PepSY_TM_like_2 - PFAM28P - GREMLIN Contacts

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PepSY_TM_like_2 - Putative PepSY_TM-like

PFAM:	PF16357	Sequences: FWLRQLHIWHWISSALFLLGLLLFAVTGITLNHAAWINPNPRVTEREGTLPAPLLAALAADAEADKLALPEALAEWLREEGGIDGAGRDAEWSDDELYVSFPGPGGDAWVTIDRATGEVEVERTDRGWIAYLNDLHKGRNTGKAWSWFIDIFAVALILLSLTGLFLLKGLKGRRRRGWPLVGLGLLIPLLLALLFVH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	197 (189)
Sequences:	4415 (3523)
Seq/√Len:	256.3
META:	0.836

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
113_D	116_T	5.137	1.00
103_G	106_G	3.265	1.00
29_I	154_V	2.660	1.00
11_W	14_S	2.561	1.00
4_R	7_H	2.419	1.00
110_V	121_V	2.399	1.00
76_W	79_E	2.383	1.00
73_L	77_L	2.100	1.00
29_I	153_A	2.094	1.00
69_L	73_L	2.093	1.00
5_Q	8_I	2.075	1.00
65_D	68_A	2.026	1.00
21_L	160_S	1.983	1.00
128_W	131_Y	1.967	1.00
8_I	11_W	1.960	1.00
33_H	150_D	1.937	1.00
163_G	166_L	1.919	1.00
14_S	17_F	1.911	1.00
128_W	132_L	1.909	1.00
7_H	14_S	1.883	1.00
158_L	162_T	1.870	1.00
71_E	74_A	1.848	1.00
96_E	111_T	1.837	1.00
127_G	131_Y	1.804	1.00
7_H	11_W	1.802	1.00
32_N	150_D	1.793	1.00
70_P	74_A	1.777	1.00
83_I	86_A	1.770	1.00
144_A	147_W	1.681	1.00
25_A	157_I	1.675	1.00
189_L	193_L	1.664	1.00
47_E	118_E	1.641	1.00
49_T	118_E	1.639	1.00
21_L	25_A	1.629	1.00
147_W	151_I	1.625	1.00
131_Y	192_A	1.596	1.00
31_L	137_K	1.586	1.00
86_A	89_D	1.585	1.00
169_G	172_G	1.574	1.00
87_G	90_A	1.562	1.00
175_R	178_W	1.558	1.00
82_G	85_G	1.527	1.00
79_E	82_G	1.466	1.00
72_A	76_W	1.440	1.00
62_A	65_D	1.421	1.00
11_W	15_A	1.410	1.00
169_G	173_R	1.406	1.00
70_P	76_W	1.399	1.00
143_K	146_S	1.355	1.00
33_H	36_W	1.340	1.00
78_R	81_G	1.333	1.00
111_T	120_E	1.323	1.00
76_W	81_G	1.321	1.00
8_I	12_I	1.317	1.00
70_P	73_L	1.314	1.00
30_T	133_N	1.313	1.00
178_W	182_G	1.305	1.00
22_L	157_I	1.300	1.00
71_E	75_E	1.286	1.00
72_A	75_E	1.283	1.00
74_A	81_G	1.281	1.00
52_A	55_L	1.272	1.00
47_E	120_E	1.270	1.00
77_L	81_G	1.268	1.00
26_V	157_I	1.263	1.00
29_I	33_H	1.245	1.00
168_K	172_G	1.227	1.00
76_W	80_E	1.219	1.00
178_W	181_V	1.213	1.00
127_G	130_A	1.167	1.00
57_A	61_D	1.166	1.00
21_L	156_L	1.165	1.00
3_L	7_H	1.155	1.00
95_D	115_A	1.155	1.00
64_A	67_L	1.153	1.00
139_R	142_G	1.148	1.00
74_A	78_R	1.147	1.00
133_N	139_R	1.144	1.00
173_R	181_V	1.134	1.00
143_K	147_W	1.132	1.00
61_D	64_A	1.114	1.00
60_A	64_A	1.112	1.00
24_F	145_W	1.105	1.00
179_P	183_L	1.096	1.00
48_G	119_V	1.093	1.00
61_D	65_D	1.091	1.00
