YFCH - ECOLI - GREMLIN Contacts

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YFCH - Epimerase family protein YfcH

UniProt:	P77775	Sequences: MNIVITGGTGLIGRHLIPRLLELGHQITVVTRNPQKASSVLGPRVTLWQGLADQSNLNGVDAVINLAGEPIADKRWTHEQKERLCQSRWNITQKLVDLINASDTPPSVLISGSATGYYGDLGEVVVTEEEPPHNEFTHKLCARWEEIACRAQSDKTRVCLLRTGVVLAPDGGILGKMLPPFRLGLGGPIGSGRQYLAWIHIDDMVNGILWLLDNELRGPFNMVSPYPVRNEQFAHALGHALHRPAILRVPATAIRLLMGESSVLVLGGQRALPKRLEEAGFAFRWYDLEEALADVVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14111
Length:	297 (274)
Sequences:	64767 (45601)
Seq/√Len:	2754.9

ECOLI - YFCH GALE YBJS GM4D RMLB2 RMLB1 FCL HLDD RMLD YEEZ QOR2 ARNA YBJT YRAR
BACSU - YFHF GALE YTCB YFNG RMLB SPSK YTBQ YESF YWNB YHFK YHEG EPSC
HALSA - Q9HSV1 Q9HSU9 Q9HRD1 Q9HSE7 Q9HML4 Q9HS50 Q9HNV3 Q9HPF1 Q9HSQ3 Q9HR86
SULSO - Q97VN5 Q97UM3 Q980W1 Q7LXG5 Q7LXE8 Q97XJ9 Q97XG1 Q7LX44 Q7LXE6 Q97XF9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_G	29_V	3.084	1.00
236_A	289_E	2.893	1.00
19_R	206_N	2.613	1.00
207_G	222_M	2.543	1.00
86_Q	90_N	2.540	1.00
2_N	26_Q	2.536	1.00
62_A	212_L	2.363	1.00
112_G	208_I	2.331	1.00
19_R	209_L	2.260	1.00
218_G	275_R	2.236	1.00
80_Q	83_R	2.192	1.00
54_Q	101_A	2.166	1.00
220_F	278_E	2.146	1.00
19_R	23_L	2.119	1.00
65_N	111_S	2.102	1.00
108_V	157_R	2.101	1.00
30_V	45_V	2.073	1.00
206_N	284_R	2.007	1.00
231_E	235_H	1.996	1.00
28_T	60_V	1.987	1.00
127_T	130_E	1.984	1.00
239_H	289_E	1.982	1.00
49_Q	52_A	1.960	1.00
148_A	158_V	1.951	1.00
4_V	60_V	1.939	1.00
64_I	212_L	1.922	1.00
2_N	28_T	1.919	1.00
93_Q	147_I	1.918	1.00
6_T	65_N	1.894	1.00
45_V	52_A	1.858	1.00
277_E	282_A	1.856	1.00
236_A	239_H	1.845	1.00
163_T	208_I	1.833	1.00
229_R	232_Q	1.824	1.00
23_L	209_L	1.773	1.00
161_L	211_L	1.754	1.00
50_G	97_D	1.748	1.00
206_N	210_W	1.739	1.00
225_P	277_E	1.726	1.00
28_T	43_P	1.716	1.00
142_A	146_E	1.713	1.00
5_I	17_I	1.707	1.00
167_L	291_A	1.689	1.00
85_C	143_R	1.686	1.00
54_Q	98_L	1.655	1.00
93_Q	97_D	1.627	1.00
90_N	93_Q	1.606	1.00
209_L	213_D	1.590	1.00
273_P	277_E	1.549	1.00
236_A	240_A	1.548	1.00
23_L	213_D	1.537	1.00
16_L	64_I	1.524	1.00
3_I	25_H	1.521	1.00
48_W	86_Q	1.519	1.00
19_R	22_E	1.509	1.00
61_D	107_S	1.506	1.00
16_L	205_V	1.492	1.00
92_T	144_W	1.491	1.00
108_V	159_C	1.486	1.00
82_E	86_Q	1.473	1.00
16_L	66_L	1.472	1.00
179_P	183_L	1.466	1.00
210_W	214_N	1.443	1.00
63_V	99_I	1.438	1.00
17_I	29_V	1.433	1.00
52_A	55_S	1.426	1.00
276_L	279_A	1.415	1.00
132_P	142_A	1.414	1.00
50_G	54_Q	1.413	1.00
12_I	166_V	1.410	1.00
163_T	204_M	1.403	1.00
128_E	275_R	1.388	1.00
19_R	205_V	1.387	1.00
66_L	112_G	1.372	1.00
112_G	163_T	1.342	1.00
100_N	154_D	1.341	1.00
137_T	141_C	1.335	1.00
50_G	94_K	1.334	1.00
