YDEH - ECOLI - GREMLIN Contacts

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YDEH - Diguanylate cyclase YdeH

UniProt:	P31129	Sequences: MIKKTTEIDAILLNLNKAIDAHYQWLVSMFHSVVARDASKPEITDNHSYGLCQFGRWIDHLGPLDNDELPYVRLMDSAHQHMHNCGRELMLAIVENHWQDAHFDAFQEGLLSFTAALTDYKIYLLTIRSNMDVLTGLPGRRVLDESFDHQLRNAEPLNLYLMLLDIDRFKLVNDTYGHLIGDVVLRTLATYLASWTRDYETVYRYGGEEFIIIVKAANDEEACRAGVRICQLVDNHAITHSEGHINITVTAGVSRAFPEEPLDVVIGRADRAMYEGKQTGRNRCMFIDEQNVINRV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11643
Length:	296 (267)
Sequences:	20879 (17923)
Seq/√Len:	1096.9

ECOLI - YDEH YEGE DOSC YDAM YEDQ GMR DOSP YEAJ YLIF YCDT YEAI YEAP YFGF YFIN CSRD YNEF YFEA ADRA YHJK YLIE YLAB YJCC RTN
BACSU - YKOW YTRP YHCK YDAK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
127_I	131_M	4.170	1.00
197_R	200_E	2.986	1.00
162_M	226_G	2.877	1.00
138_P	142_V	2.828	1.00
276_G	285_M	2.795	1.00
143_L	211_I	2.733	1.00
168_R	281_R	2.669	1.00
160_Y	255_R	2.629	1.00
147_F	262_L	2.571	1.00
279_T	285_M	2.503	1.00
31_H	115_A	2.339	1.00
162_M	251_A	2.233	1.00
137_L	189_A	2.175	1.00
34_V	112_S	2.073	1.00
142_V	146_S	2.068	1.00
183_V	186_R	2.028	1.00
143_L	203_Y	1.977	1.00
160_Y	222_A	1.975	1.00
126_T	130_N	1.935	1.00
167_D	250_T	1.899	1.00
234_D	282_N	1.885	1.00
261_P	264_V	1.874	1.00
230_C	284_C	1.865	1.00
184_V	247_I	1.840	1.00
146_S	149_H	1.817	1.00
276_G	283_R	1.817	1.00
26_L	45_D	1.805	1.00
275_E	279_T	1.796	1.00
259_E	268_R	1.787	1.00
124_L	128_R	1.745	1.00
225_A	228_R	1.717	1.00
187_T	191_Y	1.713	1.00
233_V	249_V	1.690	1.00
32_S	53_Q	1.665	1.00
150_Q	153_N	1.658	1.00
187_T	190_T	1.649	1.00
275_E	285_M	1.634	1.00
267_G	271_R	1.629	1.00
137_L	202_V	1.627	1.00
130_N	142_V	1.622	1.00
166_I	188_L	1.613	1.00
150_Q	215_K	1.601	1.00
195_W	228_R	1.588	1.00
205_Y	211_I	1.588	1.00
195_W	232_L	1.572	1.00
159_L	256_A	1.556	1.00
91_L	95_E	1.542	1.00
162_M	214_V	1.537	1.00
142_V	145_E	1.534	1.00
192_L	202_V	1.532	1.00
179_L	267_G	1.526	1.00
146_S	201_T	1.521	1.00
37_D	42_E	1.519	1.00
49_Y	52_C	1.518	1.00
146_S	203_Y	1.507	1.00
164_L	249_V	1.449	1.00
127_I	136_G	1.444	1.00
214_V	225_A	1.443	1.00
19_I	23_Y	1.438	1.00
218_N	221_E	1.430	1.00
164_L	251_A	1.423	1.00
279_T	283_R	1.419	1.00
188_L	233_V	1.413	1.00
34_V	43_I	1.400	1.00
32_S	114_T	1.399	1.00
173_N	181_G	1.395	1.00
56_R	92_A	1.383	1.00
248_T	282_N	1.374	1.00
190_T	193_A	1.373	1.00
268_R	287_I	1.371	1.00
48_S	52_C	1.366	1.00
187_T	238_I	1.366	1.00
180_I	183_V	1.353	1.00
196_T	202_V	1.350	1.00
239_T	244_H	1.347	1.00
133_V	141_R	1.344	1.00
227_V	230_C	1.334	1.00
275_E	278_Q	1.327	1.00
163_L	273_M	1.326	1.00
