PSD1 - PFAM28P - GREMLIN Contacts

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PSD1 - Protein of unknown function (DUF1553)

PFAM:	PF07587	Sequences: RRLALARWLTSPDNPLTARVIVNRVWQHHFGRGLVETPDDFGRQGEPPSHPELLDWLAVEFVESGWSLKALHRLIVTSATYRQSSRATPEALEKDPDNRLLARGPRRRLEAEVIRDAALAVSGLLDPKMGGPSVKPYQPPRKYVQSTGEDLYRRSLYTFWKRTVPPPFLETFDAPDREVCTVRRSRTNTPLQALFLLNDPFVVEAARALAERLLKEAERIERAYRLALSRPPTAEELAALLAFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	244 (242)
Sequences:	45286 (33498)
Seq/√Len:	2153.3
META:	0.961

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_H	72_H	3.733	1.00
64_S	70_A	3.403	1.00
221_E	237_L	3.054	1.00
60_E	70_A	3.013	1.00
60_E	64_S	2.912	1.00
67_S	70_A	2.878	1.00
36_E	46_E	2.759	1.00
110_E	113_V	2.758	1.00
59_V	63_E	2.745	1.00
221_E	231_P	2.694	1.00
60_E	74_L	2.633	1.00
213_L	223_A	2.627	1.00
21_I	68_L	2.586	1.00
212_R	226_L	2.511	1.00
32_R	36_E	2.492	1.00
79_A	83_Q	2.364	1.00
27_Q	38_P	2.189	1.00
91_A	102_A	2.182	1.00
60_E	63_E	2.163	1.00
3_L	7_R	2.146	1.00
22_V	71_L	2.123	1.00
225_R	231_P	2.100	1.00
73_R	77_T	2.095	1.00
124_L	205_A	2.079	1.00
88_T	91_A	2.057	1.00
64_S	74_L	2.048	1.00
87_A	92_L	1.950	1.00
124_L	208_A	1.922	1.00
29_H	76_V	1.921	1.00
118_A	202_V	1.884	1.00
222_R	226_L	1.846	1.00
238_A	242_A	1.822	1.00
221_E	232_P	1.820	1.00
12_P	62_V	1.784	1.00
25_V	71_L	1.768	1.00
74_L	77_T	1.705	1.00
146_S	150_D	1.702	1.00
70_A	74_L	1.677	1.00
209_L	227_A	1.664	1.00
90_E	93_E	1.637	1.00
56_W	74_L	1.631	1.00
59_V	62_V	1.629	1.00
230_R	236_E	1.622	1.00
218_E	221_E	1.590	1.00
216_E	222_R	1.578	1.00
25_V	72_H	1.539	1.00
90_E	94_K	1.538	1.00
234_A	238_A	1.528	1.00
61_F	68_L	1.507	1.00
208_A	211_E	1.498	1.00
224_Y	232_P	1.495	1.00
220_I	241_L	1.463	1.00
174_A	177_R	1.447	1.00
32_R	99_R	1.443	1.00
35_V	41_F	1.442	1.00
56_W	60_E	1.437	1.00
235_E	238_A	1.425	1.00
109_L	117_A	1.404	1.00
64_S	67_S	1.402	1.00
117_A	121_V	1.383	1.00
201_F	205_A	1.380	1.00
124_L	152_Y	1.369	1.00
4_A	7_R	1.368	1.00
109_L	113_V	1.360	1.00
22_V	61_F	1.353	1.00
221_E	225_R	1.340	1.00
18_A	62_V	1.335	1.00
112_E	184_R	1.335	1.00
237_L	241_L	1.320	1.00
89_P	93_E	1.317	1.00
126_D	149_E	1.314	1.00
71_L	75_I	1.310	1.00
49_S	99_R	1.284	1.00
68_L	72_H	1.283	1.00
29_H	75_I	1.270	1.00
200_P	204_E	1.268	1.00
222_R	225_R	1.262	1.00
62_V	66_W	1.258	1.00
