DUF3485 - PFAM28P - GREMLIN Contacts

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DUF3485 - Protein of unknown function (DUF3485)

PFAM:	PF11984	Sequences: LALALLLLAAAAAAAALARTEPVPLRAPLASFPLQIGGWRGGDDAPLDPWVPDVLGADDYLSRTYRNPDGRPVNLYVAYYASQRQGASLIHSPENCLPGSGWEIVSSGRVTLPVPLGGGPIPVNRYVIQKGGRRQLVLYWYQVGGRVVASEYWAKLYLVRDALRGRRTDGALVRVSTPVGDGEEAAEARLQAFARALLPALPRY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	204 (199)
Sequences:	12809 (11097)
Seq/√Len:	786.6
META:	0.947

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_T	74_N	3.368	1.00
49_P	53_D	3.332	1.00
48_D	51_V	2.872	1.00
160_R	164_R	2.861	1.00
175_V	194_A	2.790	1.00
58_D	81_A	2.667	1.00
142_Q	147_V	2.603	1.00
67_N	71_R	2.598	1.00
125_R	187_E	2.584	1.00
111_T	122_P	2.421	1.00
105_V	129_Q	2.384	1.00
35_Q	40_R	2.384	1.00
192_A	196_A	2.366	1.00
177_T	190_L	2.346	1.00
156_L	160_R	2.188	1.00
177_T	189_R	2.154	1.00
177_T	186_A	2.051	1.00
191_Q	195_R	2.042	1.00
111_T	120_P	2.021	1.00
129_Q	134_R	2.012	1.00
91_H	96_C	1.975	1.00
146_R	157_Y	1.946	1.00
136_L	179_V	1.940	1.00
142_Q	145_G	1.937	1.00
150_S	153_W	1.918	1.00
138_L	187_E	1.768	1.00
157_Y	160_R	1.760	1.00
188_A	192_A	1.683	1.00
185_A	188_A	1.647	1.00
27_A	31_S	1.621	1.00
108_G	125_R	1.612	1.00
71_R	189_R	1.601	1.00
116_L	119_G	1.594	1.00
38_G	68_P	1.591	1.00
50_W	53_D	1.588	1.00
135_Q	176_S	1.588	1.00
187_E	191_Q	1.587	1.00
155_K	158_L	1.585	1.00
153_W	157_Y	1.584	1.00
74_N	176_S	1.571	1.00
138_L	190_L	1.556	1.00
73_V	193_F	1.556	1.00
192_A	195_R	1.552	1.00
38_G	67_N	1.526	1.00
175_V	190_L	1.505	1.00
52_P	57_A	1.504	1.00
34_L	41_G	1.480	1.00
162_A	168_T	1.442	1.00
85_Q	88_S	1.435	1.00
93_P	96_C	1.429	1.00
84_R	87_A	1.399	1.00
37_G	196_A	1.387	1.00
49_P	52_P	1.379	1.00
110_V	191_Q	1.370	1.00
65_Y	193_F	1.369	1.00
12_A	15_A	1.369	1.00
148_V	157_Y	1.323	1.00
188_A	191_Q	1.322	1.00
7_L	10_A	1.298	1.00
144_G	161_D	1.298	1.00
109_R	122_P	1.298	1.00
146_R	160_R	1.294	1.00
14_A	17_L	1.291	1.00
94_E	107_S	1.270	1.00
10_A	14_A	1.268	1.00
128_I	137_V	1.266	1.00
44_D	47_L	1.262	1.00
113_P	120_P	1.258	1.00
67_N	70_G	1.247	1.00
136_L	187_E	1.246	1.00
35_Q	38_G	1.245	1.00
8_L	12_A	1.232	1.00
11_A	14_A	1.222	1.00
127_V	134_R	1.218	1.00
41_G	47_L	1.212	1.00
73_V	177_T	1.212	1.00
42_G	47_L	1.205	1.00
10_A	13_A	1.198	1.00
22_P	25_L	1.188	1.00
5_L	9_A	1.187	1.00
66_R	72_P	1.180	1.00
123_V	140_W	1.171	1.00
34_L	63_R	1.161	1.00
146_R	161_D	1.160	1.00
78_A	172_L	1.146	1.00
42_G	45_A	1.144	1.00
9_A	13_A	1.143	1.00
94_E	151_E	1.142	1.00
194_A	197_L	1.137	1.00
180_G	183_E	1.127	1.00
