YDIL - BACSU - GREMLIN Contacts

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YDIL - Putative membrane peptidase YdiL

UniProt:	O05525	Sequences: MRKQYWFIILTYIIMQFSALIAIPLLFKFGYAGGQPTDENMLHAQGLWSVISFIACLVVVLLILRTVPKETLRNGQKDSIGLSILWAIAGFFIALFSQGIAGSIEYYVFGIGRESENTQAILDVIQAVPLMIIVSSIVGPILEEIIFRKIIFGALYEKTNFFFAGLISSVIFGIVHADLKHLLLYTAMGFTFAFLYARTKRIWVPIFAHLMMNTFVVIMQLEPVRNYLEQQSTQMQLIIGGLFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	244 (207)
Sequences:	3888 (3469)
Seq/√Len:	241.1

BACSU - YDIL YYAK YPBD
HALSA - Q9HS87 Q9HMZ0 Q9HNQ5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
165_G	193_A	4.287	1.00
173_G	186_T	4.112	1.00
136_S	214_T	3.962	1.00
152_F	197_A	3.737	1.00
201_R	204_V	3.149	1.00
147_F	175_V	3.070	1.00
195_L	208_A	2.991	1.00
212_M	216_V	2.944	1.00
173_G	185_Y	2.860	1.00
170_V	186_T	2.829	1.00
139_G	210_L	2.807	1.00
156_Y	197_A	2.788	1.00
152_F	193_A	2.742	1.00
161_F	197_A	2.732	1.00
140_P	210_L	2.681	1.00
194_F	198_R	2.651	1.00
196_Y	205_P	2.638	1.00
169_S	190_F	2.486	1.00
178_D	181_H	2.303	1.00
173_G	189_G	2.218	1.00
152_F	168_S	2.215	1.00
181_H	185_Y	1.948	1.00
161_F	165_G	1.946	1.00
203_W	206_I	1.933	1.00
141_I	206_I	1.903	1.00
169_S	193_A	1.886	1.00
165_G	197_A	1.842	1.00
196_Y	199_T	1.833	1.00
169_S	186_T	1.818	1.00
168_S	193_A	1.752	1.00
153_G	156_Y	1.748	1.00
165_G	190_F	1.730	1.00
189_G	193_A	1.730	1.00
160_N	163_F	1.696	1.00
12_Y	15_M	1.641	1.00
195_L	204_V	1.632	1.00
87_A	91_F	1.600	1.00
149_K	202_I	1.551	1.00
152_F	165_G	1.544	1.00
136_S	139_G	1.526	1.00
152_F	156_Y	1.526	1.00
188_M	192_F	1.512	1.00
16_Q	19_A	1.465	1.00
15_M	19_A	1.442	1.00
169_S	173_G	1.398	1.00
164_A	168_S	1.392	1.00
162_F	166_L	1.371	1.00
140_P	213_N	1.370	1.00
159_T	163_F	1.368	1.00
82_L	85_L	1.365	1.00
149_K	153_G	1.360	1.00
136_S	217_V	1.353	1.00
19_A	22_A	1.331	1.00
166_L	190_F	1.327	1.00
192_F	205_P	1.325	1.00
193_A	197_A	1.324	1.00
66_T	69_K	1.321	1.00
168_S	196_Y	1.289	1.00
168_S	189_G	1.270	1.00
61_L	65_R	1.262	1.00
196_Y	201_R	1.261	1.00
20_L	24_P	1.251	1.00
16_Q	20_L	1.245	1.00
201_R	205_P	1.228	1.00
58_V	62_L	1.216	1.00
202_I	206_I	1.207	1.00
212_M	215_F	1.203	1.00
152_F	196_Y	1.202	1.00
132_I	217_V	1.201	1.00
12_Y	19_A	1.189	1.00
159_T	164_A	1.189	1.00
169_S	189_G	1.185	1.00
165_G	194_F	1.144	1.00
120_A	123_D	1.141	1.00
84_I	88_I	1.140	1.00
210_L	214_T	1.124	1.00
156_Y	161_F	1.122	1.00
163_F	167_I	1.118	1.00
182_L	186_T	1.112	1.00
151_I	168_S	1.103	1.00
192_F	208_A	1.101	1.00
139_G	206_I	1.099	1.00
186_T	190_F	1.095	1.00
156_Y	164_A	1.092	1.00
64_L	68_P	1.090	1.00
152_F	164_A	1.089	1.00
149_K	201_R	1.088	1.00
195_L	205_P	1.087	1.00
135_S	139_G	1.082	1.00
160_N	164_A	1.079	1.00
100_I	104_I	1.071	1.00
