRAARLRPEIVLEEIPAPQRLAPYAVALSADVTVDDDEDELATGRLVLLHDPAGQEAWDGTFRLVTYVRAELEPEMAADPLLPEVGWSWLTDALDARGAGYTAASGTVTRVSSESFGGLAGRPDTAEIEIRASWTPTDPDLGAHLEAWCDLLCTAAGLPPLPGVT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (173)
Sequences:	1993 (1107)
Seq/√Len:	84.1
META:	0.689

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_P	62_D	3.989	1.00
13_R	25_E	3.679	1.00
108_R	161_D	3.620	1.00
57_L	75_L	3.544	1.00
70_D	114_A	3.053	1.00
95_E	127_F	2.947	1.00
61_H	72_T	2.798	1.00
9_V	37_V	2.768	1.00
70_D	113_T	2.614	1.00
126_S	133_R	2.560	1.00
95_E	125_E	2.420	1.00
113_T	148_T	2.370	1.00
42_D	54_T	2.143	1.00
94_P	125_E	2.120	1.00
116_S	129_G	2.083	1.00
28_A	36_A	2.069	1.00
4_E	72_T	2.069	1.00
21_I	164_C	2.040	1.00
59_L	152_L	2.002	1.00
17_L	160_C	2.000	1.00
44_T	49_E	1.986	1.00
12_L	156_L	1.920	1.00
71_G	146_T	1.734	1.00
45_V	48_D	1.729	1.00
3_A	7_A	1.708	1.00
26_I	40_S	1.708	1.00
97_G	139_I	1.656	1.00
65_G	72_T	1.611	1.00
8_A	73_F	1.599	1.00
122_V	126_S	1.593	1.00
106_D	112_Y	1.577	1.00
79_V	166_A	1.577	1.00
83_L	139_I	1.567	1.00
2_P	6_R	1.535	1.00
103_D	106_D	1.499	0.99
112_Y	115_A	1.489	0.99
160_C	164_C	1.488	0.99
124_S	130_L	1.485	0.99
103_D	165_T	1.476	0.99
4_E	61_H	1.463	0.99
57_L	77_T	1.450	0.99
59_L	73_F	1.446	0.99
94_P	121_R	1.433	0.99
17_L	23_L	1.413	0.99
102_T	112_Y	1.404	0.99
3_A	6_R	1.403	0.99
53_A	167_A	1.382	0.99
12_L	37_V	1.381	0.99
121_R	125_E	1.362	0.99
7_A	150_P	1.354	0.99
62_D	66_Q	1.340	0.99
88_A	123_S	1.334	0.99
11_S	59_L	1.317	0.99
52_L	80_R	1.297	0.98
58_V	77_T	1.268	0.98
80_R	138_E	1.257	0.98
125_E	135_D	1.250	0.98
80_R	125_E	1.243	0.98
84_E	87_M	1.239	0.98
45_V	51_E	1.203	0.97
10_A	14_A	1.197	0.97
111_G	149_D	1.196	0.97
106_D	111_G	1.194	0.97
130_L	133_R	1.184	0.97
110_A	154_A	1.173	0.97
129_G	132_G	1.167	0.97
167_A	170_P	1.150	0.97
96_V	99_S	1.149	0.97
72_T	146_T	1.128	0.96
44_T	47_D	1.127	0.96
122_V	138_E	1.127	0.96
13_R	37_V	1.123	0.96
21_I	53_A	1.123	0.96
40_S	126_S	1.119	0.96
151_D	154_A	1.116	0.96
2_P	8_A	1.116	0.96
116_S	137_A	1.105	0.96
83_L	93_L	1.101	0.96
32_L	66_Q	1.081	0.95
161_D	164_C	1.067	0.95
108_R	157_E	1.065	0.95
77_T	143_A	1.062	0.95
61_H	146_T	1.057	0.95
79_V	162_L	1.057	0.95
118_T	124_S	1.055	0.94