168_R	171_L	1.325	1.00
153_N	215_K	1.324	1.00
232_L	235_N	1.313	1.00
79_H	82_M	1.313	1.00
183_V	187_T	1.313	1.00
253_V	286_F	1.294	1.00
34_V	50_G	1.289	1.00
163_L	205_Y	1.288	1.00
146_S	150_Q	1.285	1.00
130_N	141_R	1.271	1.00
230_C	234_D	1.244	1.00
196_T	212_I	1.243	1.00
122_I	126_T	1.239	1.00
148_D	262_L	1.229	1.00
88_E	96_N	1.227	1.00
223_C	227_V	1.226	1.00
256_A	265_V	1.220	1.00
163_L	266_I	1.219	1.00
130_N	138_P	1.215	1.00
150_Q	159_L	1.205	1.00
223_C	286_F	1.199	1.00
189_A	202_V	1.198	1.00
46_N	50_G	1.198	1.00
180_I	240_H	1.192	1.00
226_G	284_C	1.187	1.00
226_G	253_V	1.186	1.00
91_L	97_H	1.186	1.00
205_Y	266_I	1.179	1.00
194_S	232_L	1.176	1.00
23_Y	27_V	1.163	1.00
254_S	268_R	1.154	1.00
100_D	115_A	1.149	1.00
130_N	145_E	1.145	1.00
223_C	284_C	1.137	1.00
264_V	268_R	1.137	1.00
138_P	201_T	1.134	1.00
240_H	243_G	1.122	1.00
35_A	111_L	1.111	1.00
123_Y	126_T	1.105	1.00
51_L	57_W	1.105	1.00
132_D	204_R	1.105	1.00
29_M	33_V	1.101	1.00
250_T	276_G	1.098	1.00
226_G	251_A	1.096	1.00
254_S	265_V	1.094	1.00
171_L	175_T	1.089	1.00
72_V	76_D	1.087	1.00
22_H	26_L	1.086	1.00
128_R	141_R	1.083	1.00
122_I	125_L	1.080	1.00
87_R	101_A	1.075	1.00
159_L	213_I	1.070	1.00
148_D	152_R	1.069	1.00
170_K	174_D	1.067	1.00
88_E	98_W	1.061	1.00
145_E	149_H	1.060	1.00
46_N	51_L	1.057	1.00
166_I	249_V	1.055	1.00
42_E	65_D	1.055	1.00
172_V	184_V	1.049	1.00
271_R	287_I	1.047	1.00
32_S	47_H	1.042	1.00
93_I	97_H	1.040	1.00
51_L	58_I	1.036	1.00
131_M	142_V	1.032	1.00
231_Q	234_D	1.027	1.00
270_D	274_Y	1.022	1.00
217_A	221_E	1.017	1.00
36_R	112_S	1.017	1.00
230_C	282_N	1.017	1.00
254_S	269_A	1.016	1.00
154_A	159_L	1.015	1.00
227_V	231_Q	1.012	1.00
140_R	144_D	1.008	1.00
100_D	120_Y	1.002	1.00
67_D	71_Y	1.002	1.00
186_R	190_T	1.001	1.00
27_V	48_S	1.001	1.00
57_W	60_H	1.000	1.00
222_A	253_V	0.998	1.00
37_D	40_K	0.995	1.00
159_L	265_V	0.994	1.00
169_F	185_L	0.992	1.00
48_S	51_L	0.988	1.00
21_A	35_A	0.987	1.00
260_E	268_R	0.984	1.00
253_V	284_C	0.976	1.00
222_A	226_G	0.969	1.00
167_D	281_R	0.967	1.00
58_I	62_G	0.961	1.00
56_R	60_H	0.958	1.00
230_C	251_A	0.954	1.00
178_H	270_D	0.947	1.00
144_D	263_D	0.945	1.00
101_A	114_T	0.945	1.00
142_V	201_T	0.941	1.00
163_L	211_I	0.941	1.00
131_M	138_P	0.931	1.00
176_Y	243_G	0.929	1.00
45_D	58_I	0.925	1.00
144_D	262_L	0.916	1.00
94_V	97_H	0.916	1.00
256_A	259_E	0.914	1.00
90_M	96_N	0.910	1.00
124_L	127_I	0.908	1.00
164_L	212_I	0.898	1.00
36_R	43_I	0.897	1.00
280_G	283_R	0.896	1.00
226_G	230_C	0.892	1.00
135_T	185_L	0.890	1.00
161_L	266_I	0.890	1.00
143_L	213_I	0.889	1.00
133_V	144_D	0.887	1.00
211_I	266_I	0.886	1.00
79_H	83_H	0.880	1.00
