KDGD - BACSU - GREMLIN Contacts

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KDGD - Probable 5-dehydro-4-deoxyglucarate dehydratase

UniProt:	P42235	Sequences: MSRIRKAPAGILGFPVAPFNTQGKLEEEALFQNIEFLLNEGLEAIFIACGSGEFQSLSQKEYEQMVEVAVSAAGGKVPVYTGVGGNLSTALDWAQLSEKKGADGYLILPPYLVHGEQEGLYQYAKTIIESTDLNAILYQRDNAVLSVEQIKRLTECEQLVGVKDGVGNMDLNINLVYTIGDRLGWLNGMPMAEVTMPAYLPIGFHSYSSAISNYIPHISRMFYDALKNGNDELVKELYRHVILPINDIRKQRKGYAVSLIKAGMEIMGLNVRNTARPPVGPVEKDHYQQLEAILKQAADRFPKKAATV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	308 (283)
Sequences:	10374 (6868)
Seq/√Len:	408.3

ECOLI - DAPA YAGE YJHH NANA
BACSU - KDGD DAPA
HALSA - DAPAL
SULSO - Q97UF0 Q97UI2 Q97WF2 KDGA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
230_N	233_L	3.803	1.00
35_E	72_A	3.294	1.00
20_N	24_K	3.138	1.00
121_Y	152_R	3.087	1.00
266_I	291_E	3.025	1.00
31_F	72_A	2.786	1.00
27_E	64_Q	2.733	1.00
27_E	68_V	2.614	1.00
98_E	132_D	2.584	1.00
31_F	68_V	2.575	1.00
63_E	96_L	2.497	1.00
225_A	233_L	2.468	1.00
83_V	94_A	2.456	1.00
199_Y	204_F	2.374	1.00
94_A	105_Y	2.267	1.00
233_L	236_E	2.119	1.00
35_E	76_K	2.063	1.00
125_K	156_C	2.024	1.00
224_D	228_N	2.011	1.00
12_L	44_A	1.991	1.00
225_A	230_N	1.991	1.00
129_E	156_C	1.961	1.00
36_F	40_E	1.956	1.00
220_R	224_D	1.950	1.00
151_K	178_T	1.948	1.00
117_Q	149_Q	1.927	1.00
117_Q	146_S	1.918	1.00
200_L	226_L	1.917	1.00
87_L	123_Y	1.903	1.00
64_Q	67_E	1.881	1.00
291_E	295_K	1.865	1.00
26_E	29_A	1.862	1.00
43_E	224_D	1.847	1.00
125_K	129_E	1.844	1.00
262_A	287_Y	1.823	1.00
35_E	39_N	1.818	1.00
59_Q	89_T	1.817	1.00
118_E	122_Q	1.808	1.00
144_V	171_L	1.796	1.00
31_F	71_S	1.766	1.00
218_I	240_H	1.758	1.00
121_Y	125_K	1.751	1.00
118_E	152_R	1.730	1.00
40_E	217_H	1.721	1.00
34_I	69_A	1.686	1.00
70_V	79_V	1.669	1.00
67_E	71_S	1.658	1.00
136_I	161_G	1.652	1.00
30_L	69_A	1.648	1.00
64_Q	68_V	1.645	1.00
13_G	212_S	1.616	1.00
128_I	156_C	1.614	1.00
265_E	273_N	1.608	1.00
29_A	32_Q	1.595	1.00
122_Q	125_K	1.570	1.00
288_Q	291_E	1.566	1.00
150_I	162_V	1.566	1.00
107_I	127_I	1.565	1.00
61_E	276_R	1.560	1.00
47_I	69_A	1.528	1.00
68_V	72_A	1.513	1.00
94_A	131_T	1.506	1.00
66_V	81_T	1.487	1.00
146_S	149_Q	1.484	1.00
18_P	30_L	1.468	1.00
38_L	77_V	1.453	1.00
236_E	240_H	1.449	1.00
30_L	65_M	1.427	1.00
90_A	127_I	1.380	1.00
221_M	225_A	1.376	1.00
122_Q	126_T	1.365	1.00
98_E	131_T	1.358	1.00
284_K	287_Y	1.356	1.00
288_Q	292_A	1.349	1.00
284_K	288_Q	1.342	1.00
16_V	264_M	1.340	1.00
43_E	220_R	1.340	1.00
265_E	270_N	1.334	1.00
221_M	233_L	1.331	1.00
251_Q	289_Q	1.327	1.00
262_A	266_I	1.325	1.00
96_L	99_K	1.314	1.00
85_G	90_A	1.313	1.00
12_L	46_F	1.311	1.00
98_E	133_L	1.295	1.00
59_Q	92_D	1.289	1.00
68_V	71_S	1.281	1.00
217_H	221_M	1.271	1.00
