YIGL - ECOLI - GREMLIN Contacts

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YIGL - Pyridoxal phosphate phosphatase YigL

UniProt:	P27848	Sequences: MYQVVASDLDGTLLSPDHTLSPYAKETLKLLTARGINFVFATGRHHVDVGQIRDNLEIKSYMITSNGARVHDLDGNLIFAHNLDRDIASDLFGVVNDNPDIITNVYRDDEWFMNRHRPEEMRFFKEAVFQYALYEPGLLEPEGVSKVFFTCDSHEQLLPLEQAINARWGDRVNVSFSTLTCLEVMAGGVSKGHALEAVAKKLGYSLKDCIAFGDGMNDAEMLSMAGKGCIMGSAHQRLKDLHPELEVIGTNADDAVPHYLRKLYLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11470
Length:	266 (254)
Sequences:	10963 (9018)
Seq/√Len:	565.8

ECOLI - YIGL COF YIDA YBHA SUPH YBJI MPGP
BACSU - YXEH YWPJ YWTE YITU YKRA YHAX YCSE NTDB
HALSA - PGP
SULSO - PGP1 PGP2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
249_G	258_H	4.270	1.00
16_P	252_A	3.642	1.00
211_A	225_A	3.069	1.00
250_T	253_D	2.796	1.00
222_L	228_G	2.721	1.00
3_Q	208_D	2.697	1.00
21_S	254_D	2.650	1.00
23_Y	254_D	2.560	1.00
199_A	209_C	2.551	1.00
223_S	241_L	2.436	1.00
15_S	19_T	2.413	1.00
196_E	224_M	2.395	1.00
236_Q	240_D	2.387	1.00
23_Y	261_R	2.359	1.00
7_S	38_F	2.325	1.00
42_T	49_V	2.198	1.00
206_L	224_M	2.140	1.00
79_F	197_A	2.037	1.00
190_S	220_E	2.011	1.00
219_A	238_L	1.925	1.00
216_M	237_R	1.916	1.00
228_G	243_P	1.831	1.00
30_L	33_A	1.826	1.00
216_M	235_H	1.820	1.00
22_P	26_E	1.813	1.00
230_I	242_H	1.799	1.00
25_K	55_N	1.769	1.00
197_A	201_K	1.763	1.00
28_L	38_F	1.759	1.00
219_A	241_L	1.750	1.00
205_S	208_D	1.749	1.00
249_G	253_D	1.733	1.00
31_L	36_I	1.723	1.00
236_Q	239_K	1.717	1.00
30_L	261_R	1.709	1.00
84_D	87_I	1.706	1.00
4_V	39_V	1.704	1.00
227_K	246_E	1.670	1.00
196_E	200_K	1.669	1.00
227_K	243_P	1.665	1.00
30_L	34_R	1.638	1.00
6_A	195_L	1.633	1.00
197_A	200_K	1.628	1.00
229_C	259_Y	1.614	1.00
246_E	263_L	1.603	1.00
192_G	224_M	1.580	1.00
238_L	241_L	1.575	1.00
96_N	114_N	1.570	1.00
95_V	149_F	1.554	1.00
81_H	197_A	1.535	1.00
37_N	202_L	1.529	1.00
193_H	196_E	1.526	1.00
21_S	24_A	1.500	1.00
195_L	221_M	1.500	1.00
207_K	226_G	1.481	1.00
212_F	256_V	1.467	1.00
9_L	14_L	1.463	1.00
246_E	259_Y	1.463	1.00
211_A	221_M	1.457	1.00
7_S	212_F	1.456	1.00
26_E	30_L	1.455	1.00
161_E	165_N	1.455	1.00
24_A	254_D	1.426	1.00
87_I	171_R	1.417	1.00
23_Y	258_H	1.415	1.00
25_K	29_K	1.405	1.00
32_T	60_S	1.392	1.00
90_D	171_R	1.378	1.00
6_A	41_A	1.357	1.00
27_T	257_P	1.357	1.00
77_L	80_A	1.350	1.00
239_K	247_V	1.335	1.00
219_A	223_S	1.332	1.00
232_G	250_T	1.323	1.00
230_I	234_A	1.307	1.00
212_F	259_Y	1.307	1.00
199_A	206_L	1.299	1.00