213_L	222_R	1.245	1.00
18_A	66_W	1.239	1.00
12_P	63_E	1.232	1.00
115_R	155_S	1.226	1.00
211_E	215_K	1.224	1.00
204_E	207_R	1.220	1.00
72_H	76_V	1.217	1.00
89_P	92_L	1.211	1.00
140_P	143_Y	1.208	1.00
232_P	237_L	1.199	1.00
11_S	14_N	1.195	1.00
128_K	150_D	1.193	1.00
175_P	184_R	1.191	1.00
80_T	101_L	1.190	1.00
209_L	223_A	1.188	1.00
98_N	105_P	1.181	1.00
27_Q	33_G	1.169	1.00
19_R	55_D	1.161	1.00
39_D	182_V	1.158	1.00
118_A	205_A	1.156	1.00
25_V	29_H	1.153	1.00
171_T	195_F	1.151	1.00
207_R	211_E	1.150	1.00
168_F	195_F	1.139	1.00
46_E	99_R	1.137	1.00
224_Y	240_L	1.132	1.00
25_V	68_L	1.124	1.00
135_K	159_F	1.123	1.00
21_I	25_V	1.121	1.00
205_A	208_A	1.118	1.00
14_N	17_T	1.114	1.00
36_E	97_D	1.113	1.00
77_T	82_R	1.106	1.00
217_A	222_R	1.104	1.00
80_T	83_Q	1.098	1.00
21_I	61_F	1.091	1.00
220_I	240_L	1.082	1.00
7_R	10_T	1.081	1.00
141_R	144_V	1.079	1.00
104_G	107_R	1.069	1.00
9_L	17_T	1.060	1.00
239_A	242_A	1.056	1.00
206_A	209_L	1.047	1.00
60_E	71_L	1.043	1.00
107_R	186_R	1.027	1.00
30_F	75_I	1.011	1.00
120_A	127_P	1.011	1.00
135_K	146_S	1.007	1.00
121_V	227_A	0.995	1.00
214_L	219_R	0.995	1.00
128_K	149_E	0.986	1.00
140_P	144_V	0.972	1.00
5_L	9_L	0.972	1.00
88_T	102_A	0.968	1.00
166_P	169_L	0.956	1.00
155_S	158_T	0.948	1.00
40_D	44_Q	0.947	1.00
27_Q	183_R	0.947	1.00
76_V	81_Y	0.944	1.00
29_H	81_Y	0.943	1.00
95_D	98_N	0.937	1.00
55_D	58_A	0.937	1.00
238_A	241_L	0.936	1.00
71_L	74_L	0.932	1.00
219_R	222_R	0.928	1.00
235_E	239_A	0.919	1.00
20_V	41_F	0.914	1.00
199_D	202_V	0.914	1.00
234_A	237_L	0.913	1.00
87_A	102_A	0.912	1.00
101_L	105_P	0.911	1.00
134_V	158_T	0.908	1.00
137_Y	151_L	0.907	1.00
32_R	183_R	0.901	1.00
212_R	216_E	0.896	1.00
10_T	62_V	0.892	1.00
56_W	59_V	0.885	1.00
39_D	180_C	0.883	1.00
61_F	71_L	0.873	1.00
214_L	217_A	0.870	1.00
135_K	138_Q	0.870	1.00
117_A	120_A	0.867	1.00
58_A	62_V	0.867	1.00
129_M	156_L	0.864	1.00
146_S	149_E	0.858	1.00
130_G	153_R	0.855	1.00
79_A	82_R	0.850	1.00
223_A	226_L	0.842	1.00
173_D	185_S	0.842	1.00
203_V	207_R	0.840	1.00
36_E	99_R	0.835	1.00
49_S	101_L	0.827	1.00
25_V	75_I	0.825	1.00
17_T	66_W	0.825	1.00
64_S	71_L	0.824	1.00
204_E	208_A	0.821	1.00
176_D	179_V	0.814	1.00
145_Q	149_E	0.812	1.00
115_R	119_L	0.811	1.00
224_Y	228_L	0.810	1.00
91_A	100_L	0.807	1.00
55_D	59_V	0.804	1.00
39_D	183_R	0.802	1.00