14_A	18_A	1.109	1.00
28_P	59_D	1.103	1.00
41_G	44_D	1.098	1.00
62_S	76_Y	1.077	1.00
129_Q	132_G	1.075	1.00
153_W	156_L	1.071	1.00
9_A	12_A	1.064	1.00
130_K	133_R	1.054	1.00
10_A	15_A	1.047	1.00
123_V	138_L	1.041	1.00
60_Y	76_Y	1.036	1.00
41_G	46_P	1.035	1.00
107_S	124_N	1.033	1.00
40_R	66_R	1.028	1.00
6_L	9_A	1.021	1.00
194_A	198_L	0.995	1.00
90_I	141_Y	0.988	1.00
96_C	101_G	0.977	1.00
62_S	74_N	0.975	1.00
109_R	124_N	0.964	1.00
179_V	186_A	0.956	1.00
15_A	18_A	0.956	1.00
110_V	123_V	0.955	1.00
113_P	195_R	0.953	1.00
43_D	46_P	0.952	1.00
133_R	178_P	0.945	1.00
175_V	193_F	0.945	1.00
79_Y	169_D	0.941	1.00
156_L	159_V	0.938	1.00
13_A	17_L	0.938	1.00
128_I	135_Q	0.936	1.00
32_F	61_L	0.928	1.00
19_R	22_P	0.926	1.00
67_N	192_A	0.923	1.00
51_V	54_V	0.913	1.00
199_P	202_P	0.911	1.00
67_N	72_P	0.904	1.00
109_R	149_A	0.900	1.00
39_W	73_V	0.896	1.00
110_V	125_R	0.893	1.00
58_D	87_A	0.893	1.00
12_A	16_A	0.886	1.00
54_V	57_A	0.881	1.00
90_I	95_N	0.874	1.00
74_N	135_Q	0.869	1.00
50_W	54_V	0.867	1.00
104_I	126_Y	0.863	1.00
57_A	76_Y	0.861	1.00
53_D	56_G	0.856	1.00
64_T	72_P	0.855	1.00
185_A	189_R	0.854	1.00
6_L	10_A	0.854	1.00
183_E	189_R	0.848	1.00
103_E	129_Q	0.846	1.00
77_V	171_A	0.844	1.00
42_G	46_P	0.836	1.00
155_K	159_V	0.833	1.00
11_A	15_A	0.830	1.00
121_I	147_V	0.829	1.00
51_V	57_A	0.822	1.00
189_R	192_A	0.809	1.00
36_I	196_A	0.807	1.00
88_S	155_K	0.806	1.00
138_L	191_Q	0.802	1.00
9_A	14_A	0.794	1.00
83_Q	170_G	0.791	1.00
125_R	138_L	0.782	1.00
179_V	183_E	0.776	1.00
8_L	11_A	0.775	1.00
20_T	23_V	0.770	1.00
186_A	189_R	0.768	1.00
154_A	158_L	0.768	1.00
4_A	8_L	0.760	1.00
53_D	57_A	0.759	1.00
94_E	126_Y	0.758	1.00
39_W	67_N	0.750	1.00
136_L	177_T	0.747	1.00
157_Y	161_D	0.745	1.00
79_Y	171_A	0.744	1.00
112_L	123_V	0.741	1.00
16_A	19_R	0.740	1.00
190_L	194_A	0.738	1.00
4_A	7_L	0.738	1.00
196_A	200_A	0.738	1.00
13_A	16_A	0.736	1.00
43_D	64_T	0.733	1.00
197_L	200_A	0.732	1.00
52_P	55_L	0.728	1.00
148_V	154_A	0.725	1.00
57_A	78_A	0.722	1.00
143_V	154_A	0.721	1.00
110_V	187_E	0.719	1.00
91_H	101_G	0.716	1.00
126_Y	139_Y	0.709	1.00
137_V	176_S	0.705	1.00
41_G	45_A	0.700	1.00
47_L	51_V	0.699	1.00
181_D	184_E	0.685	1.00
141_Y	151_E	0.684	1.00
198_L	202_P	0.684	1.00
36_I	197_L	0.683	1.00
96_C	99_G	0.682	1.00
138_L	194_A	0.677	1.00
114_V	118_G	0.676	1.00
75_L	197_L	0.670	1.00
175_V	197_L	0.670	1.00
40_R	68_P	0.670	1.00
46_P	52_P	0.667	1.00
107_S	126_Y	0.664	1.00
18_A	21_E	0.660	1.00
82_S	85_Q	0.658	1.00
144_G	165_G	0.657	1.00
90_I	170_G	0.657	1.00
66_R	70_G	0.656	1.00
110_V	113_P	0.654	1.00
169_D	172_L	0.652	1.00