111_G	148_T	1.034	0.94
6_R	10_A	1.031	0.94
40_S	78_Y	1.031	0.94
105_L	110_A	1.006	0.93
41_A	163_L	1.000	0.93
97_G	119_V	0.995	0.93
22_V	44_T	0.989	0.92
37_V	75_L	0.987	0.92
152_L	155_H	0.983	0.92
77_T	159_W	0.981	0.92
99_S	104_A	0.980	0.92
102_T	115_A	0.975	0.92
9_V	13_R	0.974	0.92
150_P	153_G	0.961	0.91
85_P	92_L	0.943	0.90
18_R	164_C	0.940	0.90
8_A	153_G	0.929	0.90
83_L	87_M	0.917	0.89
25_E	37_V	0.917	0.89
42_D	78_Y	0.916	0.89
7_A	11_S	0.901	0.88
116_S	133_R	0.892	0.88
89_A	92_L	0.891	0.88
66_Q	147_P	0.886	0.87
26_I	53_A	0.883	0.87
46_D	49_E	0.879	0.87
97_G	113_T	0.872	0.87
152_L	156_L	0.870	0.86
110_A	139_I	0.869	0.86
17_L	32_L	0.867	0.86
61_H	73_F	0.857	0.86
40_S	80_R	0.857	0.86
58_V	66_Q	0.852	0.85
122_V	125_E	0.850	0.85
58_V	138_E	0.847	0.85
88_A	101_L	0.845	0.85
71_G	91_P	0.839	0.84
87_M	115_A	0.829	0.84
11_S	151_D	0.826	0.84
86_E	94_P	0.825	0.83
8_A	11_S	0.824	0.83
80_R	140_E	0.823	0.83
116_S	126_S	0.823	0.83
126_S	159_W	0.792	0.81
32_L	160_C	0.787	0.80
142_R	147_P	0.778	0.80
96_V	100_W	0.771	0.79
130_L	135_D	0.769	0.79
35_Y	63_P	0.758	0.78
34_P	63_P	0.756	0.78
130_L	137_A	0.755	0.78
77_T	156_L	0.755	0.78
164_C	170_P	0.752	0.77
157_E	160_C	0.752	0.77
157_E	172_L	0.746	0.77
92_L	118_T	0.736	0.76
107_A	150_P	0.735	0.76
11_S	150_P	0.726	0.75
21_I	41_A	0.723	0.75
32_L	60_L	0.718	0.74
137_A	159_W	0.717	0.74
3_A	22_V	0.716	0.74
137_A	141_I	0.715	0.74
156_L	164_C	0.711	0.73
31_R	72_T	0.707	0.73
124_S	138_E	0.706	0.73
7_A	10_A	0.704	0.73
78_Y	122_V	0.701	0.72
65_G	71_G	0.700	0.72
27_P	143_A	0.696	0.72
145_W	155_H	0.696	0.72
80_R	122_V	0.693	0.71
2_P	73_F	0.690	0.71
73_F	83_L	0.690	0.71
84_E	123_S	0.686	0.71
70_D	125_E	0.683	0.70
41_A	118_T	0.683	0.70
57_L	90_D	0.682	0.70
54_T	78_Y	0.680	0.70
66_Q	79_V	0.679	0.70
30_Q	36_A	0.678	0.70
70_D	141_I	0.677	0.70
134_P	141_I	0.671	0.69
69_W	74_R	0.668	0.69
83_L	88_A	0.666	0.68
57_L	121_R	0.665	0.68
32_L	137_A	0.654	0.67
101_L	158_A	0.654	0.67
119_V	123_S	0.651	0.67
73_F	116_S	0.650	0.66
142_R	145_W	0.646	0.66
91_P	163_L	0.645	0.66
2_P	35_Y	0.642	0.66
92_L	96_V	0.632	0.64
85_P	129_G	0.625	0.63
4_E	15_A	0.624	0.63
16_R	19_P	0.621	0.63
106_D	109_G	0.621	0.63
105_L	112_Y	0.620	0.63
