PepSY_TM - PFAM28P - GREMLIN Contacts

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PepSY_TM - PepSY-associated TM region

PFAM:	PF03929	Sequences: FRLHLWLGLVLGLFLLLLALTGALLVFRPEIDAWLNALLYPDQLFVDPYTGEVLGFRFLYRLHRSDTGRLIVGLAALLLLVLLLSGLVLWKGRRFWRDLHNVLGFWALPFLLVLALTGLYWSFPWYFGAAADRLEPPPPDPTPYDPADLPAGDRLLRWLYPLHTGDFGGLPGRILWFLLGLAGALLSVTGLLLWWRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	197 (175)
Sequences:	13779 (9394)
Seq/√Len:	710.1
META:	0.621

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_A	183_G	2.585	1.00
27_F	177_F	2.520	1.00
23_A	177_F	2.504	1.00
170_L	174_I	2.407	1.00
16_L	184_A	2.341	1.00
30_E	173_R	2.249	1.00
18_L	72_V	2.236	1.00
47_D	50_T	2.196	1.00
130_A	143_P	2.188	1.00
17_L	62_L	2.151	1.00
151_A	155_L	2.140	1.00
67_T	70_L	2.136	1.00
80_L	115_A	2.036	1.00
70_L	74_L	2.034	1.00
191_L	195_W	1.989	1.00
192_L	196_R	1.952	1.00
107_A	182_A	1.947	1.00
61_R	65_S	1.934	1.00
47_D	52_E	1.902	1.00
23_A	180_G	1.891	1.00
60_Y	64_R	1.849	1.00
114_L	176_W	1.831	1.00
160_Y	164_T	1.824	1.00
27_F	170_L	1.802	1.00
145_D	148_D	1.800	1.00
37_A	46_V	1.799	1.00
23_A	184_A	1.773	1.00
170_L	173_R	1.645	1.00
94_R	98_D	1.644	1.00
168_G	172_G	1.643	1.00
12_G	187_S	1.639	1.00
47_D	54_L	1.633	1.00
188_V	192_L	1.613	1.00
76_A	119_L	1.611	1.00
27_F	174_I	1.589	1.00
83_L	112_L	1.554	1.00
103_L	182_A	1.522	1.00
83_L	115_A	1.518	1.00
80_L	112_L	1.507	1.00
79_L	115_A	1.505	1.00
20_L	184_A	1.502	1.00
162_L	167_F	1.497	1.00
12_G	191_L	1.457	1.00
24_L	59_L	1.453	1.00
58_F	62_L	1.438	1.00
110_F	179_L	1.436	1.00
14_F	75_A	1.410	1.00
83_L	108_L	1.391	1.00
96_W	192_L	1.383	1.00
185_L	189_T	1.370	1.00
150_P	153_D	1.359	1.00
67_T	71_I	1.358	1.00
27_F	30_E	1.352	1.00
103_L	107_A	1.345	1.00
74_L	77_L	1.329	1.00
107_A	111_L	1.312	1.00
153_D	157_R	1.292	1.00
111_L	183_G	1.276	1.00
73_G	123_F	1.275	1.00
74_L	78_L	1.271	1.00
113_V	162_L	1.269	1.00
60_Y	63_H	1.265	1.00
77_L	119_L	1.252	1.00
171_P	174_I	1.246	1.00
87_L	108_L	1.227	1.00
109_P	113_V	1.224	1.00
99_L	185_L	1.209	1.00
97_R	101_N	1.208	1.00
82_L	85_S	1.193	1.00
74_L	123_F	1.176	1.00
102_V	106_W	1.174	1.00
172_G	176_W	1.169	1.00
126_Y	129_A	1.158	1.00
33_A	36_N	1.153	1.00
105_F	108_L	1.139	1.00
93_R	96_W	1.131	1.00
73_G	122_S	1.127	1.00
32_D	36_N	1.103	1.00
59_L	62_L	1.102	1.00
