YDIB - ECOLI - GREMLIN Contacts

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YDIB - Quinate/shikimate dehydrogenase

UniProt:	P0A6D5	Sequences: MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11234
Length:	288 (260)
Sequences:	6318 (4707)
Seq/√Len:	291.9

ECOLI - YDIB AROE
BACSU - AROE
HALSA - AROE
SULSO - AROE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
238_M	246_Q	4.467	1.00
15_Y	43_E	4.043	1.00
82_T	104_Y	3.080	1.00
91_I	103_G	2.838	1.00
268_T	274_D	2.827	1.00
80_E	102_R	2.810	1.00
109_T	265_E	2.745	1.00
80_E	100_Y	2.702	1.00
126_T	150_E	2.552	1.00
229_V	241_L	2.538	1.00
265_E	268_T	2.521	1.00
72_Q	137_T	2.453	1.00
96_N	101_L	2.353	1.00
128_V	197_A	2.185	1.00
78_V	103_G	2.158	1.00
8_E	62_R	2.156	1.00
139_I	232_C	2.132	1.00
78_V	94_I	2.119	1.00
240_K	244_Q	2.112	1.00
238_M	243_Q	2.101	1.00
25_M	263_G	2.094	1.00
95_V	269_L	1.996	1.00
129_L	140_G	1.989	1.00
85_A	91_I	1.988	1.00
111_H	230_T	1.955	1.00
73_L	76_E	1.933	1.00
116_K	146_E	1.907	1.00
65_G	266_Q	1.890	1.00
113_R	116_K	1.872	1.00
9_L	40_M	1.832	1.00
229_V	245_A	1.810	1.00
127_M	148_L	1.806	1.00
15_Y	45_D	1.794	1.00
242_L	252_T	1.793	1.00
64_T	94_I	1.785	1.00
137_T	170_R	1.770	1.00
15_Y	46_N	1.754	1.00
14_A	67_S	1.752	1.00
165_L	169_Q	1.724	1.00
74_A	78_V	1.709	1.00
75_C	81_L	1.698	1.00
51_G	54_E	1.692	1.00
83_P	86_K	1.692	1.00
111_H	139_I	1.687	1.00
11_G	42_F	1.687	1.00
126_T	198_D	1.649	1.00
48_S	51_G	1.612	1.00
224_H	227_L	1.608	1.00
70_N	73_L	1.607	1.00
30_L	37_F	1.606	1.00
74_A	94_I	1.602	1.00
13_M	64_T	1.594	1.00
104_Y	269_L	1.594	1.00
82_T	102_R	1.568	1.00
10_I	37_F	1.544	1.00
113_R	261_W	1.536	1.00
94_I	101_L	1.513	1.00
132_A	155_N	1.485	1.00
128_V	154_F	1.482	1.00
81_L	86_K	1.480	1.00
39_Y	65_G	1.478	1.00
93_T	106_T	1.478	1.00
10_I	30_L	1.472	1.00
135_A	232_C	1.467	1.00
78_V	91_I	1.448	1.00
50_P	54_E	1.419	1.00
152_K	197_A	1.415	1.00
126_T	152_K	1.411	1.00
88_V	108_G	1.410	1.00
114_A	230_T	1.391	1.00
55_G	58_A	1.386	1.00
150_E	180_T	1.383	1.00
16_P	19_H	1.379	1.00
12_L	41_A	1.359	1.00
10_I	62_R	1.357	1.00
45_D	48_S	1.354	1.00
243_Q	247_Q	1.354	1.00
84_A	104_Y	1.350	1.00
79_D	100_Y	1.341	1.00
68_M	205_K	1.338	1.00
9_L	38_T	1.336	1.00
114_A	257_G	1.336	1.00
56_L	61_M	1.332	1.00
87_L	145_I	1.326	1.00
84_A	145_I	1.318	1.00
28_K	32_K	1.312	1.00
157_R	162_D	1.297	1.00
15_Y	70_N	1.282	1.00
12_L	17_I	1.271	1.00
44_V	52_A	1.239	1.00
155_N	205_K	1.230	1.00