270_N	273_N	1.264	1.00
9_A	227_K	1.263	1.00
36_F	269_L	1.255	1.00
283_E	286_H	1.254	1.00
174_N	178_T	1.254	1.00
63_E	92_D	1.243	1.00
91_L	126_T	1.224	1.00
197_P	234_V	1.220	1.00
292_A	296_Q	1.219	1.00
136_I	208_S	1.216	1.00
176_V	185_W	1.212	1.00
53_E	261_K	1.212	1.00
80_Y	104_G	1.211	1.00
11_I	42_L	1.208	1.00
63_E	67_E	1.205	1.00
86_N	89_T	1.201	1.00
105_Y	131_T	1.196	1.00
226_L	231_D	1.195	1.00
66_V	97_S	1.178	1.00
60_K	64_Q	1.176	1.00
59_Q	96_L	1.168	1.00
126_T	277_P	1.167	1.00
34_I	73_A	1.148	1.00
38_L	76_K	1.147	1.00
128_I	158_Q	1.144	1.00
24_K	88_S	1.140	1.00
48_A	65_M	1.137	1.00
223_Y	227_K	1.129	1.00
184_G	205_H	1.124	1.00
126_T	129_E	1.104	1.00
292_A	295_K	1.102	1.00
70_V	103_D	1.102	1.00
231_D	235_K	1.097	1.00
67_E	96_L	1.093	1.00
263_G	294_L	1.086	1.00
20_N	26_E	1.085	1.00
63_E	99_K	1.082	1.00
73_A	79_V	1.082	1.00
95_Q	99_K	1.078	1.00
95_Q	130_S	1.072	1.00
29_A	271_V	1.069	1.00
19_F	57_L	1.067	1.00
221_M	224_D	1.066	1.00
28_E	31_F	1.064	1.00
67_E	100_K	1.061	1.00
126_T	130_S	1.059	1.00
232_E	235_K	1.053	1.00
262_A	265_E	1.051	1.00
148_E	178_T	1.046	1.00
262_A	291_E	1.042	1.00
27_E	31_F	1.042	1.00
152_R	155_E	1.026	1.00
13_G	37_L	1.025	1.00
34_I	72_A	1.024	1.00
81_T	102_A	1.016	1.00
80_Y	136_I	1.016	1.00
21_T	274_T	1.013	1.00
96_L	100_K	1.011	1.00
118_E	121_Y	1.005	1.00
105_Y	133_L	1.004	1.00
118_E	283_E	0.999	1.00
172_N	199_Y	0.992	1.00
83_V	97_S	0.990	1.00
282_V	286_H	0.989	1.00
84_G	108_L	0.989	1.00
233_L	237_L	0.989	1.00
91_L	95_Q	0.977	1.00
282_V	290_L	0.976	1.00
46_F	106_L	0.976	1.00
13_G	42_L	0.976	1.00
9_A	205_H	0.973	1.00
105_Y	135_A	0.970	1.00
201_P	231_D	0.968	1.00
189_M	194_V	0.966	1.00
287_Y	291_E	0.965	1.00
31_F	35_E	0.965	1.00
11_I	220_R	0.964	1.00
59_Q	93_W	0.961	1.00
174_N	247_D	0.958	1.00
153_L	159_L	0.945	1.00
151_K	179_I	0.945	1.00
286_H	289_Q	0.944	1.00
121_Y	149_Q	0.939	1.00
289_Q	292_A	0.938	1.00
91_L	130_S	0.936	1.00
33_N	264_M	0.927	1.00
92_D	96_L	0.926	1.00
139_Q	144_V	0.925	1.00
265_E	287_Y	0.921	1.00
235_K	239_R	0.915	1.00
232_E	236_E	0.915	1.00
117_Q	152_R	0.914	1.00
128_I	135_A	0.913	1.00
70_V	102_A	0.912	1.00
154_T	183_L	0.910	1.00
244_P	296_Q	0.910	1.00
137_L	150_I	0.907	1.00
15_P	37_L	0.906	1.00
211_I	246_N	0.904	1.00
23_G	88_S	0.903	1.00
200_L	223_Y	0.903	1.00
43_E	223_Y	0.903	1.00
60_K	92_D	0.901	1.00
62_Y	93_W	0.898	1.00
19_F	276_R	0.895	1.00
151_K	155_E	0.892	1.00
85_G	89_T	0.890	1.00
83_V	105_Y	0.885	1.00
225_A	237_L	0.880	1.00
122_Q	280_G	0.880	1.00
109_P	143_A	0.879	1.00
293_I	296_Q	0.876	1.00
70_V	100_K	0.876	1.00
38_L	73_A	0.874	1.00
34_I	68_V	0.870	1.00
92_D	95_Q	0.869	1.00
120_L	143_A	0.868	1.00
266_I	295_K	0.867	1.00
209_S	212_S	0.863	1.00
23_G	277_P	0.859	1.00