93_R	196_R	1.101	1.00
28_R	32_D	1.097	1.00
56_F	59_L	1.096	1.00
167_F	176_W	1.092	1.00
184_A	187_S	1.078	1.00
103_L	185_L	1.073	1.00
90_W	105_F	1.070	1.00
64_R	69_R	1.067	1.00
192_L	195_W	1.061	1.00
28_R	60_Y	1.060	1.00
15_L	79_L	1.057	1.00
92_G	95_F	1.056	1.00
149_L	154_R	1.053	1.00
93_R	97_R	1.053	1.00
2_R	5_L	1.047	1.00
149_L	157_R	1.023	1.00
58_F	61_R	1.019	1.00
7_L	78_L	1.019	1.00
66_D	70_L	1.001	1.00
114_L	179_L	0.999	1.00
120_Y	159_L	0.998	1.00
70_L	123_F	0.997	1.00
58_F	63_H	0.984	1.00
16_L	187_S	0.979	1.00
84_L	88_V	0.973	1.00
96_W	196_R	0.973	1.00
68_G	72_V	0.964	1.00
183_G	187_S	0.964	1.00
117_T	159_L	0.961	1.00
149_L	153_D	0.960	1.00
94_R	97_R	0.946	1.00
123_F	126_Y	0.938	1.00
105_F	109_P	0.935	1.00
72_V	76_A	0.934	1.00
99_L	103_L	0.930	1.00
157_R	161_P	0.925	1.00
172_G	175_L	0.905	1.00
11_L	75_A	0.905	1.00
110_F	114_L	0.900	1.00
181_L	185_L	0.896	1.00
107_A	110_F	0.895	1.00
57_R	61_R	0.883	1.00
80_L	116_L	0.881	1.00
20_L	24_L	0.878	1.00
25_L	60_Y	0.876	1.00
23_A	26_V	0.875	1.00
95_F	99_L	0.872	1.00
61_R	64_R	0.866	1.00
19_A	184_A	0.865	1.00
72_V	118_G	0.865	1.00
17_L	21_T	0.858	1.00
25_L	28_R	0.844	1.00
98_D	102_V	0.828	1.00
146_P	154_R	0.822	1.00
59_L	64_R	0.817	1.00
18_L	75_A	0.815	1.00
155_L	159_L	0.813	1.00
26_V	177_F	0.813	1.00
124_P	127_F	0.807	1.00
81_V	85_S	0.803	1.00
167_F	172_G	0.802	1.00
168_G	171_P	0.796	1.00
174_I	178_L	0.795	1.00
59_L	63_H	0.793	1.00
155_L	158_W	0.791	1.00
56_F	60_Y	0.785	1.00
174_I	177_F	0.782	1.00
108_L	111_L	0.777	1.00
164_T	168_G	0.775	1.00
21_T	62_L	0.774	1.00
84_L	112_L	0.770	1.00
125_W	129_A	0.769	1.00
120_Y	156_L	0.769	1.00
87_L	105_F	0.769	1.00
7_L	10_V	0.767	1.00
91_K	94_R	0.766	1.00
153_D	156_L	0.761	1.00
15_L	19_A	0.760	1.00
47_D	51_G	0.760	1.00
144_Y	149_L	0.754	1.00
29_P	32_D	0.751	1.00
171_P	175_L	0.750	1.00
79_L	183_G	0.749	1.00
10_V	14_F	0.749	1.00
14_F	18_L	0.747	1.00
69_R	122_S	0.737	1.00
184_A	192_L	0.734	1.00
124_P	128_G	0.731	1.00
169_G	172_G	0.729	1.00
26_V	176_W	0.729	1.00
50_T	53_V	0.720	1.00
90_W	101_N	0.718	1.00
8_G	176_W	0.717	1.00
23_A	181_L	0.716	1.00
152_G	156_L	0.714	1.00
177_F	180_G	0.708	1.00
49_Y	53_V	0.707	1.00
158_W	167_F	0.703	1.00
75_A	79_L	0.699	1.00
26_V	172_G	0.696	1.00
11_L	78_L	0.690	1.00
48_P	51_G	0.679	1.00
144_Y	147_A	0.679	1.00
154_R	158_W	0.679	1.00
