YAGL - ECOLI - GREMLIN Contacts

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YAGL - Uncharacterized protein YagL

UniProt:	P77607	Sequences: MRGKILLYQLKYRWQSLSIFGCFLCKMTLFRYQKIIYDTGVHQMRSFFYTICSSEQQESITDHHSLAEICQKFNILPEHVVIEQVDIKEVVSEQRLLRQLIHHEMNRQDTLVIPDLSCLGRTVEDLQNILFFCLQKEMFIYSYHPASRIEPSAESCLSFLIARQDTIDIHNLKSTKSRYRHVKKKLGRKEGSKYRRDITILKKGGFTQAEIAKKLSISLSTVKRHWNNGIIG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13551
Length:	232 (183)
Sequences:	7961 (6036)
Seq/√Len:	446.2

ECOLI - YAGL PINR PINE PINQ YBCK
BACSU - YOKA CISA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_V	104_E	3.374	1.00
96_L	99_Q	3.335	1.00
201_L	214_K	3.013	1.00
83_E	96_L	2.520	1.00
50_T	63_H	2.509	1.00
197_D	201_L	2.483	1.00
48_F	66_L	2.419	1.00
100_L	111_L	2.375	1.00
63_H	67_A	2.324	1.00
63_H	82_I	2.152	1.00
206_F	214_K	2.079	1.00
68_E	72_K	2.068	1.00
178_R	182_V	1.994	1.00
168_D	171_N	1.939	1.00
201_L	206_F	1.921	1.00
179_Y	184_K	1.879	1.00
156_C	167_I	1.877	1.00
124_E	131_F	1.827	1.00
209_A	213_K	1.809	1.00
63_H	80_V	1.807	1.00
208_Q	223_K	1.800	1.00
212_A	222_V	1.778	1.00
54_S	57_Q	1.774	1.00
159_F	163_R	1.760	1.00
123_V	159_F	1.752	1.00
64_H	68_E	1.717	1.00
47_F	104_E	1.676	1.00
169_I	173_K	1.670	1.00
202_K	226_W	1.665	1.00
79_H	99_Q	1.648	1.00
126_L	162_A	1.645	1.00
133_C	138_M	1.630	1.00
223_K	227_N	1.614	1.00
127_Q	159_F	1.587	1.00
105_M	111_L	1.573	1.00
47_F	100_L	1.561	1.00
206_F	210_E	1.552	1.00
130_L	158_S	1.546	1.00
45_R	109_D	1.535	1.00
132_F	136_K	1.518	1.00
134_L	155_S	1.490	1.00
46_S	75_I	1.478	1.00
124_E	128_N	1.471	1.00
48_F	80_V	1.441	1.00
97_L	129_I	1.439	1.00
142_S	145_P	1.437	1.00
172_L	176_K	1.426	1.00
155_S	166_T	1.425	1.00
105_M	138_M	1.407	1.00
151_P	154_E	1.407	1.00
156_C	163_R	1.401	1.00
207_T	210_E	1.387	1.00
70_C	77_P	1.384	1.00
120_G	126_L	1.382	1.00
200_I	204_G	1.380	1.00
197_D	214_K	1.353	1.00
113_I	140_I	1.344	1.00
67_A	80_V	1.334	1.00
202_K	211_I	1.318	1.00
177_S	181_H	1.298	1.00
123_V	127_Q	1.297	1.00
113_I	142_S	1.294	1.00
175_T	179_Y	1.281	1.00
117_S	165_D	1.264	1.00
201_L	211_I	1.263	1.00
209_A	219_L	1.248	1.00
93_E	98_R	1.227	1.00
90_V	125_D	1.211	1.00
45_R	76_L	1.208	1.00
219_L	223_K	1.194	1.00
178_R	181_H	1.184	1.00
85_V	95_R	1.182	1.00
69_I	73_F	1.181	1.00
67_A	71_Q	1.144	1.00
65_S	114_P	1.140	1.00
64_H	178_R	1.139	1.00
106_N	132_F	1.137	1.00
66_L	112_V	1.132	1.00
131_F	135_Q	1.118	1.00
197_D	200_I	1.117	1.00
123_V	162_A	1.116	1.00
97_L	100_L	1.109	1.00