65_G	128_G	0.620	0.63
93_L	96_V	0.618	0.63
111_G	157_E	0.609	0.61
81_A	101_L	0.608	0.61
156_L	161_D	0.607	0.61
26_I	141_I	0.603	0.61
48_D	51_E	0.598	0.60
62_D	120_T	0.597	0.60
15_A	21_I	0.596	0.60
107_A	161_D	0.593	0.59
45_V	49_E	0.589	0.59
46_D	51_E	0.589	0.59
109_G	139_I	0.585	0.58
27_P	159_W	0.584	0.58
53_A	116_S	0.583	0.58
22_V	32_L	0.581	0.58
43_V	169_L	0.578	0.58
25_E	39_L	0.578	0.58
66_Q	75_L	0.577	0.57
94_P	137_A	0.572	0.57
115_A	119_V	0.569	0.56
7_A	14_A	0.561	0.55
32_L	133_R	0.560	0.55
144_S	147_P	0.560	0.55
53_A	77_T	0.559	0.55
125_E	129_G	0.558	0.55
25_E	70_D	0.558	0.55
81_A	139_I	0.556	0.55
75_L	116_S	0.555	0.54
4_E	73_F	0.553	0.54
75_L	141_I	0.551	0.54
15_A	40_S	0.550	0.54
32_L	118_T	0.550	0.54
20_E	169_L	0.549	0.54
161_D	165_T	0.547	0.53
89_A	121_R	0.546	0.53
24_E	80_R	0.545	0.53
24_E	30_Q	0.545	0.53
149_D	154_A	0.544	0.53
68_A	72_T	0.543	0.53
57_L	156_L	0.539	0.52
77_T	130_L	0.537	0.52
20_E	164_C	0.534	0.52
94_P	115_A	0.532	0.51
73_F	80_R	0.532	0.51
18_R	169_L	0.528	0.51
15_A	160_C	0.527	0.51
27_P	39_L	0.526	0.51
62_D	147_P	0.526	0.51
26_I	32_L	0.526	0.51
77_T	138_E	0.526	0.51
58_V	124_S	0.526	0.51
10_A	132_G	0.525	0.51
116_S	159_W	0.524	0.50
8_A	59_L	0.523	0.50
93_L	139_I	0.523	0.50
113_T	141_I	0.522	0.50
53_A	121_R	0.522	0.50
48_D	151_D	0.520	0.50
8_A	12_L	0.519	0.50
10_A	13_R	0.519	0.50
42_D	146_T	0.518	0.50
64_A	72_T	0.518	0.50
115_A	164_C	0.516	0.49
66_Q	130_L	0.516	0.49
16_R	157_E	0.515	0.49
53_A	122_V	0.515	0.49
12_L	58_V	0.513	0.49
57_L	93_L	0.512	0.49
13_R	26_I	0.512	0.49
46_D	102_T	0.510	0.49
43_V	143_A	0.509	0.48
160_C	166_A	0.508	0.48
4_E	150_P	0.506	0.48
94_P	123_S	0.505	0.48
26_I	133_R	0.500	0.47

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
3emxA	1	0.4091	6.9	0.964	Contact Map
4nzsA	4	0.4602	4.7	0.967	Contact Map
3hlzA	1	0.733	4.2	0.968	Contact Map
2vugA	2	0.2841	4	0.968	Contact Map
2c0cA	1	0.3409	3.4	0.969	Contact Map
4ubtA	3	0.4886	3.3	0.969	Contact Map
4o9aA	4	0.4489	3.3	0.969	Contact Map
3nwmA	1	0.267	3.3	0.969	Contact Map
4j56E	1	0.3239	3.1	0.969	Contact Map
4p56A	1	0.2159	2.9	0.97	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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