74_A	85_G	1.087	1.00
17_F	21_L	1.086	1.00
164_L	181_V	1.082	1.00
95_D	114_R	1.076	1.00
13_S	19_L	1.071	1.00
7_H	12_I	1.070	1.00
165_F	168_K	1.063	1.00
138_G	149_I	1.055	1.00
69_L	77_L	1.047	1.00
170_L	173_R	1.042	1.00
99_V	102_P	1.035	1.00
59_A	63_E	1.024	1.00
67_L	71_E	1.017	1.00
70_P	79_E	1.016	1.00
174_R	178_W	0.999	1.00
45_E	120_E	0.995	1.00
29_I	157_I	0.975	1.00
64_A	68_A	0.971	1.00
151_I	154_V	0.969	1.00
77_L	80_E	0.959	1.00
93_S	96_E	0.958	1.00
138_G	141_T	0.946	1.00
75_E	79_E	0.946	1.00
40_N	43_V	0.944	1.00
60_A	63_E	0.944	1.00
15_A	18_L	0.933	1.00
100_S	109_W	0.927	1.00
79_E	84_D	0.916	1.00
74_A	77_L	0.905	1.00
189_L	192_A	0.898	1.00
81_G	85_G	0.896	1.00
161_L	165_F	0.889	1.00
141_T	146_S	0.886	1.00
165_F	169_G	0.884	1.00
78_R	85_G	0.884	1.00
3_L	8_I	0.883	1.00
81_G	119_V	0.883	1.00
73_L	76_W	0.883	1.00
30_T	37_I	0.876	1.00
31_L	138_G	0.871	1.00
84_D	87_G	0.868	1.00
11_W	17_F	0.866	1.00
28_G	153_A	0.865	1.00
3_L	165_F	0.864	1.00
79_E	85_G	0.862	1.00
7_H	13_S	0.858	0.99
15_A	19_L	0.853	0.99
74_A	79_E	0.851	0.99
90_A	97_L	0.849	0.99
56_A	59_A	0.848	0.99
21_L	152_F	0.847	0.99
80_E	83_I	0.845	0.99
27_T	133_N	0.843	0.99
176_R	180_L	0.838	0.99
6_L	158_L	0.832	0.99
100_S	103_G	0.830	0.99
80_E	84_D	0.825	0.99
111_T	122_E	0.823	0.99
4_R	8_I	0.819	0.99
190_L	193_L	0.812	0.99
112_I	119_V	0.807	0.99
91_E	94_D	0.806	0.99
12_I	15_A	0.805	0.99
50_L	54_L	0.805	0.99
190_L	194_L	0.803	0.99
86_A	90_A	0.796	0.99
14_S	19_L	0.795	0.99
75_E	80_E	0.794	0.99
22_L	26_V	0.794	0.99
171_K	176_R	0.793	0.99
125_D	128_W	0.791	0.99
61_D	66_K	0.783	0.99
44_T	123_R	0.782	0.99
78_R	82_G	0.779	0.99
70_P	78_R	0.778	0.99
109_W	122_E	0.778	0.99
50_L	53_P	0.777	0.99
11_W	18_L	0.777	0.99
72_A	77_L	0.777	0.99
30_T	139_R	0.776	0.99
63_E	66_K	0.769	0.99
81_G	87_G	0.766	0.99
186_L	190_L	0.764	0.99
176_R	179_P	0.763	0.99
95_D	113_D	0.762	0.99
33_H	145_W	0.762	0.99
14_S	18_L	0.762	0.99
85_G	89_D	0.757	0.99
110_V	119_V	0.756	0.99
69_L	72_A	0.756	0.99
55_L	59_A	0.751	0.99
75_E	78_R	0.750	0.99
13_S	18_L	0.746	0.99
130_A	134_D	0.746	0.99
134_D	139_R	0.739	0.98
145_W	150_D	0.735	0.98
24_F	137_K	0.735	0.98
70_P	77_L	0.734	0.98
74_A	86_A	0.730	0.98
172_G	175_R	0.730	0.98
98_Y	102_P	0.728	0.98
126_R	130_A	0.725	0.98
111_T	115_A	0.721	0.98
108_A	111_T	0.720	0.98
8_I	14_S	0.712	0.98
81_G	86_A	0.708	0.98
181_V	185_L	0.708	0.98
72_A	81_G	0.707	0.98
64_A	69_L	0.704	0.98
164_L	184_G	0.702	0.98
174_R	181_V	0.692	0.98
167_L	181_V	0.692	0.98