222_F	237_L	0.857	1.00
79_V	102_A	0.855	1.00
285_D	288_Q	0.850	1.00
196_M	207_Y	0.848	1.00
273_N	287_Y	0.847	1.00
95_Q	98_E	0.847	1.00
248_I	293_I	0.846	1.00
107_I	135_A	0.843	1.00
47_I	65_M	0.843	1.00
26_E	270_N	0.841	1.00
147_V	178_T	0.839	1.00
11_I	207_Y	0.831	1.00
186_L	206_S	0.826	1.00
42_L	216_P	0.826	1.00
87_L	91_L	0.825	1.00
201_P	226_L	0.824	1.00
128_I	159_L	0.823	1.00
11_I	223_Y	0.821	1.00
29_A	270_N	0.814	1.00
201_P	235_K	0.807	1.00
28_E	32_Q	0.806	1.00
285_D	289_Q	0.805	1.00
156_C	159_L	0.804	1.00
198_A	201_P	0.802	1.00
32_Q	269_L	0.799	1.00
23_G	274_T	0.794	1.00
121_Y	156_C	0.793	1.00
60_K	63_E	0.789	1.00
215_I	245_I	0.787	1.00
15_P	45_I	0.782	1.00
66_V	102_A	0.782	1.00
40_E	216_P	0.775	1.00
273_N	281_P	0.770	1.00
48_A	81_T	0.770	1.00
147_V	171_L	0.768	1.00
265_E	271_V	0.767	1.00
147_V	174_N	0.766	1.00
11_I	212_S	0.764	1.00
243_L	247_D	0.764	1.00
97_S	102_A	0.763	1.00
50_G	112_L	0.763	1.00
266_I	287_Y	0.757	1.00
147_V	151_K	0.756	1.00
88_S	92_D	0.755	1.00
229_G	232_E	0.751	1.00
66_V	100_K	0.748	1.00
197_P	226_L	0.748	1.00
15_P	30_L	0.746	1.00
187_N	199_Y	0.744	1.00
57_L	65_M	0.742	1.00
179_I	205_H	0.737	1.00
30_L	34_I	0.735	1.00
215_I	218_I	0.731	1.00
215_I	242_I	0.731	1.00
138_Y	163_K	0.728	1.00
101_G	133_L	0.727	1.00
122_Q	277_P	0.726	1.00
34_I	45_I	0.719	1.00
44_A	80_Y	0.718	1.00
90_A	107_I	0.717	1.00
198_A	202_I	0.705	1.00
221_M	237_L	0.702	1.00
25_L	30_L	0.701	1.00
20_N	28_E	0.699	1.00
45_I	73_A	0.698	1.00
238_Y	243_L	0.698	1.00
78_P	103_D	0.696	1.00
117_Q	148_E	0.694	1.00
73_A	76_K	0.692	1.00
87_L	126_T	0.689	1.00
228_N	233_L	0.686	1.00
109_P	145_L	0.686	1.00
274_T	281_P	0.685	1.00
172_N	185_W	0.684	1.00
150_I	175_L	0.682	1.00
155_E	182_R	0.682	1.00
20_N	274_T	0.681	1.00
251_Q	286_H	0.679	1.00
38_L	72_A	0.676	0.99
174_N	177_Y	0.674	0.99
222_F	226_L	0.674	0.99
83_V	107_I	0.672	0.99
145_L	150_I	0.672	0.99
217_H	267_M	0.672	0.99
36_F	267_M	0.669	0.99
258_S	275_A	0.668	0.99
148_E	174_N	0.668	0.99
218_I	221_M	0.668	0.99
63_E	93_W	0.666	0.99
170_D	194_V	0.666	0.99
59_Q	63_E	0.663	0.99
37_L	42_L	0.660	0.99
173_I	177_Y	0.660	0.99
54_F	82_G	0.659	0.99
155_E	180_G	0.656	0.99
48_A	57_L	0.655	0.99
258_S	282_V	0.653	0.99
116_E	258_S	0.651	0.99
63_E	100_K	0.650	0.99
73_A	77_V	0.649	0.99
275_A	279_V	0.648	0.99
37_L	40_E	0.647	0.99
63_E	97_S	0.646	0.99
125_K	152_R	0.645	0.99
12_L	80_Y	0.645	0.99
196_M	222_F	0.644	0.99
271_V	274_T	0.644	0.99
33_N	37_L	0.644	0.99
20_N	23_G	0.642	0.99
137_L	145_L	0.640	0.99
144_V	168_N	0.639	0.99
8_P	104_G	0.638	0.99
58_S	88_S	0.638	0.99
139_Q	164_D	0.638	0.99
15_P	69_A	0.636	0.99
266_I	294_L	0.635	0.99
119_G	280_G	0.634	0.99
289_Q	293_I	0.633	0.99
172_N	176_V	0.630	0.99
176_V	179_I	0.627	0.99
