YIDA - ECOLI - GREMLIN Contacts

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YIDA - Sugar phosphatase YidA

UniProt:	P0A8Y5	Sequences: MAIKLIAIDMDGTLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYNGALVQKAADGSTVAQTALSYDDYRFLEKLSREVGSHFHALDRTTLYTANRDISYYTVHESFVATIPLVFCEAEKMDPNTQFLKVMMIDEPAILDQAIARIPQEVKEKYTVLKSAPYFLEILDKRVNKGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAMDNAIPSVKEVANFVTKSNLEDGVAFAIEKYVLN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11195
Length:	270 (256)
Sequences:	10974 (9017)
Seq/√Len:	563.6

ECOLI - YIDA SUPH YBJI YBHA YIGL COF MPGP
BACSU - YXEH YHAX YWPJ YKRA YWTE YITU 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
253_K	262_F	4.095	1.00
17_P	256_L	3.543	1.00
217_A	231_A	3.131	1.00
254_S	257_E	2.977	1.00
228_I	234_G	2.886	1.00
22_S	258_D	2.768	1.00
4_K	214_E	2.742	1.00
24_A	258_D	2.603	1.00
205_A	215_I	2.541	1.00
24_A	265_E	2.471	1.00
8_I	39_V	2.427	1.00
242_P	246_E	2.408	1.00
43_T	50_V	2.402	1.00
16_L	20_T	2.347	1.00
229_E	247_V	2.253	1.00
202_K	230_Y	2.186	1.00
212_P	230_Y	2.041	1.00
76_K	79_D	2.024	1.00
196_N	226_A	2.010	1.00
23_P	27_N	1.933	1.00
31_A	34_A	1.909	1.00
225_I	244_V	1.888	1.00
84_A	203_S	1.819	1.00
222_E	243_S	1.811	1.00
253_K	257_E	1.808	1.00
225_I	247_V	1.802	1.00
236_A	248_A	1.793	1.00
242_P	245_K	1.791	1.00
5_L	40_V	1.767	1.00
31_A	265_E	1.761	1.00
29_I	39_V	1.747	1.00
222_E	241_I	1.745	1.00
26_K	56_E	1.738	1.00
3_I	216_M	1.728	1.00
234_G	249_N	1.721	1.00
7_A	201_V	1.715	1.00
32_A	37_V	1.701	1.00
211_K	214_E	1.698	1.00
202_K	206_D	1.686	1.00
31_A	35_R	1.684	1.00
89_S	92_D	1.680	1.00
76_K	81_S	1.621	1.00
203_S	206_D	1.620	1.00
250_F	267_Y	1.599	1.00
235_V	263_A	1.588	1.00
244_V	247_V	1.587	1.00
233_V	249_N	1.579	1.00
203_S	207_V	1.564	1.00
233_V	250_F	1.559	1.00
10_M	15_L	1.558	1.00
8_I	218_I	1.543	1.00
199_T	202_K	1.521	1.00
22_S	25_V	1.513	1.00
38_N	208_L	1.511	1.00
86_T	203_S	1.510	1.00
3_I	37_V	1.510	1.00
198_G	230_Y	1.505	1.00
201_V	227_M	1.494	1.00
218_I	260_V	1.444	1.00
101_R	118_A	1.442	1.00
27_N	31_A	1.431	1.00
250_F	263_A	1.430	1.00
217_A	227_M	1.425	1.00
95_F	177_K	1.422	1.00
100_S	156_M	1.417	1.00
25_V	258_D	1.399	1.00
167_I	171_P	1.396	1.00
141_E	144_K	1.373	1.00
33_R	60_E	1.365	1.00
213_E	232_G	1.358	1.00
24_A	262_F	1.349	1.00
3_I	214_E	1.346	1.00
236_A	240_A	1.344	1.00
3_I	233_V	1.343	1.00
218_I	263_A	1.324	1.00
92_D	177_K	1.321	1.00
26_K	30_A	1.313	1.00
85_Q	150_Q	1.290	1.00
238_D	254_S	1.285	1.00