162_A	166_R	0.651	1.00
139_Y	172_L	0.651	1.00
125_R	136_L	0.647	1.00
38_G	196_A	0.646	1.00
187_E	190_L	0.640	1.00
83_Q	90_I	0.637	1.00
21_E	24_P	0.636	1.00
83_Q	88_S	0.634	1.00
17_L	20_T	0.630	1.00
14_A	20_T	0.627	1.00
3_L	7_L	0.627	1.00
51_V	56_G	0.626	1.00
75_L	193_F	0.626	1.00
96_C	139_Y	0.625	1.00
17_L	21_E	0.624	1.00
15_A	20_T	0.623	1.00
32_F	197_L	0.622	1.00
90_I	154_A	0.620	1.00
38_G	192_A	0.620	1.00
22_P	26_R	0.612	1.00
58_D	61_L	0.611	1.00
151_E	154_A	0.609	1.00
57_A	60_Y	0.608	1.00
181_D	185_A	0.607	1.00
154_A	157_Y	0.604	1.00
189_R	196_A	0.604	1.00
20_T	25_L	0.602	1.00
32_F	63_R	0.602	1.00
127_V	136_L	0.601	1.00
105_V	134_R	0.600	1.00
121_I	198_L	0.596	1.00
143_V	170_G	0.593	1.00
12_A	17_L	0.591	1.00
190_L	193_F	0.590	1.00
52_P	60_Y	0.587	1.00
186_A	190_L	0.582	1.00
87_A	90_I	0.578	1.00
195_R	199_P	0.573	1.00
14_A	19_R	0.571	1.00
158_L	168_T	0.569	1.00
71_R	180_G	0.567	1.00
135_Q	178_P	0.567	1.00
3_L	6_L	0.564	1.00
148_V	151_E	0.561	1.00
92_S	95_N	0.560	1.00
80_Y	90_I	0.559	1.00
146_R	153_W	0.558	1.00
74_N	97_L	0.553	1.00
139_Y	174_R	0.552	1.00
161_D	166_R	0.549	1.00
47_L	60_Y	0.549	1.00
5_L	8_L	0.546	1.00
71_R	185_A	0.545	1.00
7_L	11_A	0.544	1.00
51_V	55_L	0.543	1.00
110_V	138_L	0.542	1.00
42_G	66_R	0.542	1.00
34_L	42_G	0.541	1.00
62_S	66_R	0.541	1.00
6_L	11_A	0.535	1.00
195_R	198_L	0.533	1.00
73_V	189_R	0.533	1.00
104_I	107_S	0.531	1.00
88_S	154_A	0.529	1.00
29_L	59_D	0.529	1.00
14_A	21_E	0.529	1.00
33_P	65_Y	0.525	1.00
137_V	174_R	0.523	1.00
123_V	128_I	0.523	1.00
143_V	158_L	0.522	1.00
61_L	65_Y	0.521	1.00
73_V	175_V	0.520	1.00
179_V	185_A	0.519	1.00
124_N	149_A	0.519	1.00
179_V	182_G	0.518	1.00
52_P	56_G	0.518	1.00
41_G	63_R	0.517	1.00
122_P	147_V	0.517	1.00
8_L	13_A	0.517	1.00
85_Q	158_L	0.517	1.00
15_A	21_E	0.513	1.00
80_Y	83_Q	0.512	1.00
77_V	173_V	0.512	1.00
104_I	128_I	0.511	1.00
54_V	172_L	0.509	1.00
115_P	119_G	0.508	1.00
152_Y	156_L	0.507	1.00
20_T	26_R	0.506	1.00
83_Q	169_D	0.505	1.00
29_L	32_F	0.504	1.00
48_D	53_D	0.504	1.00
45_A	64_T	0.500	1.00

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
1z21A	1	0.3382	13.6	0.925	Contact Map
5a1uH	1	0.3775	5.6	0.937	Contact Map
1kdlA	1	0.0686	5.5	0.938	Contact Map
4p6zM	1	0.3873	4.3	0.941	Contact Map
4hmyS	1	0.3873	4.3	0.941	Contact Map
2vglS	1	0.3873	3.7	0.943	Contact Map
2ggtA	1	0.4461	3.6	0.943	Contact Map
1jrmA	1	0.3235	3.4	0.944	Contact Map
3j7yb	1	0.2696	3.3	0.944	Contact Map
2vglM	1	0.3873	3.1	0.945	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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