154_A	256_A	0.878	1.00
144_D	148_D	0.878	1.00
162_M	253_V	0.877	1.00
191_Y	237_A	0.873	1.00
221_E	224_R	0.872	1.00
196_T	200_E	0.870	1.00
165_D	277_K	0.867	1.00
32_S	50_G	0.867	1.00
157_L	216_A	0.859	1.00
209_E	270_D	0.858	1.00
183_V	241_S	0.858	1.00
224_R	228_R	0.856	1.00
180_I	243_G	0.854	1.00
200_E	225_A	0.852	1.00
164_L	192_L	0.848	1.00
191_Y	238_I	0.842	1.00
151_L	256_A	0.840	1.00
70_P	74_L	0.838	1.00
138_P	203_Y	0.835	1.00
179_L	263_D	0.830	1.00
165_D	208_E	0.830	1.00
22_H	25_W	0.830	1.00
50_G	54_F	0.829	1.00
206_G	209_E	0.826	1.00
147_F	213_I	0.826	1.00
176_Y	245_I	0.823	1.00
252_G	269_A	0.818	1.00
37_D	44_T	0.816	1.00
191_Y	232_L	0.815	1.00
142_V	203_Y	0.811	1.00
98_W	121_K	0.807	1.00
196_T	229_I	0.807	1.00
262_L	266_I	0.803	1.00
207_G	274_Y	0.796	1.00
24_Q	28_S	0.795	1.00
258_P	286_F	0.793	1.00
219_D	255_R	0.790	1.00
117_L	121_K	0.789	1.00
162_M	212_I	0.786	1.00
170_K	274_Y	0.785	1.00
172_V	245_I	0.784	1.00
143_L	147_F	0.783	1.00
264_V	267_G	0.781	1.00
179_L	183_V	0.777	1.00
160_Y	253_V	0.775	1.00
69_L	72_V	0.775	1.00
77_S	80_Q	0.773	1.00
260_E	264_V	0.762	1.00
163_L	269_A	0.762	1.00
196_T	225_A	0.750	1.00
103_F	110_L	0.750	1.00
276_G	280_G	0.748	1.00
255_R	286_F	0.748	1.00
34_V	114_T	0.748	1.00
111_L	116_A	0.746	1.00
184_V	238_I	0.744	1.00
238_I	247_I	0.741	1.00
173_N	207_G	0.740	1.00
31_H	49_Y	0.730	1.00
237_A	246_N	0.729	1.00
271_R	275_E	0.729	1.00
86_G	121_K	0.727	1.00
46_N	61_L	0.726	1.00
68_E	72_V	0.723	1.00
186_R	189_A	0.722	1.00
127_I	130_N	0.721	1.00
26_L	33_V	0.714	1.00
71_Y	74_L	0.713	1.00
165_D	274_Y	0.713	1.00
214_V	222_A	0.712	1.00
39_S	42_E	0.711	1.00
217_A	222_A	0.711	1.00
112_S	116_A	0.708	1.00
192_L	229_I	0.707	1.00
167_D	248_T	0.703	1.00
202_V	212_I	0.700	1.00
20_D	24_Q	0.699	1.00
160_Y	226_G	0.698	1.00
36_R	110_L	0.690	1.00
154_A	158_N	0.689	1.00
191_Y	195_W	0.687	1.00
222_A	255_R	0.685	1.00
32_S	49_Y	0.683	1.00
258_P	268_R	0.680	1.00
63_P	66_N	0.678	1.00
239_T	242_E	0.677	1.00
231_Q	235_N	0.675	1.00
36_R	66_N	0.670	1.00
134_L	185_L	0.666	1.00
161_L	265_V	0.664	1.00
78_A	82_M	0.664	1.00
173_N	182_D	0.663	1.00
240_H	245_I	0.661	1.00
220_E	223_C	0.660	1.00
192_L	212_I	0.659	1.00
193_A	202_V	0.657	1.00
77_S	81_H	0.653	1.00
146_S	213_I	0.652	1.00
50_G	114_T	0.647	1.00
140_R	182_D	0.644	1.00
147_F	151_L	0.641	1.00
183_V	240_H	0.638	1.00
60_H	92_A	0.636	1.00
251_A	284_C	0.632	1.00
35_A	45_D	0.630	1.00
70_P	73_R	0.628	1.00
99_Q	114_T	0.627	1.00
110_L	113_F	0.625	1.00
212_I	229_I	0.624	1.00
190_T	194_S	0.624	1.00
134_L	186_R	0.623	1.00
93_I	96_N	0.618	1.00
227_V	284_C	0.618	1.00
200_E	214_V	0.618	1.00