205_A	212_P	1.281	1.00
92_D	95_F	1.259	1.00
28_A	261_A	1.256	1.00
228_I	244_V	1.253	1.00
7_A	42_T	1.249	1.00
103_V	169_R	1.244	1.00
82_T	85_Q	1.241	1.00
212_P	215_I	1.240	1.00
225_I	229_E	1.237	1.00
179_T	226_A	1.231	1.00
99_L	103_V	1.229	1.00
250_F	266_K	1.229	1.00
90_Y	94_R	1.222	1.00
243_S	246_E	1.220	1.00
263_A	267_Y	1.219	1.00
86_T	192_D	1.197	1.00
92_D	178_Y	1.195	1.00
216_M	267_Y	1.191	1.00
24_A	28_A	1.182	1.00
6_I	264_I	1.177	1.00
73_L	82_T	1.164	1.00
28_A	265_E	1.163	1.00
162_I	165_Q	1.156	1.00
245_K	251_V	1.154	1.00
215_I	231_A	1.154	1.00
30_A	34_A	1.152	1.00
67_I	200_G	1.149	1.00
164_D	168_A	1.148	1.00
40_V	204_L	1.127	1.00
85_Q	152_L	1.115	1.00
164_D	182_K	1.109	1.00
6_I	32_A	1.109	1.00
179_T	194_R	1.109	1.00
252_T	259_G	1.106	1.00
217_A	228_I	1.103	1.00
260_V	264_I	1.102	1.00
5_L	205_A	1.100	1.00
5_L	210_I	1.093	1.00
7_A	215_I	1.087	1.00
181_L	191_L	1.086	1.00
252_T	263_A	1.083	1.00
153_K	189_E	1.081	1.00
239_N	255_N	1.080	1.00
17_P	255_N	1.075	1.00
231_A	234_G	1.066	1.00
74_V	203_S	1.062	1.00
6_I	37_V	1.058	1.00
212_P	232_G	1.056	1.00
23_P	26_K	1.051	1.00
122_I	126_T	1.051	1.00
192_D	195_V	1.050	1.00
10_M	53_Y	1.049	1.00
235_V	252_T	1.043	1.00
16_L	256_L	1.040	1.00
261_A	265_E	1.033	1.00
241_I	244_V	1.033	1.00
14_L	25_V	1.021	1.00
177_K	193_K	1.014	1.00
237_M	259_G	1.012	1.00
158_D	162_I	1.011	1.00
5_L	215_I	1.005	1.00
74_V	84_A	1.005	1.00
30_A	33_R	1.004	1.00
196_N	199_T	1.001	1.00
201_V	231_A	0.995	1.00
98_K	102_E	0.991	1.00
205_A	230_Y	0.990	1.00
262_F	266_K	0.982	1.00
235_V	250_F	0.981	1.00
221_Q	241_I	0.978	1.00
216_M	233_V	0.975	1.00
240_A	245_K	0.968	1.00
216_M	263_A	0.967	1.00
30_A	58_H	0.962	1.00
216_M	235_V	0.960	1.00
165_Q	168_A	0.956	1.00
51_H	80_G	0.951	1.00
99_L	102_E	0.951	1.00
204_L	208_L	0.949	1.00
168_A	171_P	0.944	1.00
237_M	252_T	0.944	1.00
205_A	232_G	0.938	1.00
238_D	245_K	0.937	1.00
253_K	259_G	0.937	1.00
86_T	194_R	0.934	1.00
263_A	266_K	0.930	1.00
198_G	226_A	0.927	1.00
14_L	29_I	0.927	1.00
85_Q	112_R	0.924	1.00
32_A	39_V	0.920	1.00
202_K	212_P	0.919	1.00
47_Y	68_T	0.918	1.00
236_A	244_V	0.917	1.00
8_I	260_V	0.914	1.00
94_R	98_K	0.910	1.00
205_A	210_I	0.908	1.00
222_E	225_I	0.908	1.00
43_T	68_T	0.904	1.00
238_D	253_K	0.889	1.00
27_N	30_A	0.888	1.00
191_L	196_N	0.887	1.00
74_V	200_G	0.885	1.00
72_A	195_V	0.880	1.00
165_Q	169_R	0.877	1.00
262_F	265_E	0.872	1.00
7_A	40_V	0.869	1.00
238_D	257_E	0.863	1.00
87_A	150_Q	0.860	1.00
158_D	163_L	0.858	1.00