250_P	253_A	1.328	1.00
113_S	117_Y	1.320	1.00
146_E	149_C	1.311	1.00
54_Q	102_S	1.311	1.00
195_Y	227_P	1.305	1.00
180_P	185_L	1.302	1.00
149_C	160_L	1.298	1.00
96_V	151_A	1.291	1.00
232_Q	235_H	1.289	1.00
25_H	213_D	1.279	1.00
164_G	271_A	1.276	1.00
58_N	102_S	1.276	1.00
18_P	170_D	1.274	1.00
200_H	291_A	1.264	1.00
201_I	205_V	1.253	1.00
8_G	17_I	1.248	1.00
111_S	144_W	1.243	1.00
97_D	100_N	1.217	1.00
62_A	108_V	1.213	1.00
139_K	143_R	1.212	1.00
64_I	208_I	1.208	1.00
47_L	91_I	1.203	1.00
199_I	204_M	1.193	1.00
161_L	208_I	1.193	1.00
88_R	140_L	1.186	1.00
147_I	150_R	1.186	1.00
65_N	92_T	1.185	1.00
4_V	30_V	1.175	1.00
275_R	278_E	1.174	1.00
127_T	272_L	1.167	1.00
20_L	209_L	1.161	1.00
76_W	80_Q	1.143	1.00
111_S	148_A	1.133	1.00
3_I	62_A	1.132	1.00
126_V	130_E	1.123	1.00
3_I	20_L	1.119	1.00
19_R	202_D	1.113	1.00
210_W	279_A	1.107	1.00
118_Y	221_N	1.106	1.00
57_L	60_V	1.104	1.00
95_L	109_L	1.098	1.00
193_R	231_E	1.097	1.00
110_I	161_L	1.092	1.00
207_G	276_L	1.091	1.00
9_T	31_T	1.085	1.00
206_N	281_F	1.084	1.00
129_E	275_R	1.084	1.00
123_E	127_T	1.080	1.00
149_C	158_V	1.080	1.00
218_G	278_E	1.078	1.00
162_R	219_P	1.076	1.00
200_H	285_W	1.075	1.00
94_K	97_D	1.075	1.00
111_S	160_L	1.074	1.00
15_H	201_I	1.073	1.00
123_E	130_E	1.071	1.00
193_R	229_R	1.070	1.00
99_I	109_L	1.069	1.00
15_H	202_D	1.065	1.00
188_P	248_R	1.063	1.00
55_S	58_N	1.056	1.00
197_A	225_P	1.055	1.00
47_L	67_A	1.052	1.00
273_P	283_F	1.048	1.00
238_G	245_A	1.048	1.00
149_C	219_P	1.048	1.00
18_P	22_E	1.047	1.00
235_H	238_G	1.044	1.00
228_V	288_L	1.035	1.00
96_V	109_L	1.030	1.00
97_D	101_A	1.026	1.00
11_L	168_A	1.026	1.00
98_L	101_A	1.024	1.00
238_G	244_P	1.023	1.00
223_V	271_A	1.017	1.00
69_E	87_S	1.015	1.00
90_N	94_K	1.014	1.00
54_Q	58_N	1.013	1.00
173_I	177_M	1.009	1.00
145_E	162_R	1.009	1.00
53_D	98_L	1.009	1.00
98_L	102_S	1.008	1.00
89_W	143_R	1.007	1.00
85_C	89_W	1.007	1.00
6_T	95_L	1.004	1.00
227_P	270_R	0.997	1.00
228_V	232_Q	0.996	1.00
14_R	170_D	0.985	1.00
57_L	98_L	0.981	1.00
166_V	204_M	0.973	1.00
33_N	36_K	0.970	1.00
85_C	90_N	0.970	1.00
30_V	56_N	0.966	1.00
195_Y	229_R	0.965	1.00
84_L	140_L	0.965	1.00
11_L	201_I	0.961	1.00
99_I	106_P	0.956	1.00
87_S	91_I	0.956	1.00
220_F	275_R	0.956	1.00
247_L	250_P	0.955	1.00
100_N	156_T	0.948	1.00
206_N	209_L	0.947	1.00
227_P	268_G	0.936	1.00
28_T	59_G	0.934	1.00
109_L	148_A	0.931	1.00
15_H	18_P	0.930	1.00
66_L	208_I	0.923	1.00
57_L	63_V	0.921	1.00
96_V	148_A	0.920	1.00
162_R	221_N	0.918	1.00
143_R	146_E	0.911	1.00
2_N	25_H	0.910	1.00
167_L	200_H	0.909	1.00
210_W	213_D	0.908	1.00
200_H	203_D	0.906	1.00
2_N	60_V	0.903	1.00
51_L	55_S	0.896	1.00
157_R	216_L	0.892	1.00
15_H	19_R	0.884	1.00