16_L	21_L	0.690	0.98
57_A	64_A	0.685	0.98
134_D	137_K	0.684	0.98
133_N	137_K	0.684	0.98
164_L	167_L	0.677	0.97
171_K	180_L	0.668	0.97
32_N	149_I	0.664	0.97
42_R	47_E	0.661	0.97
116_T	119_V	0.658	0.97
102_P	107_D	0.658	0.97
12_I	16_L	0.651	0.97
82_G	86_A	0.647	0.97
167_L	177_G	0.646	0.96
66_K	70_P	0.645	0.96
26_V	132_L	0.639	0.96
25_A	152_F	0.638	0.96
150_D	153_A	0.635	0.96
25_A	153_A	0.634	0.96
18_L	185_L	0.629	0.96
188_P	191_L	0.629	0.96
48_G	51_P	0.629	0.96
25_A	156_L	0.626	0.96
62_A	67_L	0.623	0.96
185_L	189_L	0.619	0.96
45_E	122_E	0.616	0.95
90_A	93_S	0.615	0.95
67_L	70_P	0.614	0.95
62_A	66_K	0.612	0.95
27_T	141_T	0.611	0.95
77_L	85_G	0.610	0.95
130_A	137_K	0.609	0.95
13_S	159_L	0.607	0.95
171_K	174_R	0.606	0.95
7_H	170_L	0.605	0.95
141_T	152_F	0.603	0.95
172_G	176_R	0.603	0.95
147_W	154_V	0.602	0.95
77_L	119_V	0.602	0.95
24_F	149_I	0.601	0.95
13_S	17_F	0.600	0.95
113_D	118_E	0.598	0.95
28_G	31_L	0.596	0.95
21_L	159_L	0.593	0.94
101_F	104_P	0.593	0.94
49_T	52_A	0.586	0.94
67_L	75_E	0.586	0.94
18_L	21_L	0.585	0.94
59_A	62_A	0.582	0.94
51_P	76_W	0.576	0.94
166_L	170_L	0.569	0.93
8_I	13_S	0.568	0.93
157_I	161_L	0.565	0.93
171_K	178_W	0.564	0.93
74_A	83_I	0.564	0.93
58_L	61_D	0.561	0.93
58_L	63_E	0.561	0.93
72_A	79_E	0.559	0.92
77_L	83_I	0.555	0.92
134_D	142_G	0.555	0.92
57_A	62_A	0.543	0.91
88_R	94_D	0.541	0.91
104_P	107_D	0.540	0.91
69_L	76_W	0.539	0.91
6_L	12_I	0.538	0.91
61_D	68_A	0.536	0.91
102_P	105_G	0.535	0.91
173_R	178_W	0.534	0.91
57_A	63_E	0.534	0.91
31_L	134_D	0.532	0.91
175_R	179_P	0.532	0.91
136_H	163_G	0.531	0.90
173_R	176_R	0.528	0.90
83_I	87_G	0.527	0.90
13_S	16_L	0.526	0.90
154_V	158_L	0.526	0.90
59_A	67_L	0.521	0.90
22_L	161_L	0.519	0.89
111_T	166_L	0.518	0.89
30_T	129_I	0.514	0.89
103_G	108_A	0.509	0.89
102_P	139_R	0.509	0.89
35_A	38_N	0.506	0.88
69_L	85_G	0.504	0.88
168_K	173_R	0.504	0.88
64_A	72_A	0.501	0.88
78_R	83_I	0.500	0.88

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
4or2A	2	0.7665	34.9	0.923	Contact Map
2l2tA	2	0.2132	8.8	0.942	Contact Map
4wd8A	3	0.269	7.8	0.943	Contact Map
4ea3A	2	0.7107	7.2	0.944	Contact Map
2kgyA	1	0.4518	5	0.948	Contact Map
3c02A	3	0.2741	4.3	0.95	Contact Map
1kqfC	3	0.3299	3.8	0.951	Contact Map
2mpnA	2	0.3198	3.8	0.951	Contact Map
2gsmB	1	0.401	3.7	0.951	Contact Map
2jwaA	2	0.2234	2.8	0.954	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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