83_V	207_V	0.856	1.00
25_V	261_A	0.854	1.00
215_I	232_G	0.852	1.00
16_L	22_S	0.851	1.00
51_H	55_K	0.847	1.00
88_L	192_D	0.844	1.00
68_T	73_L	0.837	1.00
232_G	249_N	0.836	1.00
95_F	98_K	0.834	1.00
228_I	247_V	0.833	1.00
75_Q	82_T	0.833	1.00
98_K	143_E	0.830	1.00
91_D	95_F	0.823	1.00
122_I	125_Y	0.821	1.00
176_E	193_K	0.820	1.00
243_S	247_V	0.816	1.00
67_I	204_L	0.815	1.00
99_L	174_V	0.812	1.00
75_Q	80_G	0.812	1.00
217_A	234_G	0.808	1.00
42_T	67_I	0.807	1.00
180_V	190_I	0.805	1.00
8_I	14_L	0.800	1.00
159_E	162_I	0.790	1.00
167_I	182_K	0.790	1.00
37_V	216_M	0.788	1.00
6_I	216_M	0.785	1.00
253_K	266_K	0.784	1.00
32_A	264_I	0.784	1.00
14_L	21_I	0.783	1.00
215_I	230_Y	0.781	1.00
47_Y	75_Q	0.776	1.00
102_E	169_R	0.776	1.00
10_M	41_L	0.772	1.00
28_A	31_A	0.771	1.00
87_A	152_L	0.761	1.00
46_P	69_Y	0.761	1.00
240_A	244_V	0.757	1.00
68_T	75_Q	0.757	1.00
25_V	28_A	0.753	1.00
237_M	240_A	0.751	1.00
160_P	164_D	0.748	1.00
40_V	61_Q	0.741	1.00
95_F	99_L	0.741	1.00
24_A	261_A	0.736	1.00
179_T	196_N	0.735	1.00
142_A	145_M	0.735	1.00
164_D	167_I	0.734	1.00
97_E	101_R	0.734	1.00
228_I	248_A	0.728	1.00
18_D	256_L	0.725	1.00
201_V	217_A	0.724	1.00
81_S	207_V	0.724	1.00
16_L	255_N	0.715	1.00
50_V	68_T	0.712	1.00
220_D	240_A	0.709	1.00
220_D	237_M	0.709	1.00
41_L	50_V	0.706	1.00
103_V	165_Q	0.705	1.00
214_E	232_G	0.703	1.00
95_F	174_V	0.700	1.00
94_R	143_E	0.699	1.00
101_R	107_F	0.698	1.00
111_D	151_F	0.696	1.00
14_L	255_N	0.695	1.00
135_I	139_F	0.687	1.00
195_V	199_T	0.685	1.00
199_T	203_S	0.684	1.00
250_F	262_F	0.684	1.00
234_G	244_V	0.682	1.00
72_A	192_D	0.682	1.00
179_T	193_K	0.681	1.00
50_V	66_C	0.680	1.00
140_C	144_K	0.676	1.00
140_C	143_E	0.675	1.00
12_G	237_M	0.671	1.00
99_L	169_R	0.670	1.00
202_K	205_A	0.663	1.00
70_N	189_E	0.660	1.00
250_F	253_K	0.658	1.00
155_M	189_E	0.657	1.00
169_R	172_Q	0.655	1.00
234_G	248_A	0.653	1.00
90_Y	150_Q	0.652	1.00
42_T	227_M	0.651	1.00
93_Y	151_F	0.650	1.00
24_A	27_N	0.648	1.00
10_M	14_L	0.644	1.00
218_I	235_V	0.643	1.00
91_D	94_R	0.643	1.00
174_V	177_K	0.637	1.00
104_G	162_I	0.636	1.00
252_T	262_F	0.630	1.00
47_Y	51_H	0.630	1.00
5_L	204_L	0.625	1.00
236_A	247_V	0.622	1.00
226_A	229_E	0.621	1.00
73_L	152_L	0.618	1.00
94_R	147_P	0.614	1.00
239_N	245_K	0.613	1.00
10_M	50_V	0.610	1.00
171_P	180_V	0.610	1.00
168_A	172_Q	0.610	1.00
112_R	150_Q	0.607	1.00
258_D	261_A	0.606	1.00
111_D	149_T	0.605	1.00
33_R	61_Q	0.604	1.00
153_K	183_S	0.600	1.00
82_T	112_R	0.600	1.00