87_I	90_D	1.292	1.00
259_Y	263_L	1.284	1.00
85_R	89_S	1.267	1.00
81_H	186_A	1.261	1.00
156_Q	159_P	1.253	1.00
222_L	238_L	1.248	1.00
27_T	261_R	1.246	1.00
32_T	59_K	1.242	1.00
206_L	209_C	1.234	1.00
237_R	240_D	1.233	1.00
173_N	220_E	1.231	1.00
80_A	145_S	1.230	1.00
29_K	33_A	1.216	1.00
246_E	262_K	1.214	1.00
80_A	143_G	1.211	1.00
69_R	77_L	1.195	1.00
87_I	172_V	1.195	1.00
4_V	204_Y	1.176	1.00
257_P	261_R	1.174	1.00
256_V	260_L	1.166	1.00
39_V	198_V	1.160	1.00
5_V	260_L	1.160	1.00
63_I	194_A	1.158	1.00
5_V	31_L	1.147	1.00
61_Y	202_L	1.139	1.00
209_C	225_A	1.123	1.00
211_A	222_L	1.120	1.00
15_S	252_A	1.119	1.00
16_P	251_N	1.112	1.00
5_V	36_I	1.108	1.00
158_L	162_Q	1.106	1.00
248_I	259_Y	1.098	1.00
23_Y	27_T	1.095	1.00
70_V	197_A	1.089	1.00
210_I	227_K	1.082	1.00
173_N	188_G	1.082	1.00
39_V	61_Y	1.071	1.00
175_S	185_M	1.070	1.00
158_L	176_F	1.069	1.00
229_C	248_I	1.069	1.00
4_V	199_A	1.064	1.00
210_I	263_L	1.058	1.00
206_L	226_G	1.053	1.00
259_Y	262_K	1.050	1.00
22_P	25_K	1.042	1.00
235_H	238_L	1.039	1.00
190_S	193_H	1.039	1.00
29_K	32_T	1.037	1.00
229_C	246_E	1.027	1.00
196_E	206_L	1.022	1.00
29_K	57_E	1.017	1.00
225_A	228_G	1.016	1.00
192_G	220_E	1.015	1.00
231_M	255_A	1.013	1.00
195_L	225_A	1.013	1.00
151_C	156_Q	1.009	1.00
171_R	187_G	1.000	1.00
199_A	224_M	0.999	1.00
258_H	262_K	0.999	1.00
6_A	209_C	0.993	1.00
94_V	97_D	0.992	1.00
70_V	79_F	0.991	1.00
9_L	52_I	0.991	1.00
13_L	24_A	0.990	1.00
89_S	93_G	0.978	1.00
68_A	189_V	0.978	1.00
198_V	202_L	0.974	1.00
186_A	189_V	0.973	1.00
215_G	235_H	0.971	1.00
210_I	259_Y	0.971	1.00
81_H	188_G	0.970	1.00
234_A	239_K	0.961	1.00
248_I	255_A	0.957	1.00
13_L	28_L	0.957	1.00
82_N	143_G	0.955	1.00
237_R	241_L	0.953	1.00
210_I	229_C	0.953	1.00
232_G	239_K	0.951	1.00
46_H	64_T	0.950	1.00
70_V	194_A	0.948	1.00
151_C	157_L	0.947	1.00
232_G	249_G	0.945	1.00
4_V	209_C	0.937	1.00
80_A	108_D	0.936	1.00
93_G	97_D	0.935	1.00
159_P	162_Q	0.934	1.00
230_I	238_L	0.930	1.00
216_M	219_A	0.930	1.00
233_S	251_N	0.927	1.00
99_P	163_A	0.924	1.00
50_G	75_G	0.924	1.00
258_H	261_R	0.919	1.00
94_V	99_P	0.917	1.00
146_K	183_E	0.917	1.00
71_H	77_L	0.913	1.00
64_T	69_R	0.913	1.00
7_S	256_V	0.912	1.00
199_A	204_Y	0.910	1.00
26_E	29_K	0.905	1.00
162_Q	165_N	0.905	1.00
90_D	93_G	0.890	1.00
243_P	246_E	0.887	1.00
36_I	210_I	0.883	1.00
6_A	39_V	0.877	1.00
174_V	184_V	0.874	1.00
31_L	38_F	0.870	1.00
42_T	64_T	0.865	1.00
50_G	54_D	0.863	1.00
249_G	255_A	0.862	1.00