204_V	207_F	1.069	1.00
153_G	196_Y	1.053	1.00
79_S	82_L	1.017	1.00
141_I	210_L	1.005	1.00
86_W	90_G	0.992	1.00
182_L	185_Y	0.991	1.00
202_I	205_P	0.982	1.00
190_F	193_A	0.979	1.00
119_Q	123_D	0.972	1.00
80_I	83_S	0.967	1.00
206_I	210_L	0.953	1.00
131_M	135_S	0.953	1.00
92_F	96_F	0.943	1.00
85_L	89_A	0.939	1.00
102_G	106_Y	0.938	1.00
81_G	85_L	0.938	1.00
155_L	159_T	0.937	1.00
137_I	141_I	0.933	1.00
151_I	171_I	0.932	1.00
91_F	211_M	0.932	1.00
12_Y	16_Q	0.930	1.00
24_P	28_K	0.919	1.00
101_A	105_E	0.913	1.00
108_V	111_I	0.911	1.00
132_I	136_S	0.906	1.00
185_Y	189_G	0.896	1.00
13_I	16_Q	0.892	1.00
66_T	70_E	0.889	1.00
78_D	82_L	0.888	1.00
200_K	205_P	0.887	1.00
20_L	27_F	0.881	0.99
91_F	94_A	0.878	0.99
178_D	185_Y	0.875	0.99
38_D	41_M	0.868	0.99
19_A	23_I	0.867	0.99
154_A	157_E	0.866	0.99
39_E	48_W	0.864	0.99
145_I	206_I	0.859	0.99
147_F	172_F	0.853	0.99
128_V	131_M	0.851	0.99
136_S	140_P	0.840	0.99
94_A	98_Q	0.839	0.99
183_L	187_A	0.834	0.99
53_F	57_L	0.832	0.99
135_S	217_V	0.832	0.99
178_D	182_L	0.828	0.99
117_N	121_I	0.821	0.99
83_S	86_W	0.815	0.99
207_F	211_M	0.814	0.99
180_K	183_L	0.811	0.99
176_H	209_H	0.811	0.99
118_T	122_L	0.810	0.99
41_M	44_A	0.807	0.99
181_H	184_L	0.805	0.99
173_G	181_H	0.802	0.99
207_F	210_L	0.799	0.99
46_G	49_S	0.799	0.99
155_L	167_I	0.796	0.99
173_G	182_L	0.795	0.99
139_G	142_L	0.793	0.99
82_L	86_W	0.792	0.99
172_F	176_H	0.790	0.99
184_L	212_M	0.781	0.99
90_G	191_T	0.780	0.99
199_T	204_V	0.779	0.99
45_Q	49_S	0.772	0.99
79_S	83_S	0.771	0.99
25_L	29_F	0.771	0.99
14_I	19_A	0.771	0.99
180_K	184_L	0.769	0.99
185_Y	188_M	0.763	0.99
76_Q	80_I	0.762	0.98
116_E	119_Q	0.757	0.98
54_I	57_L	0.757	0.98
89_A	93_I	0.756	0.98
150_I	154_A	0.751	0.98
60_V	64_L	0.749	0.98
95_L	98_Q	0.744	0.98
177_A	182_L	0.742	0.98
154_A	179_L	0.738	0.98
117_N	185_Y	0.737	0.98
95_L	99_G	0.734	0.98
117_N	120_A	0.728	0.98
156_Y	200_K	0.724	0.98
130_L	134_V	0.723	0.98
32_A	36_P	0.719	0.98
52_S	56_C	0.719	0.98
149_K	156_Y	0.718	0.98
136_S	210_L	0.717	0.98
129_P	133_I	0.713	0.98
162_F	190_F	0.711	0.98
62_L	66_T	0.709	0.98
54_I	58_V	0.708	0.98
89_A	96_F	0.703	0.97
125_I	129_P	0.700	0.97
190_F	194_F	0.699	0.97
22_A	26_L	0.695	0.97
99_G	103_S	0.694	0.97
156_Y	160_N	0.693	0.97
184_L	187_A	0.691	0.97
192_F	195_L	0.691	0.97
60_V	63_I	0.686	0.97
45_Q	48_W	0.685	0.97
161_F	164_A	0.680	0.97
88_I	92_F	0.678	0.97
15_M	18_S	0.677	0.97
164_A	185_Y	0.677	0.97
211_M	214_T	0.676	0.97
194_F	204_V	0.674	0.97
78_D	83_S	0.671	0.97
196_Y	200_K	0.670	0.97
14_I	17_F	0.669	0.97
137_I	140_P	0.669	0.97
115_S	118_T	0.654	0.96
61_L	64_L	0.652	0.96
14_I	18_S	0.651	0.96
76_Q	84_I	0.650	0.96
24_P	27_F	0.649	0.96
74_N	77_K	0.649	0.96
196_Y	204_V	0.648	0.96
18_S	22_A	0.644	0.96