198_I	211_I	1.106	1.00
114_P	174_S	1.100	1.00
99_Q	104_E	1.100	1.00
81_V	100_L	1.095	1.00
101_I	129_I	1.091	1.00
201_L	204_G	1.065	1.00
50_T	59_S	1.062	1.00
50_T	80_V	1.060	1.00
130_L	140_I	1.058	1.00
110_T	141_Y	1.049	1.00
81_V	96_L	1.042	1.00
202_K	208_Q	1.037	1.00
46_S	110_T	1.037	1.00
61_T	114_P	1.012	1.00
110_T	139_F	0.997	1.00
176_K	186_L	0.988	1.00
70_C	75_I	0.976	1.00
218_S	221_T	0.971	1.00
65_S	174_S	0.966	1.00
79_H	104_E	0.965	1.00
48_F	77_P	0.961	1.00
177_S	180_R	0.959	1.00
117_S	171_N	0.958	1.00
47_F	81_V	0.956	1.00
89_E	93_E	0.950	1.00
106_N	136_K	0.944	1.00
50_T	82_I	0.940	1.00
113_I	119_L	0.936	1.00
77_P	80_V	0.933	1.00
156_C	164_Q	0.933	1.00
87_I	121_R	0.925	1.00
198_I	225_H	0.915	1.00
156_C	160_L	0.912	1.00
68_E	71_Q	0.912	1.00
61_T	174_S	0.905	1.00
85_V	89_E	0.901	1.00
198_I	222_V	0.890	1.00
222_V	225_H	0.889	1.00
119_L	129_I	0.888	1.00
160_L	163_R	0.883	1.00
111_L	133_C	0.880	1.00
176_K	180_R	0.877	1.00
180_R	186_L	0.875	1.00
152_S	170_H	0.874	1.00
116_L	165_D	0.874	1.00
87_I	120_G	0.873	1.00
65_S	68_E	0.871	1.00
164_Q	167_I	0.869	1.00
101_I	132_F	0.866	1.00
44_M	109_D	0.856	1.00
160_L	164_Q	0.852	1.00
107_R	137_E	0.847	1.00
97_L	119_L	0.847	1.00
210_E	214_K	0.844	1.00
52_C	57_Q	0.834	1.00
50_T	66_L	0.829	1.00
169_I	172_L	0.825	1.00
59_S	82_I	0.825	1.00
115_D	144_H	0.824	1.00
52_C	84_Q	0.819	1.00
115_D	171_N	0.813	1.00
173_K	176_K	0.813	1.00
139_F	150_E	0.809	1.00
70_C	112_V	0.804	1.00
208_Q	219_L	0.801	1.00
59_S	84_Q	0.799	1.00
69_I	112_V	0.799	1.00
198_I	215_L	0.795	1.00
199_T	202_K	0.793	1.00
141_Y	148_R	0.792	1.00
61_T	178_R	0.792	1.00
217_I	222_V	0.788	1.00
200_I	203_K	0.787	1.00
120_G	129_I	0.786	1.00
211_I	222_V	0.785	1.00
69_I	143_Y	0.784	1.00
176_K	179_Y	0.783	1.00
128_N	132_F	0.778	1.00
225_H	228_N	0.777	1.00
44_M	139_F	0.770	1.00
212_A	219_L	0.769	1.00
210_E	213_K	0.765	1.00
88_K	169_I	0.764	1.00
153_A	156_C	0.763	1.00
211_I	215_L	0.761	1.00
125_D	128_N	0.760	1.00
61_T	115_D	0.755	1.00
69_I	141_Y	0.750	1.00
60_I	64_H	0.742	1.00
100_L	105_M	0.740	1.00
217_I	225_H	0.736	1.00
49_Y	83_E	0.736	1.00
116_L	142_S	0.733	1.00
122_T	125_D	0.733	1.00
82_I	96_L	0.732	1.00
196_R	200_I	0.731	1.00
122_T	131_F	0.726	1.00
185_K	190_E	0.725	1.00
45_R	78_E	0.722	1.00
139_F	148_R	0.717	1.00
196_R	199_T	0.715	1.00
205_G	211_I	0.715	1.00
208_Q	212_A	0.714	1.00
212_A	216_S	0.704	1.00
220_S	224_R	0.701	1.00
172_L	175_T	0.699	1.00
159_F	166_T	0.693	1.00
171_N	174_S	0.687	1.00