288_Q	295_K	0.625	0.99
55_Q	113_V	0.625	0.99
173_I	202_I	0.623	0.99
154_T	179_I	0.623	0.99
25_L	65_M	0.623	0.99
252_R	286_H	0.621	0.99
67_E	99_K	0.620	0.99
264_M	267_M	0.620	0.99
197_P	231_D	0.620	0.99
89_T	92_D	0.618	0.99
176_V	205_H	0.615	0.99
50_G	138_Y	0.614	0.99
132_D	158_Q	0.613	0.99
198_A	238_Y	0.613	0.99
264_M	269_L	0.611	0.99
66_V	70_V	0.610	0.99
177_Y	239_R	0.608	0.99
225_A	228_N	0.608	0.99
293_I	297_A	0.603	0.99
35_E	38_L	0.596	0.99
48_A	62_Y	0.595	0.99
263_G	266_I	0.594	0.99
173_I	238_Y	0.594	0.99
282_V	287_Y	0.591	0.99
27_E	72_A	0.590	0.99
136_I	160_V	0.585	0.99
47_I	79_V	0.580	0.98
25_L	68_V	0.577	0.98
116_E	119_G	0.577	0.98
197_P	238_Y	0.577	0.98
179_I	182_R	0.576	0.98
9_A	43_E	0.575	0.98
164_D	172_N	0.574	0.98
200_L	227_K	0.568	0.98
253_K	259_L	0.568	0.98
21_T	271_V	0.567	0.98
262_A	275_A	0.566	0.98
224_D	227_K	0.565	0.98
145_L	149_Q	0.565	0.98
149_Q	152_R	0.565	0.98
275_A	280_G	0.565	0.98
214_Y	263_G	0.563	0.98
148_E	151_K	0.560	0.98
41_G	220_R	0.558	0.98
75_G	103_D	0.555	0.98
14_F	210_A	0.553	0.98
160_V	184_G	0.549	0.98
161_G	184_G	0.547	0.98
129_E	158_Q	0.546	0.98
16_V	260_I	0.544	0.98
226_L	234_V	0.543	0.98
102_A	133_L	0.542	0.98
71_S	74_G	0.542	0.98
80_Y	106_L	0.542	0.98
42_L	220_R	0.540	0.98
218_I	237_L	0.539	0.98
109_P	124_A	0.538	0.97
19_F	61_E	0.538	0.97
284_K	291_E	0.538	0.97
60_K	96_L	0.537	0.97
169_M	195_T	0.536	0.97
46_F	80_Y	0.535	0.97
225_A	234_V	0.533	0.97
94_A	127_I	0.531	0.97
214_Y	260_I	0.529	0.97
173_I	198_A	0.527	0.97
168_N	171_L	0.527	0.97
14_F	209_S	0.527	0.97
118_E	280_G	0.525	0.97
236_E	239_R	0.525	0.97
237_L	240_H	0.523	0.97
81_T	97_S	0.523	0.97
210_A	260_I	0.522	0.97
116_E	252_R	0.522	0.97
196_M	219_S	0.522	0.97
196_M	223_Y	0.521	0.97
123_Y	126_T	0.520	0.97
177_Y	244_P	0.518	0.97
33_N	269_L	0.518	0.97
124_A	159_L	0.517	0.97
14_F	190_P	0.516	0.97
90_A	94_A	0.516	0.97
24_K	64_Q	0.515	0.97
48_A	66_V	0.512	0.97
49_C	138_Y	0.511	0.97
85_G	93_W	0.511	0.97
185_W	199_Y	0.510	0.97
107_I	124_A	0.510	0.97
15_P	34_I	0.508	0.96
161_G	183_L	0.506	0.96
62_Y	89_T	0.505	0.96
249_R	260_I	0.505	0.96
91_L	127_I	0.504	0.96
263_G	290_L	0.504	0.96
36_F	216_P	0.503	0.96
62_Y	96_L	0.500	0.96

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
4i7wA	3	0.9286	100	0.089	Contact Map
3si9A	3	0.9383	100	0.089	Contact Map
3na8A	3	0.9286	100	0.093	Contact Map
3eb2A	3	0.9318	100	0.094	Contact Map
2ojpA	2	0.9286	100	0.094	Contact Map
3l21A	5	0.9448	100	0.095	Contact Map
4oe7A	3	0.9383	100	0.096	Contact Map
4fhaA	3	0.9578	100	0.096	Contact Map
3qzeA	2	0.9286	100	0.097	Contact Map
4pfmA	2	0.9416	100	0.097	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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