DUF1538 - PFAM28P - GREMLIN Contacts

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DUF1538 - Protein of unknown function (DUF1538)

PFAM:	PF07556	Sequences: IVLIVLIFQLFVLRLPIPNLLRILIGLVLVIIGLTLFLLGLELGLFPLGELIGSQLAKKGSLWLLLLFGFLLGFGTTIAEPALIVLAKQVEEVSGGAIPAKGLRLTVAIGVGLAIALGVLRILFGIPLHYLLIPGYLLVLILTFFAPKEFVGIAFDSGGVTTGPVTVPFVLALGLGLASAIGGRNPLIDGFGLIALASLGPIIAVLILGLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	211 (210)
Sequences:	8850 (5037)
Seq/√Len:	347.6
META:	0.884

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
126_I	131_L	3.493	1.00
135_G	199_L	3.365	1.00
7_I	11_F	3.247	1.00
69_G	119_V	3.128	1.00
70_F	116_A	3.083	1.00
161_T	198_S	3.002	1.00
130_Y	134_P	2.845	1.00
120_L	124_F	2.828	1.00
66_L	116_A	2.822	1.00
141_I	145_F	2.811	1.00
142_L	207_I	2.631	1.00
139_V	199_L	2.569	1.00
63_W	67_L	2.406	1.00
87_A	103_L	2.393	1.00
101_K	105_L	2.369	1.00
88_K	100_A	2.321	1.00
127_P	130_Y	2.321	1.00
83_L	107_V	2.292	1.00
31_I	35_T	2.249	1.00
202_I	206_L	2.190	1.00
137_L	141_I	2.100	1.00
146_A	206_L	2.074	1.00
131_L	196_L	2.005	1.00
74_F	105_L	1.973	1.00
91_E	100_A	1.969	1.00
8_F	11_F	1.954	1.00
70_F	112_G	1.951	1.00
166_T	197_A	1.900	1.00
102_G	208_L	1.892	1.00
117_L	131_L	1.803	1.00
6_L	10_L	1.791	1.00
2_V	27_L	1.783	1.00
17_I	21_L	1.775	1.00
129_H	133_I	1.775	1.00
69_G	115_I	1.732	1.00
90_V	153_I	1.722	1.00
50_E	54_S	1.694	1.00
99_P	102_G	1.668	1.00
20_L	24_L	1.655	1.00
21_L	25_I	1.644	1.00
159_G	198_S	1.624	1.00
24_L	28_V	1.611	1.00
77_T	198_S	1.608	1.00
132_L	195_A	1.594	1.00
25_I	29_L	1.594	1.00
146_A	210_L	1.594	1.00
106_T	204_A	1.573	1.00
55_Q	58_K	1.535	1.00
134_P	137_L	1.528	1.00
66_L	120_L	1.517	1.00
77_T	161_T	1.489	1.00
119_V	177_L	1.482	1.00
140_L	144_F	1.462	1.00
103_L	205_V	1.441	1.00
122_I	174_G	1.405	1.00
115_I	170_V	1.404	1.00
19_N	22_R	1.389	1.00
185_N	188_I	1.388	1.00
90_V	103_L	1.360	1.00
74_F	112_G	1.356	1.00
143_T	155_F	1.341	1.00
65_L	177_L	1.334	1.00
87_A	100_A	1.320	1.00
128_L	132_L	1.316	1.00
87_A	104_R	1.314	1.00
44_G	47_P	1.303	1.00
3_L	7_I	1.295	1.00
51_L	55_Q	1.291	1.00
140_L	143_T	1.279	1.00
9_Q	16_P	1.270	1.00
102_G	106_T	1.269	1.00
111_V	166_T	1.246	1.00
84_I	100_A	1.245	1.00
168_P	172_A	1.228	1.00
82_A	198_S	1.220	1.00
174_G	193_L	1.205	1.00
138_L	203_I	1.200	1.00
112_G	116_A	1.198	1.00
39_L	43_L	1.171	1.00
91_E	99_P	1.147	1.00
11_F	14_R	1.129	1.00
105_L	109_I	1.126	1.00
161_T	166_T	1.100	1.00
150_F	209_G	1.096	1.00
70_F	74_F	1.093	1.00
54_S	179_S	1.080	1.00
122_I	193_L	1.078	1.00
106_T	208_L	1.074	1.00
35_T	39_L	1.070	1.00
9_Q	20_L	1.068	1.00
22_R	25_I	1.063	1.00
134_P	138_L	1.057	1.00
131_L	135_G	1.050	1.00
160_V	164_P	1.048	1.00
18_P	21_L	1.041	1.00
9_Q	14_R	1.034	1.00