67_A	77_P	0.685	1.00
64_H	67_A	0.683	1.00
61_T	65_S	0.681	1.00
199_T	203_K	0.679	1.00
116_L	158_S	0.675	1.00
100_L	104_E	0.671	1.00
191_G	194_Y	0.662	1.00
212_A	217_I	0.658	1.00
99_Q	102_H	0.654	1.00
44_M	110_T	0.653	1.00
203_K	206_F	0.646	0.99
114_P	144_H	0.644	0.99
129_I	133_C	0.639	0.99
157_L	164_Q	0.634	0.99
199_T	228_N	0.631	0.99
145_P	161_I	0.629	0.99
46_S	70_C	0.623	0.99
152_S	167_I	0.618	0.99
208_Q	222_V	0.618	0.99
198_I	201_L	0.618	0.99
126_L	158_S	0.612	0.99
221_T	224_R	0.611	0.99
206_F	211_I	0.607	0.99
170_H	174_S	0.607	0.99
173_K	177_S	0.607	0.99
179_Y	186_L	0.606	0.99
98_R	102_H	0.604	0.99
174_S	178_R	0.600	0.99
202_K	222_V	0.596	0.99
157_L	161_I	0.592	0.99
105_M	133_C	0.591	0.99
120_G	125_D	0.591	0.99
97_L	101_I	0.589	0.99
192_S	215_L	0.589	0.99
156_C	159_F	0.585	0.99
102_H	107_R	0.584	0.99
198_I	202_K	0.580	0.99
169_I	176_K	0.578	0.99
153_A	167_I	0.577	0.99
104_E	107_R	0.577	0.99
188_R	193_K	0.577	0.99
81_V	99_Q	0.577	0.99
208_Q	226_W	0.574	0.99
218_S	223_K	0.573	0.99
188_R	191_G	0.568	0.99
174_S	177_S	0.567	0.99
157_L	160_L	0.566	0.99
192_S	225_H	0.563	0.99
123_V	163_R	0.563	0.99
202_K	207_T	0.562	0.99
207_T	213_K	0.556	0.98
153_A	157_L	0.555	0.98
161_I	164_Q	0.555	0.98
222_V	226_W	0.554	0.98
123_V	166_T	0.548	0.98
212_A	215_L	0.547	0.98
124_E	127_Q	0.545	0.98
132_F	135_Q	0.545	0.98
97_L	125_D	0.544	0.98
47_F	78_E	0.541	0.98
66_L	143_Y	0.540	0.98
150_E	154_E	0.535	0.98
198_I	217_I	0.530	0.98
190_E	193_K	0.526	0.98
127_Q	131_F	0.525	0.98
176_K	185_K	0.525	0.98
200_I	214_K	0.524	0.98
197_D	215_L	0.524	0.98
201_L	205_G	0.520	0.98
90_V	97_L	0.518	0.98
220_S	223_K	0.518	0.98
58_E	84_Q	0.518	0.98
46_S	141_Y	0.517	0.98
192_S	217_I	0.516	0.98
221_T	225_H	0.511	0.97
120_G	162_A	0.508	0.97
158_S	162_A	0.506	0.97
200_I	205_G	0.505	0.97
217_I	221_T	0.504	0.97
46_S	112_V	0.504	0.97
90_V	120_G	0.502	0.97
185_K	188_R	0.501	0.97
112_V	141_Y	0.501	0.97
215_L	222_V	0.500	0.97

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
1gdtA	2	0.7716	100	0.316	Contact Map
2r0qC	3	0.7371	100	0.342	Contact Map
4bqqA	2	0.7759	100	0.352	Contact Map
3uj3X	2	0.5172	100	0.358	Contact Map
3g13A	2	0.6336	100	0.43	Contact Map
3guvA	2	0.5862	100	0.432	Contact Map
3lhkA	2	0.5948	100	0.518	Contact Map
2gm5A	4	0.5172	100	0.52	Contact Map
3bvpA	4	0.5474	100	0.526	Contact Map
3ilxA	2	0.5431	100	0.543	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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