151_A	154_R	0.678	1.00
66_D	69_R	0.672	1.00
79_L	83_L	0.671	1.00
98_D	101_N	0.667	1.00
116_L	120_Y	0.664	1.00
16_L	20_L	0.659	1.00
79_L	111_L	0.658	1.00
11_L	15_L	0.658	1.00
165_G	168_G	0.655	1.00
158_W	161_P	0.652	1.00
73_G	77_L	0.640	1.00
85_S	88_V	0.637	1.00
123_F	128_G	0.637	1.00
125_W	128_G	0.634	1.00
123_F	129_A	0.632	1.00
148_D	151_A	0.626	1.00
193_L	196_R	0.621	1.00
51_G	54_L	0.617	1.00
120_Y	127_F	0.617	1.00
7_L	82_L	0.615	1.00
30_E	170_L	0.612	1.00
19_A	180_G	0.612	1.00
57_R	60_Y	0.611	1.00
14_F	72_V	0.611	1.00
19_A	23_A	0.611	1.00
92_G	96_W	0.604	1.00
65_S	69_R	0.604	1.00
68_G	76_A	0.601	1.00
186_L	189_T	0.600	1.00
19_A	187_S	0.596	1.00
71_I	75_A	0.593	1.00
108_L	112_L	0.591	1.00
180_G	184_A	0.588	1.00
83_L	89_L	0.588	1.00
72_V	75_A	0.585	1.00
182_A	185_L	0.584	1.00
96_W	189_T	0.583	1.00
164_T	176_W	0.582	1.00
52_E	55_G	0.580	1.00
152_G	155_L	0.575	1.00
111_L	186_L	0.573	1.00
73_G	119_L	0.573	1.00
33_A	46_V	0.566	1.00
26_V	165_G	0.560	1.00
15_L	115_A	0.559	1.00
59_L	65_S	0.557	1.00
179_L	183_G	0.556	1.00
80_L	83_L	0.553	1.00
68_G	73_G	0.553	1.00
26_V	173_R	0.550	1.00
156_L	160_Y	0.545	1.00
187_S	191_L	0.543	1.00
72_V	122_S	0.542	1.00
16_L	19_A	0.541	1.00
49_Y	55_G	0.538	1.00
25_L	121_W	0.535	1.00
156_L	161_P	0.535	1.00
13_L	17_L	0.531	1.00
68_G	71_I	0.531	1.00
161_P	166_D	0.530	1.00
160_Y	166_D	0.528	1.00
91_K	97_R	0.528	1.00
99_L	189_T	0.526	1.00
127_F	156_L	0.521	1.00
68_G	90_W	0.517	1.00
10_V	13_L	0.517	1.00
121_W	160_Y	0.516	1.00
128_G	153_D	0.514	1.00
93_R	197_R	0.511	1.00
188_V	194_W	0.510	0.99
107_A	179_L	0.510	0.99
12_G	190_G	0.510	0.99
175_L	179_L	0.509	0.99
182_A	186_L	0.505	0.99
119_L	123_F	0.505	0.99
56_F	61_R	0.504	0.99
6_W	10_V	0.501	0.99
121_W	127_F	0.500	0.99
189_T	193_L	0.500	0.99

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
4gd3A	2	0.4924	78.5	0.896	Contact Map
4o6yA	2	0.5025	70.6	0.903	Contact Map
1kqfC	3	0.6091	68.5	0.904	Contact Map
2qjyA	2	0.8782	40.9	0.919	Contact Map
1pp9C	2	0.8426	37.9	0.92	Contact Map
3cx5C	2	0.8528	32.8	0.923	Contact Map
4ogqA	2	0.8731	15.9	0.933	Contact Map
2wdqC	1	0.4061	11.4	0.938	Contact Map
2m20A	2	0.1472	5.6	0.946	Contact Map
2l9uA	2	0.1574	4.4	0.949	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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