2_N	61_D	0.882	1.00
94_K	98_L	0.879	1.00
195_Y	268_G	0.878	1.00
159_C	211_L	0.878	1.00
285_W	290_E	0.874	1.00
51_L	54_Q	0.872	1.00
176_K	179_P	0.868	1.00
21_L	27_I	0.867	1.00
50_G	101_A	0.866	1.00
203_D	224_S	0.865	1.00
202_D	285_W	0.864	1.00
16_L	20_L	0.863	1.00
30_V	52_A	0.863	1.00
69_E	83_R	0.861	1.00
17_I	27_I	0.858	1.00
238_G	243_R	0.854	1.00
52_A	56_N	0.850	1.00
43_P	56_N	0.848	1.00
100_N	155_K	0.844	1.00
161_L	222_M	0.843	1.00
34_P	44_R	0.840	1.00
33_N	44_R	0.835	1.00
57_L	102_S	0.834	1.00
186_G	248_R	0.831	1.00
166_V	199_I	0.825	1.00
248_R	251_A	0.822	1.00
149_C	152_Q	0.821	1.00
232_Q	236_A	0.821	1.00
115_T	164_G	0.820	1.00
160_L	219_P	0.818	1.00
6_T	67_A	0.818	1.00
124_V	130_E	0.809	1.00
223_V	273_P	0.805	1.00
96_V	147_I	0.805	1.00
63_V	95_L	0.805	1.00
3_I	64_I	0.804	1.00
146_E	150_R	0.802	1.00
176_K	180_P	0.802	1.00
113_S	145_E	0.801	1.00
192_G	231_E	0.797	1.00
81_K	139_K	0.796	1.00
92_T	148_A	0.795	1.00
49_Q	53_D	0.795	1.00
240_A	289_E	0.791	1.00
30_V	53_D	0.791	1.00
274_K	277_E	0.791	1.00
186_G	246_I	0.791	1.00
39_S	42_G	0.788	1.00
115_T	271_A	0.788	1.00
207_G	281_F	0.787	1.00
249_V	253_A	0.785	1.00
206_N	285_W	0.781	1.00
285_W	291_A	0.776	1.00
179_P	182_R	0.769	1.00
83_R	86_Q	0.763	1.00
48_W	87_S	0.757	1.00
85_C	140_L	0.756	1.00
203_D	206_N	0.756	1.00
65_N	95_L	0.748	1.00
91_I	94_K	0.746	1.00
225_P	273_P	0.745	1.00
103_D	106_P	0.743	1.00
100_N	151_A	0.739	1.00
97_D	151_A	0.736	1.00
151_A	154_D	0.736	1.00
211_L	276_L	0.736	1.00
169_P	200_H	0.734	1.00
53_D	94_K	0.732	1.00
181_F	238_G	0.731	1.00
249_V	252_T	0.731	1.00
33_N	38_S	0.728	1.00
135_E	138_H	0.726	1.00
133_H	138_H	0.725	1.00
16_L	208_I	0.721	1.00
143_R	147_I	0.720	1.00
210_W	281_F	0.720	1.00
195_Y	270_R	0.716	1.00
3_I	212_L	0.713	1.00
77_T	84_L	0.711	1.00
69_E	84_L	0.710	1.00
38_S	41_L	0.708	1.00
172_G	175_G	0.703	1.00
38_S	42_G	0.702	1.00
32_R	46_T	0.699	1.00
228_V	233_F	0.698	1.00
188_P	250_P	0.696	1.00
14_R	18_P	0.694	1.00
136_F	139_K	0.693	1.00
15_H	205_V	0.691	1.00
108_V	215_E	0.690	1.00
63_V	109_L	0.690	1.00
25_H	61_D	0.687	1.00
83_R	87_S	0.685	1.00
92_T	96_V	0.684	1.00
210_W	280_G	0.684	1.00
211_L	279_A	0.682	1.00
57_L	99_I	0.681	1.00
231_E	249_V	0.678	1.00
107_S	157_R	0.676	1.00
139_K	146_E	0.676	1.00
144_W	148_A	0.676	1.00
128_E	276_L	0.675	1.00
222_M	276_L	0.673	1.00
147_I	151_A	0.672	1.00
164_G	223_V	0.671	1.00
277_E	283_F	0.669	1.00
125_V	270_R	0.668	1.00
150_R	153_S	0.668	1.00
125_V	272_L	0.665	1.00
12_I	204_M	0.662	1.00
235_H	239_H	0.659	1.00
81_K	136_F	0.652	1.00
122_G	130_E	0.647	1.00
247_L	251_A	0.641	1.00
236_A	288_L	0.637	1.00
163_T	166_V	0.635	1.00
46_T	49_Q	0.631	1.00
102_S	106_P	0.627	1.00