49_S	52_S	0.643	0.96
42_L	45_Q	0.642	0.96
17_F	20_L	0.640	0.96
93_I	96_F	0.637	0.95
165_G	169_S	0.636	0.95
94_A	104_I	0.635	0.95
205_P	213_N	0.633	0.95
49_S	53_F	0.633	0.95
162_F	194_F	0.631	0.95
140_P	206_I	0.627	0.95
93_I	106_Y	0.623	0.95
87_A	208_A	0.618	0.95
14_I	30_G	0.607	0.94
92_F	103_S	0.606	0.94
152_F	161_F	0.604	0.94
67_V	70_E	0.601	0.94
17_F	41_M	0.598	0.94
44_A	47_L	0.596	0.94
172_F	209_H	0.596	0.94
103_S	106_Y	0.596	0.94
143_E	176_H	0.593	0.93
97_S	187_A	0.592	0.93
48_W	55_A	0.591	0.93
67_V	71_T	0.591	0.93
188_M	212_M	0.590	0.93
214_T	218_I	0.589	0.93
39_E	42_L	0.588	0.93
162_F	165_G	0.587	0.93
81_G	218_I	0.584	0.93
12_Y	24_P	0.584	0.93
57_L	60_V	0.583	0.93
28_K	191_T	0.583	0.93
53_F	61_L	0.581	0.93
142_L	145_I	0.580	0.93
140_P	221_L	0.573	0.92
29_F	39_E	0.571	0.92
155_L	201_R	0.570	0.92
93_I	97_S	0.568	0.92
168_S	182_L	0.566	0.92
57_L	61_L	0.565	0.92
45_Q	50_V	0.563	0.92
65_R	69_K	0.563	0.92
18_S	33_G	0.562	0.91
62_L	65_R	0.559	0.91
154_A	164_A	0.558	0.91
174_I	177_A	0.557	0.91
84_I	87_A	0.551	0.91
27_F	32_A	0.550	0.91
138_V	213_N	0.548	0.90
13_I	70_E	0.548	0.90
20_L	30_G	0.547	0.90
164_A	203_W	0.544	0.90
101_A	104_I	0.544	0.90
23_I	27_F	0.543	0.90
217_V	221_L	0.542	0.90
17_F	27_F	0.541	0.90
184_L	216_V	0.540	0.90
68_P	71_T	0.540	0.90
115_S	122_L	0.536	0.89
133_I	137_I	0.536	0.89
90_G	195_L	0.535	0.89
136_S	216_V	0.535	0.89
137_I	210_L	0.534	0.89
83_S	87_A	0.533	0.89
143_E	209_H	0.532	0.89
150_I	161_F	0.532	0.89
183_L	186_T	0.531	0.89
96_F	103_S	0.531	0.89
43_H	47_L	0.530	0.89
197_A	212_M	0.527	0.89
42_L	47_L	0.525	0.89
14_I	26_L	0.524	0.88
46_G	62_L	0.523	0.88
28_K	32_A	0.522	0.88
185_Y	196_Y	0.522	0.88
197_A	201_R	0.520	0.88
146_I	150_I	0.519	0.88
50_V	54_I	0.518	0.88
82_L	89_A	0.518	0.88
55_A	58_V	0.517	0.88
162_F	169_S	0.517	0.88
175_V	180_K	0.516	0.88
65_R	70_E	0.514	0.87
14_I	31_Y	0.514	0.87
17_F	21_I	0.512	0.87
196_Y	203_W	0.509	0.87
181_H	188_M	0.509	0.87
43_H	46_G	0.509	0.87
198_R	204_V	0.508	0.87
103_S	108_V	0.508	0.87
161_F	193_A	0.507	0.87
192_F	196_Y	0.507	0.87
98_Q	101_A	0.506	0.87
116_E	122_L	0.506	0.87
42_L	56_C	0.505	0.87
163_F	166_L	0.504	0.86
91_F	208_A	0.504	0.86
90_G	208_A	0.500	0.86

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
4cadC	1	0.8975	99.9	0.482	Contact Map
4c7rA	3	0.7992	12.3	0.938	Contact Map
4ev6A	3	0.25	5.1	0.948	Contact Map
4i0uA	4	0.2418	5	0.948	Contact Map
1afoA	2	0.1639	3.8	0.951	Contact Map
2wswA	3	0.8115	3.6	0.952	Contact Map
3aqpA	1	0.2541	2.8	0.954	Contact Map
3o7qA	1	0.6393	2.4	0.956	Contact Map
3rkoK	1	0.3156	2.2	0.957	Contact Map
2mofA	1	0.1721	1.9	0.958	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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