30_F	101_L	0.801	1.00
129_M	133_S	0.799	1.00
225_R	229_S	0.799	1.00
160_W	177_R	0.799	1.00
129_M	153_R	0.798	1.00
160_W	174_A	0.789	1.00
43_R	47_P	0.786	1.00
169_L	174_A	0.783	1.00
120_A	125_L	0.780	1.00
32_R	97_D	0.779	1.00
209_L	213_L	0.779	1.00
37_T	46_E	0.772	1.00
18_A	58_A	0.767	1.00
138_Q	164_V	0.766	1.00
209_L	226_L	0.764	1.00
165_P	170_E	0.764	1.00
70_A	77_T	0.761	1.00
145_Q	148_G	0.758	1.00
163_T	178_E	0.758	1.00
129_M	132_P	0.754	1.00
206_A	210_A	0.754	1.00
136_P	158_T	0.754	1.00
233_T	237_L	0.753	1.00
135_K	144_V	0.751	1.00
25_V	28_H	0.748	1.00
65_G	70_A	0.747	1.00
94_K	102_A	0.747	1.00
83_Q	91_A	0.740	1.00
231_P	234_A	0.738	1.00
145_Q	151_L	0.733	1.00
6_A	10_T	0.729	1.00
128_K	131_G	0.725	1.00
87_A	103_R	0.724	1.00
121_V	209_L	0.722	1.00
228_L	231_P	0.719	1.00
10_T	17_T	0.719	1.00
91_A	94_K	0.716	1.00
147_T	150_D	0.716	1.00
18_A	21_I	0.715	1.00
154_R	157_Y	0.714	1.00
224_Y	236_E	0.710	1.00
231_P	237_L	0.710	1.00
119_L	125_L	0.706	1.00
72_H	75_I	0.704	1.00
122_S	205_A	0.698	1.00
111_A	174_A	0.696	1.00
135_K	139_P	0.696	1.00
133_S	136_P	0.696	1.00
30_F	80_T	0.696	1.00
155_S	169_L	0.694	1.00
6_A	9_L	0.693	1.00
237_L	240_L	0.691	1.00
146_S	151_L	0.690	1.00
211_E	214_L	0.688	1.00
75_I	78_S	0.679	1.00
51_P	55_D	0.678	1.00
168_F	171_T	0.678	1.00
172_F	192_Q	0.676	1.00
220_I	224_Y	0.675	1.00
168_F	202_V	0.674	1.00
85_S	104_G	0.673	1.00
161_K	164_V	0.672	1.00
61_F	65_G	0.671	1.00
25_V	61_F	0.666	1.00
121_V	226_L	0.666	1.00
70_A	73_R	0.665	1.00
144_V	147_T	0.663	1.00
27_Q	32_R	0.657	1.00
145_Q	150_D	0.657	1.00
50_H	53_L	0.655	1.00
131_G	153_R	0.654	1.00
122_S	208_A	0.654	1.00
16_L	20_V	0.652	1.00
22_V	58_A	0.651	1.00
208_A	212_R	0.651	1.00
10_T	14_N	0.651	1.00
28_H	110_E	0.646	1.00
113_V	117_A	0.637	1.00
87_A	91_A	0.633	1.00
21_I	29_H	0.632	1.00
218_E	222_R	0.631	1.00
158_T	169_L	0.630	1.00
15_P	19_R	0.629	1.00
126_D	129_M	0.628	1.00
233_T	236_E	0.628	1.00
136_P	139_P	0.626	1.00
213_L	219_R	0.621	1.00
33_G	39_D	0.616	1.00
151_L	158_T	0.615	1.00
137_Y	145_Q	0.612	1.00
166_P	201_F	0.612	1.00
161_K	177_R	0.612	1.00
220_I	237_L	0.610	1.00
48_P	51_P	0.609	1.00
165_P	174_A	0.608	1.00
107_R	110_E	0.608	1.00
170_E	176_D	0.604	1.00
9_L	14_N	0.604	1.00
209_L	212_R	0.604	1.00
28_H	113_V	0.603	1.00
220_I	232_P	0.603	1.00
114_I	172_F	0.601	1.00
199_D	203_V	0.600	1.00