20_L	212_L	0.627	1.00
25_H	62_A	0.627	1.00
184_G	187_G	0.625	1.00
62_A	110_I	0.621	1.00
99_I	102_S	0.619	1.00
127_T	274_K	0.618	1.00
116_G	138_H	0.614	1.00
205_V	209_L	0.614	1.00
15_H	170_D	0.612	1.00
182_R	185_L	0.610	1.00
78_H	136_F	0.608	1.00
183_L	186_G	0.605	1.00
117_Y	145_E	0.605	1.00
85_C	139_K	0.603	1.00
110_I	212_L	0.602	1.00
117_Y	132_P	0.601	1.00
110_I	208_I	0.600	1.00
102_S	107_S	0.599	1.00
45_V	53_D	0.598	1.00
50_G	98_L	0.598	1.00
177_M	181_F	0.597	1.00
238_G	241_L	0.596	1.00
17_I	21_L	0.596	1.00
121_L	126_V	0.593	1.00
4_V	56_N	0.591	1.00
68_G	88_R	0.589	1.00
65_N	109_L	0.586	1.00
177_M	180_P	0.584	1.00
228_V	236_A	0.584	1.00
11_L	15_H	0.583	1.00
233_F	288_L	0.582	1.00
89_W	93_Q	0.582	1.00
204_M	208_I	0.579	1.00
151_A	156_T	0.579	1.00
11_L	170_D	0.578	1.00
2_N	59_G	0.577	1.00
178_L	237_L	0.574	1.00
178_L	182_R	0.571	1.00
5_I	20_L	0.570	1.00
9_T	33_N	0.569	1.00
133_H	142_A	0.568	1.00
165_V	196_L	0.567	1.00
4_V	63_V	0.567	1.00
4_V	57_L	0.565	1.00
194_Q	230_N	0.564	1.00
62_A	107_S	0.562	1.00
23_L	210_W	0.561	1.00
140_L	144_W	0.560	1.00
234_A	238_G	0.560	1.00
124_V	268_G	0.558	1.00
184_G	243_R	0.557	1.00
266_L	269_Q	0.557	1.00
114_A	141_C	0.556	1.00
161_L	207_G	0.556	1.00
21_L	24_G	0.554	1.00
276_L	283_F	0.550	1.00
4_V	45_V	0.548	1.00
157_R	215_E	0.548	1.00
23_L	206_N	0.547	1.00
59_G	102_S	0.547	1.00
171_G	175_G	0.544	1.00
180_P	188_P	0.538	1.00
197_A	224_S	0.538	1.00
139_K	150_R	0.533	1.00
53_D	57_L	0.533	1.00
243_R	246_I	0.531	1.00
93_Q	150_R	0.530	1.00
242_H	245_A	0.529	1.00
47_L	53_D	0.528	1.00
110_I	211_L	0.527	1.00
284_R	290_E	0.527	1.00
15_H	169_P	0.526	1.00
43_P	52_A	0.526	1.00
92_T	111_S	0.526	1.00
69_E	88_R	0.525	1.00
174_L	177_M	0.523	1.00
96_V	100_N	0.522	1.00
121_L	124_V	0.522	1.00
247_L	253_A	0.521	1.00
81_K	85_C	0.520	1.00
132_P	146_E	0.520	1.00
204_M	222_M	0.518	1.00
159_C	220_F	0.518	1.00
50_G	53_D	0.516	1.00
216_L	220_F	0.515	1.00
9_T	29_V	0.514	1.00
56_N	60_V	0.513	1.00
175_G	179_P	0.509	1.00
18_P	202_D	0.507	1.00
220_F	276_L	0.506	1.00
197_A	227_P	0.505	1.00
148_A	160_L	0.504	1.00
117_Y	162_R	0.504	1.00
172_G	176_K	0.503	1.00
57_L	95_L	0.501	1.00
28_T	56_N	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
1rkxA	3	0.9428	100	0.219	Contact Map
1sb8A	2	0.9663	100	0.225	Contact Map
1rpnA	4	0.9596	100	0.227	Contact Map
3rufA	2	0.9529	100	0.228	Contact Map
3m2pA	2	0.9327	100	0.231	Contact Map
1orrA	3	0.9562	100	0.238	Contact Map
3slgA	4	0.9562	100	0.239	Contact Map
3oh8A	1	0.8754	100	0.239	Contact Map
2c20A	2	0.9562	100	0.24	Contact Map
2z1mA	4	0.9832	100	0.24	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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