185_M	190_S	0.856	1.00
159_P	163_A	0.856	1.00
24_A	257_P	0.854	1.00
226_G	243_P	0.846	1.00
94_V	163_A	0.843	1.00
92_F	96_N	0.843	1.00
27_T	30_L	0.838	1.00
5_V	210_I	0.832	1.00
41_A	63_I	0.830	1.00
71_H	75_G	0.829	1.00
83_L	186_A	0.829	1.00
37_N	61_Y	0.826	1.00
23_Y	257_P	0.826	1.00
118_P	122_R	0.824	1.00
63_I	198_V	0.822	1.00
249_G	262_K	0.822	1.00
110_E	132_A	0.820	1.00
173_N	190_S	0.819	1.00
46_H	71_H	0.819	1.00
209_C	226_G	0.818	1.00
154_H	158_L	0.817	1.00
61_Y	198_V	0.814	1.00
158_L	161_E	0.814	1.00
78_I	201_K	0.810	1.00
209_C	224_M	0.808	1.00
37_N	60_S	0.804	1.00
86_D	90_D	0.803	1.00
7_S	13_L	0.800	1.00
82_N	145_S	0.798	1.00
15_S	21_S	0.795	1.00
161_E	176_F	0.794	1.00
94_V	168_W	0.794	1.00
199_A	226_G	0.793	1.00
232_G	253_D	0.789	1.00
222_L	241_L	0.787	1.00
90_D	94_V	0.783	1.00
24_A	27_T	0.782	1.00
231_M	248_I	0.774	1.00
31_L	260_L	0.771	1.00
121_M	125_K	0.767	1.00
45_H	65_S	0.765	1.00
193_H	197_A	0.761	1.00
64_T	71_H	0.756	1.00
36_I	208_D	0.753	1.00
170_D	187_G	0.749	1.00
211_A	228_G	0.749	1.00
108_D	143_G	0.742	1.00
13_L	20_L	0.740	1.00
123_F	126_E	0.738	1.00
49_V	64_T	0.738	1.00
163_A	166_A	0.733	1.00
9_L	40_F	0.732	1.00
97_D	163_A	0.729	1.00
99_P	159_P	0.727	1.00
243_P	247_V	0.724	1.00
90_D	168_W	0.723	1.00
231_M	234_A	0.720	1.00
234_A	238_L	0.718	1.00
195_L	211_A	0.715	1.00
23_Y	26_E	0.711	1.00
173_N	187_G	0.711	1.00
196_E	199_A	0.710	1.00
123_F	127_A	0.709	1.00
69_R	145_S	0.703	1.00
222_L	242_H	0.701	1.00
66_N	183_E	0.700	1.00
49_V	62_M	0.695	1.00
96_N	103_T	0.694	1.00
41_A	221_M	0.693	1.00
214_D	234_A	0.686	1.00
13_L	251_N	0.684	1.00
220_E	223_S	0.681	1.00
208_D	226_G	0.681	1.00
189_V	193_H	0.677	1.00
89_S	140_E	0.677	1.00
88_A	144_V	0.672	1.00
85_R	143_G	0.672	1.00
40_F	49_V	0.670	1.00
100_D	156_Q	0.668	1.00
68_A	186_A	0.667	1.00
254_D	257_P	0.663	1.00
228_G	238_L	0.663	1.00
192_G	196_E	0.662	1.00
246_E	258_H	0.660	1.00
246_E	249_G	0.660	1.00
46_H	50_G	0.658	1.00
11_G	231_M	0.658	1.00
219_A	222_L	0.656	1.00
122_R	125_K	0.656	1.00
157_L	161_E	0.655	1.00
76_N	201_K	0.654	1.00
15_S	251_N	0.649	1.00
248_I	258_H	0.648	1.00
137_G	140_E	0.642	1.00
227_K	259_Y	0.637	1.00
9_L	49_V	0.636	1.00
53_R	62_M	0.636	1.00
17_D	252_A	0.635	1.00
124_F	131_Y	0.634	1.00
9_L	13_L	0.633	1.00
5_V	212_F	0.633	1.00
118_P	121_M	0.633	1.00
216_M	238_L	0.631	1.00
86_D	89_S	0.630	1.00
92_F	105_V	0.628	1.00
148_F	183_E	0.626	1.00
254_D	258_H	0.624	1.00
70_V	198_V	0.624	1.00
228_G	242_H	0.622	1.00