141_I	144_F	1.032	1.00
6_L	20_L	1.029	1.00
116_A	120_L	1.021	1.00
82_A	161_T	1.019	1.00
51_L	54_S	1.007	1.00
182_G	185_N	1.000	1.00
43_L	47_P	1.000	1.00
67_L	71_L	0.995	1.00
62_L	66_L	0.992	1.00
71_L	75_G	0.991	1.00
107_V	157_S	0.991	1.00
164_P	194_I	0.990	1.00
16_P	19_N	0.977	1.00
114_A	200_G	0.976	1.00
59_K	62_L	0.973	1.00
102_G	105_L	0.970	1.00
120_L	131_L	0.969	1.00
128_L	195_A	0.963	1.00
200_G	204_A	0.957	1.00
54_S	180_A	0.957	1.00
66_L	123_L	0.945	1.00
133_I	137_L	0.942	1.00
5_V	23_I	0.941	1.00
125_G	185_N	0.940	1.00
89_Q	92_E	0.928	1.00
139_V	203_I	0.924	1.00
65_L	123_L	0.909	1.00
56_L	68_F	0.906	1.00
86_L	157_S	0.902	1.00
185_N	189_D	0.894	1.00
69_G	116_A	0.894	1.00
198_S	202_I	0.882	1.00
79_A	165_V	0.881	1.00
175_L	178_A	0.876	1.00
136_Y	199_L	0.871	1.00
143_T	206_L	0.870	1.00
115_I	197_A	0.868	1.00
181_I	184_R	0.865	1.00
82_A	159_G	0.864	1.00
119_V	174_G	0.851	1.00
5_V	9_Q	0.847	1.00
159_G	202_I	0.845	1.00
9_Q	13_L	0.844	1.00
61_S	64_L	0.837	1.00
62_L	67_L	0.836	1.00
186_P	189_D	0.833	1.00
50_E	179_S	0.826	1.00
207_I	210_L	0.825	1.00
77_T	108_A	0.823	1.00
143_T	151_V	0.819	1.00
78_I	104_R	0.818	1.00
174_G	201_P	0.817	1.00
146_A	209_G	0.815	1.00
64_L	67_L	0.813	1.00
111_V	196_L	0.810	1.00
120_L	126_I	0.808	1.00
82_A	164_P	0.807	1.00
54_S	58_K	0.804	1.00
77_T	111_V	0.802	1.00
135_G	139_V	0.795	1.00
159_G	167_V	0.794	1.00
24_L	27_L	0.784	1.00
88_K	92_E	0.782	1.00
18_P	22_R	0.772	1.00
84_I	88_K	0.764	1.00
110_G	200_G	0.762	1.00
146_A	150_F	0.758	1.00
111_V	197_A	0.756	1.00
59_K	64_L	0.753	1.00
84_I	104_R	0.748	1.00
82_A	166_T	0.744	1.00
55_Q	59_K	0.741	1.00
166_T	198_S	0.741	1.00
17_I	20_L	0.738	1.00
167_V	175_L	0.737	1.00
110_G	204_A	0.735	0.99
178_A	184_R	0.734	0.99
118_G	193_L	0.724	0.99
76_T	111_V	0.724	0.99
63_W	66_L	0.722	0.99
204_A	207_I	0.722	0.99
70_F	113_L	0.716	0.99
25_I	28_V	0.715	0.99
12_V	16_P	0.713	0.99
76_T	112_G	0.705	0.99
100_A	104_R	0.703	0.99
195_A	200_G	0.702	0.99
159_G	166_T	0.695	0.99
115_I	173_L	0.693	0.99
204_A	208_L	0.691	0.99
183_G	186_P	0.690	0.99
5_V	20_L	0.689	0.99
82_A	160_V	0.686	0.99
23_I	27_L	0.686	0.99
126_I	134_P	0.686	0.99
129_H	132_L	0.683	0.99
45_L	48_L	0.683	0.99
181_I	190_G	0.682	0.99
168_P	174_G	0.682	0.99
63_W	119_V	0.681	0.99
130_Y	133_I	0.681	0.99
57_A	181_I	0.670	0.99
156_D	198_S	0.670	0.99
162_T	202_I	0.670	0.99
62_L	123_L	0.666	0.99
148_K	151_V	0.666	0.99
158_G	201_P	0.665	0.99
57_A	180_A	0.659	0.99
174_G	197_A	0.658	0.99
74_F	108_A	0.656	0.99
3_L	6_L	0.656	0.99
28_V	32_I	0.656	0.99
165_V	168_P	0.653	0.99
41_L	45_L	0.649	0.99
153_I	159_G	0.644	0.99
18_P	28_V	0.641	0.99
114_A	135_G	0.640	0.99
181_I	187_L	0.639	0.99
91_E	94_S	0.636	0.99
1_I	9_Q	0.635	0.99
111_V	198_S	0.634	0.99