62_V	65_G	0.597	1.00
158_T	166_P	0.596	1.00
45_G	49_S	0.595	1.00
175_P	181_T	0.592	1.00
213_L	217_A	0.589	1.00
49_S	52_E	0.588	1.00
152_Y	205_A	0.587	1.00
213_L	226_L	0.584	1.00
215_K	218_E	0.582	1.00
196_L	202_V	0.579	1.00
36_E	183_R	0.579	1.00
111_A	169_L	0.578	1.00
119_L	126_D	0.578	1.00
17_T	21_I	0.575	1.00
174_A	178_E	0.574	1.00
112_E	175_P	0.568	1.00
37_T	45_G	0.567	1.00
164_V	167_P	0.567	1.00
134_V	137_Y	0.567	1.00
133_S	159_F	0.567	1.00
15_P	18_A	0.567	1.00
114_I	117_A	0.567	1.00
33_G	36_E	0.565	1.00
195_F	199_D	0.561	1.00
212_R	222_R	0.560	1.00
32_R	105_P	0.558	1.00
153_R	157_Y	0.556	1.00
110_E	114_I	0.554	1.00
35_V	46_E	0.552	1.00
167_P	170_E	0.552	1.00
148_G	151_L	0.552	1.00
239_A	243_F	0.550	1.00
50_H	101_L	0.548	1.00
38_P	182_V	0.548	1.00
141_R	164_V	0.547	1.00
170_E	174_A	0.546	1.00
88_T	92_L	0.543	1.00
46_E	49_S	0.543	1.00
194_L	198_N	0.542	1.00
134_V	139_P	0.542	1.00
221_E	234_A	0.542	1.00
160_W	165_P	0.541	1.00
21_I	24_R	0.541	1.00
128_K	132_P	0.539	1.00
12_P	65_G	0.539	1.00
210_A	213_L	0.539	1.00
95_D	103_R	0.538	1.00
160_W	163_T	0.538	1.00
139_P	143_Y	0.537	1.00
88_T	94_K	0.535	1.00
28_H	72_H	0.534	1.00
147_T	151_L	0.534	1.00
50_H	100_L	0.533	1.00
81_Y	104_G	0.533	1.00
7_R	11_S	0.528	1.00
126_D	153_R	0.528	1.00
148_G	152_Y	0.528	1.00
134_V	151_L	0.527	1.00
52_E	55_D	0.527	1.00
53_L	56_W	0.524	1.00
14_N	18_A	0.524	1.00
152_Y	208_A	0.524	1.00
44_Q	47_P	0.523	1.00
135_K	145_Q	0.521	1.00
126_D	150_D	0.521	1.00
36_E	101_L	0.519	1.00
27_Q	36_E	0.517	1.00
205_A	209_L	0.516	1.00
118_A	122_S	0.515	1.00
141_R	161_K	0.514	1.00
60_E	65_G	0.513	1.00
101_L	104_G	0.512	1.00
114_I	196_L	0.510	1.00
153_R	158_T	0.508	1.00
76_V	82_R	0.506	1.00
163_T	166_P	0.505	1.00
152_Y	204_E	0.501	1.00
195_F	201_F	0.500	1.00
121_V	228_L	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
2zc2A	1	0.1107	18.9	0.956	Contact Map
1h3lA	1	0.2664	12	0.96	Contact Map
2ysrA	1	0.2377	11.2	0.961	Contact Map
2maoA	1	0.3033	10.2	0.961	Contact Map
1or7A	2	0.3115	8.9	0.962	Contact Map
4cxfA	1	0.291	8.3	0.963	Contact Map
4qb3A	1	0.4303	7.7	0.963	Contact Map
1ufzA	1	0.2213	6.9	0.964	Contact Map
1o7xA	2	0.2664	6.7	0.964	Contact Map
2khvA	1	0.209	6.5	0.965	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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