233_S	250_T	0.621	1.00
168_W	171_R	0.621	1.00
212_F	248_I	0.620	1.00
20_L	25_K	0.618	1.00
233_S	239_K	0.616	1.00
27_T	31_L	0.616	1.00
104_N	148_F	0.614	1.00
188_G	193_H	0.611	1.00
212_F	229_C	0.608	1.00
173_N	185_M	0.606	1.00
154_H	179_L	0.605	1.00
162_Q	166_A	0.601	1.00
4_V	198_V	0.600	1.00
77_L	108_D	0.599	1.00
51_Q	54_D	0.599	1.00
69_R	108_D	0.598	1.00
107_R	110_E	0.590	1.00
24_A	28_L	0.590	1.00
214_D	231_M	0.587	1.00
238_L	242_H	0.587	1.00
174_V	182_L	0.586	1.00
40_F	53_R	0.585	1.00
124_F	127_A	0.582	1.00
65_S	145_S	0.581	1.00
116_H	133_L	0.578	1.00
257_P	260_L	0.576	1.00
107_R	142_E	0.574	1.00
21_S	257_P	0.574	1.00
157_L	176_F	0.574	1.00
70_V	201_K	0.570	0.99
116_H	121_M	0.569	0.99
165_N	174_V	0.568	0.99
249_G	259_Y	0.567	0.99
14_L	251_N	0.562	0.99
231_M	251_N	0.562	0.99
88_A	92_F	0.562	0.99
105_V	144_V	0.562	0.99
204_Y	226_G	0.560	0.99
13_L	40_F	0.560	0.99
151_C	160_L	0.554	0.99
3_Q	36_I	0.553	0.99
154_H	176_F	0.552	0.99
135_E	138_L	0.551	0.99
155_E	159_P	0.548	0.99
150_T	181_C	0.547	0.99
4_V	37_N	0.543	0.99
123_F	128_V	0.543	0.99
28_L	260_L	0.542	0.99
50_G	53_R	0.541	0.99
125_K	128_V	0.541	0.99
122_R	126_E	0.540	0.99
81_H	189_V	0.540	0.99
94_V	164_I	0.537	0.99
101_I	149_F	0.537	0.99
15_S	254_D	0.535	0.99
93_G	137_G	0.534	0.99
146_K	177_S	0.530	0.99
31_L	257_P	0.530	0.99
107_R	144_V	0.529	0.99
103_T	147_V	0.529	0.99
230_I	241_L	0.527	0.99
151_C	154_H	0.525	0.99
104_N	111_W	0.523	0.99
204_Y	208_D	0.522	0.99
157_L	182_L	0.520	0.99
212_F	260_L	0.520	0.99
108_D	145_S	0.518	0.99
229_C	243_P	0.518	0.99
26_E	261_R	0.515	0.99
28_L	32_T	0.515	0.99
121_M	124_F	0.514	0.99
108_D	142_E	0.512	0.99
53_R	58_I	0.512	0.99
6_A	199_A	0.510	0.99
149_F	184_V	0.508	0.99
91_L	184_V	0.508	0.99
45_H	48_D	0.507	0.99
37_N	204_Y	0.506	0.99
107_R	112_F	0.505	0.99
49_V	52_I	0.505	0.99
19_T	55_N	0.504	0.99
177_S	183_E	0.504	0.99
41_A	66_N	0.502	0.99
232_G	247_V	0.502	0.99
195_L	209_C	0.501	0.99
235_H	239_K	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
3pgvA	3	0.9737	100	0.179	Contact Map
1nrwA	1	0.9699	100	0.203	Contact Map
4qjbA	1	0.985	100	0.225	Contact Map
1nf2A	4	0.9812	100	0.226	Contact Map
3l7yA	1	0.9812	100	0.228	Contact Map
2b30A	2	0.9812	100	0.231	Contact Map
1rkqA	1	0.985	100	0.237	Contact Map
2rbkA	1	0.9586	100	0.239	Contact Map
3daoA	1	0.9737	100	0.239	Contact Map
4dw8A	1	0.9774	100	0.249	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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