18_R	43_E	1.224	1.00
97_D	100_Y	1.222	1.00
246_Q	252_T	1.221	1.00
227_L	250_C	1.218	1.00
136_S	203_G	1.209	1.00
181_V	184_L	1.209	1.00
11_G	64_T	1.205	1.00
57_K	96_N	1.200	1.00
125_K	198_D	1.199	1.00
57_K	101_L	1.193	1.00
108_G	142_Q	1.176	1.00
56_L	64_T	1.174	1.00
228_L	253_I	1.170	1.00
95_V	104_Y	1.160	1.00
13_M	66_V	1.158	1.00
267_F	271_T	1.155	1.00
81_L	103_G	1.147	1.00
245_A	250_C	1.146	1.00
261_W	277_L	1.139	1.00
141_A	145_I	1.136	1.00
120_F	228_L	1.132	1.00
127_M	143_G	1.126	1.00
207_G	233_V	1.123	1.00
275_F	280_V	1.122	1.00
81_L	85_A	1.119	1.00
117_E	261_W	1.115	1.00
32_K	279_Y	1.102	1.00
148_L	151_I	1.085	1.00
30_L	267_F	1.083	1.00
143_G	201_T	1.081	1.00
24_E	28_K	1.072	1.00
244_Q	247_Q	1.062	1.00
87_L	141_A	1.060	1.00
49_F	74_A	1.059	1.00
244_Q	248_A	1.042	1.00
17_I	43_E	1.035	1.00
28_K	31_E	1.027	1.00
109_T	113_R	1.025	1.00
111_H	201_T	1.021	1.00
166_A	170_R	1.018	1.00
35_L	271_T	1.016	1.00
276_P	279_Y	1.004	1.00
81_L	91_I	1.002	1.00
27_N	38_T	0.998	1.00
17_I	20_S	0.983	1.00
50_P	77_Y	0.981	1.00
57_K	79_D	0.974	1.00
47_D	73_L	0.971	1.00
129_L	136_S	0.968	1.00
74_A	91_I	0.964	1.00
152_K	182_T	0.964	1.00
157_R	163_K	0.961	1.00
97_D	102_R	0.956	1.00
203_G	232_C	0.953	1.00
49_F	77_Y	0.953	1.00
240_K	243_Q	0.953	1.00
72_Q	163_K	0.952	1.00
78_V	81_L	0.950	1.00
278_E	282_Q	0.949	1.00
42_F	61_M	0.941	1.00
75_C	78_V	0.941	1.00
113_R	265_E	0.939	1.00
162_D	166_A	0.937	1.00
162_D	165_L	0.934	1.00
264_A	277_L	0.933	1.00
140_G	171_V	0.929	1.00
44_V	70_N	0.928	1.00
132_A	153_L	0.928	1.00
21_L	24_E	0.925	1.00
140_G	151_I	0.922	1.00
46_N	73_L	0.918	1.00
57_K	60_K	0.917	1.00
112_I	116_K	0.917	1.00
257_G	261_W	0.915	1.00
95_V	102_R	0.912	1.00
134_G	138_A	0.911	1.00
50_P	73_L	0.910	1.00
118_S	253_I	0.903	1.00
33_A	273_K	0.903	1.00
260_L	264_A	0.895	1.00
163_K	166_A	0.894	1.00
55_G	59_L	0.887	1.00
27_N	31_E	0.886	1.00
33_A	267_F	0.885	1.00
14_A	17_I	0.883	1.00
215_S	244_Q	0.869	1.00
112_I	142_Q	0.869	1.00
204_T	207_G	0.868	1.00
29_A	33_A	0.855	1.00
112_I	145_I	0.843	1.00
126_T	196_S	0.841	1.00
25_M	259_L	0.840	1.00
53_I	77_Y	0.838	1.00
66_V	70_N	0.836	1.00
200_L	227_L	0.833	1.00
220_I	247_Q	0.832	1.00
114_A	261_W	0.826	1.00
9_L	59_L	0.823	1.00
135_A	203_G	0.817	1.00
113_R	117_E	0.816	1.00
96_N	99_G	0.813	1.00
233_V	239_T	0.807	1.00
28_K	279_Y	0.796	0.99
154_F	182_T	0.794	0.99
110_G	258_M	0.791	0.99
18_R	41_A	0.789	0.99
62_R	97_D	0.787	0.99
83_P	87_L	0.782	0.99