233_V	263_A	0.599	1.00
37_V	214_E	0.595	1.00
97_E	109_A	0.595	1.00
218_I	252_T	0.594	1.00
163_L	182_K	0.594	1.00
33_R	58_H	0.592	1.00
179_T	191_L	0.592	1.00
128_H	134_T	0.592	1.00
52_N	55_K	0.591	1.00
222_E	244_V	0.591	1.00
14_L	41_L	0.589	1.00
244_V	248_A	0.586	1.00
76_K	83_V	0.585	1.00
180_V	188_L	0.584	1.00
28_A	32_A	0.583	1.00
237_M	255_N	0.581	1.00
160_P	185_P	0.580	1.00
218_I	264_I	0.579	1.00
22_S	261_A	0.578	1.00
74_V	204_L	0.575	1.00
109_A	151_F	0.574	0.99
210_I	215_I	0.573	0.99
123_S	126_T	0.572	0.99
194_R	199_T	0.571	0.99
198_G	202_K	0.569	0.99
253_K	263_A	0.568	0.99
112_R	149_T	0.568	0.99
90_Y	148_N	0.567	0.99
108_H	155_M	0.566	0.99
54_L	66_C	0.566	0.99
235_V	249_N	0.564	0.99
41_L	54_L	0.563	0.99
261_A	264_I	0.562	0.99
128_H	131_F	0.560	0.99
6_I	218_I	0.558	0.99
210_I	232_G	0.558	0.99
21_I	26_K	0.558	0.99
132_V	136_P	0.557	0.99
225_I	228_I	0.556	0.99
74_V	207_V	0.556	0.99
15_L	255_N	0.555	0.99
184_A	221_Q	0.553	0.99
112_R	152_L	0.549	0.99
69_Y	152_L	0.546	0.99
258_D	262_F	0.544	0.99
155_M	187_F	0.544	0.99
239_N	254_S	0.542	0.99
119_N	140_C	0.541	0.99
126_T	129_E	0.540	0.99
29_I	264_I	0.538	0.99
241_I	245_K	0.538	0.99
76_K	207_V	0.536	0.99
32_A	261_A	0.535	0.99
8_I	32_A	0.532	0.99
163_L	188_L	0.532	0.99
50_V	53_Y	0.532	0.99
105_S	156_M	0.532	0.99
99_L	170_I	0.531	0.99
25_V	29_I	0.530	0.99
27_N	265_E	0.530	0.99
4_K	37_V	0.529	0.99
105_S	166_A	0.528	0.99
69_Y	187_F	0.528	0.99
93_Y	97_E	0.525	0.99
161_A	165_Q	0.524	0.99
127_V	131_F	0.523	0.99
3_I	38_N	0.522	0.99
69_Y	72_A	0.521	0.99
212_P	231_A	0.520	0.99
163_L	167_I	0.520	0.99
17_P	254_S	0.518	0.99
126_T	130_S	0.518	0.99
73_L	112_R	0.517	0.99
201_V	205_A	0.512	0.99
5_L	38_N	0.511	0.99
231_A	249_N	0.510	0.99
70_N	183_S	0.510	0.99
128_H	132_V	0.509	0.99
198_G	215_I	0.509	0.99
147_P	150_Q	0.506	0.99
21_I	45_R	0.503	0.99
12_G	16_L	0.503	0.99
33_R	39_V	0.502	0.99
107_F	154_V	0.501	0.99
158_D	166_A	0.501	0.99
42_T	70_N	0.500	0.99
183_S	189_E	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
1rkqA	1	1	100	0.218	Contact Map
3pgvA	3	0.9519	100	0.225	Contact Map
2b30A	2	0.9926	100	0.233	Contact Map
3l7yA	1	0.9667	100	0.238	Contact Map
3mpoA	1	0.9889	100	0.242	Contact Map
1nrwA	1	0.963	100	0.243	Contact Map
3daoA	1	0.9704	100	0.25	Contact Map
1nf2A	4	0.9741	100	0.253	Contact Map
4dw8A	1	0.9852	100	0.255	Contact Map
1rlmA	1	0.9667	100	0.259	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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