53_G	163_G	0.627	0.98
70_F	109_I	0.627	0.98
2_V	8_F	0.626	0.98
139_V	202_I	0.626	0.98
48_L	51_L	0.617	0.98
70_F	77_T	0.615	0.98
178_A	186_P	0.615	0.98
74_F	109_I	0.611	0.98
181_I	189_D	0.610	0.98
74_F	78_I	0.609	0.98
58_K	180_A	0.607	0.98
203_I	206_L	0.606	0.98
8_F	12_V	0.606	0.98
138_L	141_I	0.605	0.98
49_G	136_Y	0.603	0.98
145_F	210_L	0.603	0.98
178_A	194_I	0.601	0.98
32_I	35_T	0.600	0.98
154_A	206_L	0.598	0.98
48_L	57_A	0.597	0.98
117_L	135_G	0.595	0.98
47_P	50_E	0.594	0.98
91_E	98_I	0.593	0.98
42_E	50_E	0.592	0.98
2_V	7_I	0.591	0.98
6_L	24_L	0.585	0.98
156_D	166_T	0.580	0.97
82_A	165_V	0.578	0.97
30_V	34_L	0.575	0.97
178_A	190_G	0.572	0.97
6_L	17_I	0.572	0.97
2_V	24_L	0.571	0.97
51_L	59_K	0.570	0.97
142_L	203_I	0.569	0.97
114_A	132_L	0.568	0.97
97_A	131_L	0.567	0.97
163_G	171_L	0.566	0.97
86_L	160_V	0.566	0.97
21_L	24_L	0.563	0.97
114_A	153_I	0.563	0.97
142_L	210_L	0.563	0.97
9_Q	15_L	0.562	0.97
13_L	16_P	0.559	0.97
77_T	162_T	0.558	0.97
54_S	57_A	0.558	0.97
156_D	159_G	0.557	0.97
184_R	187_L	0.556	0.97
57_A	177_L	0.554	0.97
48_L	104_R	0.553	0.97
126_I	130_Y	0.552	0.96
114_A	196_L	0.552	0.96
125_G	181_I	0.550	0.96
4_I	9_Q	0.549	0.96
5_V	10_L	0.549	0.96
77_T	82_A	0.547	0.96
48_L	168_P	0.546	0.96
17_I	23_I	0.545	0.96
46_F	175_L	0.545	0.96
87_A	107_V	0.545	0.96
181_I	186_P	0.544	0.96
122_I	185_N	0.544	0.96
5_V	15_L	0.543	0.96
119_V	123_L	0.543	0.96
147_P	210_L	0.538	0.96
175_L	179_S	0.537	0.96
158_G	196_L	0.536	0.96
78_I	82_A	0.534	0.96
83_L	161_T	0.534	0.96
198_S	205_V	0.531	0.96
14_R	17_I	0.531	0.96
95_G	136_Y	0.531	0.96
5_V	8_F	0.529	0.96
113_L	200_G	0.528	0.95
18_P	25_I	0.528	0.95
10_L	14_R	0.524	0.95
37_F	41_L	0.523	0.95
7_I	12_V	0.523	0.95
144_F	148_K	0.523	0.95
22_R	29_L	0.522	0.95
38_L	42_E	0.521	0.95
76_T	164_P	0.520	0.95
180_A	183_G	0.518	0.95
60_G	64_L	0.515	0.95
202_I	205_V	0.514	0.95
168_P	173_L	0.513	0.95
125_G	189_D	0.513	0.95
83_L	177_L	0.513	0.95
15_L	20_L	0.513	0.95
129_H	188_I	0.511	0.95
155_F	170_V	0.511	0.95
111_V	155_F	0.510	0.95
15_L	19_N	0.509	0.95
162_T	174_G	0.508	0.94
56_L	119_V	0.503	0.94
187_L	190_G	0.503	0.94
139_V	206_L	0.502	0.94
173_L	194_I	0.501	0.94
84_I	164_P	0.500	0.94

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
2a65A	2	0.7962	4.7	0.962	Contact Map
4xp4A	1	0.8389	3.8	0.964	Contact Map
2gfpA	2	0.6114	2.8	0.966	Contact Map
2cfqA	1	0.6967	2.2	0.968	Contact Map
4us3A	1	0.6588	1.9	0.969	Contact Map
3o7qA	1	0.872	1.7	0.97	Contact Map
4n7wA	2	0.3886	1.6	0.97	Contact Map
4f35D	2	0.7062	1.6	0.97	Contact Map
1pw4A	1	0.891	1.5	0.971	Contact Map
2kluA	1	0.1232	1.3	0.972	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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