120_F	199_I	0.781	0.99
29_A	267_F	0.775	0.99
143_G	148_L	0.775	0.99
52_A	55_G	0.774	0.99
168_A	172_N	0.773	0.99
210_P	240_K	0.769	0.99
64_T	74_A	0.765	0.99
52_A	59_L	0.762	0.99
13_M	52_A	0.751	0.99
35_L	267_F	0.751	0.99
265_E	269_L	0.750	0.99
90_A	105_N	0.748	0.99
223_L	229_V	0.745	0.99
49_F	73_L	0.743	0.99
53_I	74_A	0.742	0.99
238_M	242_L	0.742	0.99
26_Q	263_G	0.742	0.99
221_S	248_A	0.741	0.99
53_I	57_K	0.739	0.99
220_I	244_Q	0.738	0.99
68_M	208_M	0.734	0.99
72_Q	76_E	0.733	0.99
128_V	200_L	0.732	0.99
130_L	184_L	0.730	0.99
164_A	167_F	0.729	0.99
80_E	86_K	0.728	0.99
29_A	280_V	0.728	0.99
64_T	96_N	0.724	0.99
232_C	258_M	0.723	0.99
199_I	228_L	0.720	0.99
10_I	271_T	0.718	0.99
117_E	257_G	0.717	0.99
215_S	240_K	0.717	0.99
228_L	251_K	0.717	0.99
136_S	140_G	0.714	0.99
233_V	254_D	0.712	0.99
78_V	101_L	0.711	0.99
9_L	42_F	0.709	0.99
126_T	149_K	0.706	0.99
223_L	250_C	0.705	0.99
21_L	235_N	0.705	0.99
90_A	138_A	0.704	0.99
88_V	138_A	0.702	0.99
168_A	181_V	0.699	0.99
26_Q	93_T	0.697	0.99
224_H	250_C	0.697	0.99
88_V	141_A	0.696	0.99
155_N	163_K	0.696	0.99
253_I	257_G	0.694	0.99
13_M	44_V	0.694	0.99
140_G	153_L	0.693	0.99
172_N	175_T	0.691	0.98
237_H	254_D	0.689	0.98
130_L	204_T	0.688	0.98
125_K	149_K	0.687	0.98
229_V	242_L	0.687	0.98
49_F	70_N	0.686	0.98
28_K	280_V	0.681	0.98
238_M	252_T	0.681	0.98
32_K	276_P	0.677	0.98
74_A	77_Y	0.677	0.98
208_M	233_V	0.677	0.98
114_A	118_S	0.676	0.98
112_I	146_E	0.672	0.98
202_N	241_L	0.671	0.98
79_D	101_L	0.671	0.98
19_H	68_M	0.668	0.98
42_F	52_A	0.665	0.98
219_D	222_L	0.658	0.98
39_Y	93_T	0.657	0.98
45_D	70_N	0.656	0.98
11_G	41_A	0.649	0.98
54_E	57_K	0.648	0.98
214_E	217_V	0.648	0.98
226_G	250_C	0.646	0.98
82_T	269_L	0.646	0.98
130_L	154_F	0.645	0.98
83_P	145_I	0.644	0.98
108_G	145_I	0.640	0.98
220_I	248_A	0.640	0.98
50_P	76_E	0.638	0.97
93_T	266_Q	0.637	0.97
26_Q	30_L	0.636	0.97
129_L	153_L	0.636	0.97
144_A	151_I	0.636	0.97
12_L	65_G	0.633	0.97
113_R	268_T	0.632	0.97
144_A	171_V	0.632	0.97
256_Y	260_L	0.631	0.97
257_G	281_K	0.630	0.97
118_S	257_G	0.625	0.97
128_V	194_L	0.625	0.97
108_G	112_I	0.622	0.97
88_V	105_N	0.622	0.97
157_R	205_K	0.619	0.97
194_L	197_A	0.617	0.97
51_G	55_G	0.616	0.97
155_N	164_A	0.611	0.97
108_G	141_A	0.610	0.97
122_I	125_K	0.608	0.97
122_I	148_L	0.605	0.97
265_E	274_D	0.603	0.96
11_G	61_M	0.602	0.96
13_M	49_F	0.598	0.96
132_A	157_R	0.597	0.96
13_M	70_N	0.594	0.96
223_L	244_Q	0.594	0.96