219_D	223_C	0.615	1.00
268_R	272_A	0.614	1.00
161_L	211_I	0.610	1.00
153_N	157_L	0.610	1.00
180_I	245_I	0.608	1.00
272_A	287_I	0.608	1.00
184_V	240_H	0.605	1.00
172_V	180_I	0.601	1.00
69_L	75_M	0.601	1.00
197_R	225_A	0.601	1.00
68_E	71_Y	0.600	1.00
144_D	203_Y	0.600	1.00
125_L	128_R	0.600	1.00
155_E	260_E	0.599	1.00
188_L	247_I	0.599	1.00
48_S	58_I	0.599	1.00
237_A	244_H	0.598	1.00
160_Y	217_A	0.598	1.00
86_G	100_D	0.598	1.00
151_L	159_L	0.598	1.00
71_Y	76_D	0.597	1.00
150_Q	201_T	0.596	1.00
233_V	238_I	0.595	1.00
25_W	28_S	0.593	1.00
24_Q	27_V	0.592	1.00
141_R	144_D	0.590	1.00
129_S	139_G	0.589	1.00
188_L	192_L	0.589	1.00
136_G	186_R	0.585	1.00
250_T	281_R	0.585	1.00
174_D	274_Y	0.585	1.00
25_W	111_L	0.583	1.00
165_D	173_N	0.579	1.00
178_H	274_Y	0.577	1.00
70_P	76_D	0.574	1.00
69_L	73_R	0.572	1.00
197_R	228_R	0.571	1.00
263_D	267_G	0.570	1.00
74_L	78_A	0.569	1.00
157_L	199_Y	0.568	1.00
78_A	83_H	0.567	1.00
69_L	74_L	0.566	1.00
103_F	106_F	0.563	1.00
184_V	208_E	0.563	1.00
172_V	240_H	0.561	1.00
217_A	255_R	0.560	1.00
230_C	249_V	0.558	1.00
179_L	241_S	0.554	1.00
110_L	114_T	0.552	1.00
150_Q	213_I	0.548	1.00
167_D	280_G	0.548	1.00
149_H	153_N	0.548	1.00
24_Q	111_L	0.548	1.00
29_M	32_S	0.547	1.00
19_I	22_H	0.547	1.00
123_Y	127_I	0.547	1.00
78_A	81_H	0.547	1.00
176_Y	180_I	0.545	1.00
143_L	205_Y	0.541	1.00
35_A	44_T	0.541	1.00
131_M	137_L	0.535	1.00
145_E	148_D	0.535	1.00
103_F	112_S	0.532	1.00
72_V	78_A	0.531	1.00
178_H	181_G	0.531	1.00
211_I	269_A	0.530	1.00
33_V	113_F	0.529	1.00
25_W	35_A	0.528	1.00
33_V	45_D	0.528	1.00
259_E	264_V	0.526	1.00
150_Q	154_A	0.525	1.00
21_A	25_W	0.524	1.00
146_S	215_K	0.524	1.00
153_N	156_P	0.523	1.00
36_R	103_F	0.522	1.00
166_I	185_L	0.519	1.00
149_H	215_K	0.517	1.00
69_L	76_D	0.515	1.00
188_L	238_I	0.514	1.00
23_Y	45_D	0.513	1.00
201_T	213_I	0.513	1.00
272_A	276_G	0.509	1.00
163_L	208_E	0.509	1.00
26_L	47_H	0.508	1.00
43_I	47_H	0.508	1.00
156_P	199_Y	0.508	1.00
46_N	54_F	0.507	1.00
268_R	271_R	0.506	1.00
73_R	76_D	0.503	1.00
155_E	256_A	0.502	1.00
25_W	29_M	0.502	1.00
56_R	61_L	0.500	1.00

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
4h54A	2	0.9358	100	0.35	Contact Map
1w25A	2	0.9797	100	0.367	Contact Map
4j40A	2	0.0068	100	0.405	Contact Map
3tvkA	1	0.5777	100	0.415	Contact Map
3pjxA	1	0.598	100	0.416	Contact Map
3mtkA	2	0.5473	100	0.418	Contact Map
3ezuA	2	0.8682	100	0.428	Contact Map
3ignA	1	0.5507	100	0.436	Contact Map
4rnhA	2	0.5473	100	0.437	Contact Map
3i5cA	2	0.6351	100	0.442	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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