115_I	253_I	0.593	0.96
114_A	253_I	0.592	0.96
130_L	200_L	0.592	0.96
15_Y	19_H	0.592	0.96
164_A	168_A	0.591	0.96
127_M	201_T	0.591	0.96
185_A	191_A	0.590	0.96
242_L	254_D	0.588	0.96
110_G	114_A	0.587	0.96
201_T	232_C	0.586	0.96
276_P	280_V	0.583	0.96
126_T	197_A	0.583	0.96
9_L	60_K	0.580	0.96
267_F	275_F	0.580	0.96
170_R	174_N	0.577	0.95
142_Q	146_E	0.576	0.95
223_L	245_A	0.574	0.95
8_E	271_T	0.573	0.95
264_A	280_V	0.572	0.95
238_M	254_D	0.571	0.95
117_E	281_K	0.571	0.95
35_L	273_K	0.571	0.95
197_A	200_L	0.571	0.95
118_S	251_K	0.570	0.95
202_N	233_V	0.570	0.95
210_P	213_N	0.570	0.95
266_Q	270_W	0.570	0.95
127_M	199_I	0.566	0.95
51_G	58_A	0.566	0.95
223_L	248_A	0.565	0.95
268_T	275_F	0.565	0.95
75_C	85_A	0.564	0.95
29_A	275_F	0.563	0.95
235_N	259_L	0.561	0.95
209_K	235_N	0.560	0.95
115_I	143_G	0.559	0.95
87_L	170_R	0.556	0.94
94_I	103_G	0.555	0.94
206_V	233_V	0.555	0.94
200_L	229_V	0.552	0.94
54_E	58_A	0.547	0.94
60_K	96_N	0.546	0.94
124_G	149_K	0.544	0.94
17_I	235_N	0.544	0.94
12_L	20_S	0.544	0.94
30_L	270_W	0.544	0.94
123_K	147_G	0.542	0.94
27_N	36_P	0.541	0.94
24_E	41_A	0.540	0.94
16_P	70_N	0.540	0.94
68_M	233_V	0.539	0.94
213_N	240_K	0.538	0.93
121_D	125_K	0.536	0.93
237_H	256_Y	0.534	0.93
9_L	55_G	0.533	0.93
27_N	40_M	0.533	0.93
204_T	208_M	0.533	0.93
61_M	64_T	0.532	0.93
53_I	101_L	0.531	0.93
135_A	138_A	0.531	0.93
66_V	94_I	0.531	0.93
207_G	210_P	0.528	0.93
84_A	141_A	0.528	0.93
108_G	139_I	0.527	0.93
129_L	143_G	0.527	0.93
9_L	41_A	0.527	0.93
141_A	171_V	0.527	0.93
17_I	67_S	0.524	0.93
22_S	259_L	0.524	0.93
96_N	100_Y	0.520	0.92
115_I	228_L	0.520	0.92
87_L	174_N	0.520	0.92
38_T	41_A	0.519	0.92
129_L	203_G	0.519	0.92
139_I	201_T	0.517	0.92
84_A	108_G	0.515	0.92
118_S	230_T	0.515	0.92
22_S	234_Y	0.513	0.92
153_L	168_A	0.511	0.92
132_A	136_S	0.509	0.91
65_G	93_T	0.506	0.91
277_L	281_K	0.505	0.91
87_L	144_A	0.503	0.91
130_L	218_N	0.500	0.91

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
3t4eA	2	0.9896	100	0.205	Contact Map
1npyA	1	0.9236	100	0.208	Contact Map
4xijA	1	0.9236	100	0.227	Contact Map
3tnlA	2	0.9757	100	0.237	Contact Map
2o7sA	2	0.9062	100	0.264	Contact Map
3phhA	1	0.875	100	0.273	Contact Map
3jyoA	2	0.9583	100	0.277	Contact Map
3fbtA	2	0.9271	100	0.285	Contact Map
3pwzA	1	0.9306	100	0.289	Contact Map
2d5cA	2	0.9062	100	0.294	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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