YFHF - BACSU - GREMLIN Contacts

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YFHF - Epimerase family protein YfhF

UniProt:	O31574	Sequences: MNIAMTGGTGFLGQHLTGVLTRQGHHVYILSRNARETEQKNMTYVQWLSEGAAPEQELPHIDVWINLAGKSIFGRWTEKTKQHILSSRINATREVQRLIQKQKEKPKTLIQASAVGIYGTSLEKTFTEDSATSDEDFLSHTAHLWEKEGQHIEAMGIRTVYARFGVMLGEKGALPLMILPYKFLAGGTIGTGRQWLSWIHVEDAAQMIRYAVENAGISGPMNVTAPNPVDMKQFGKTIARVKHRPHWLPVPEFFLSKALGEMSLLIVKGQRALPKKAITSGFRFTYSDLEFALSQLIADRKTV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	303 (281)
Sequences:	65402 (46076)
Seq/√Len:	2748.6

ECOLI - YFCH GALE RMLB2 RMLB1 YBJS GM4D FCL HLDD RMLD YEEZ QOR2 YBJT YRAR ARNA
BACSU - YFHF YTCB GALE YFNG RMLB SPSK YTBQ YWNB YHFK YESF YHEG
HALSA - Q9HSV1 Q9HSU9 Q9HRD1 Q9HSE7 Q9HS50 Q9HML4 Q9HNV3 Q9HSQ3 Q9HPF1 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
237_T	290_E	2.954	1.00
8_G	29_I	2.901	1.00
19_V	206_Q	2.543	1.00
2_N	26_H	2.510	1.00
86_S	90_N	2.475	1.00
207_M	223_V	2.420	1.00
219_G	276_K	2.338	1.00
112_A	208_I	2.296	1.00
63_V	212_V	2.284	1.00
19_V	209_R	2.229	1.00
55_E	101_K	2.199	1.00
80_T	83_H	2.121	1.00
19_V	23_Q	2.096	1.00
30_L	47_W	2.089	1.00
241_V	294_S	2.082	1.00
108_T	158_R	2.037	1.00
66_N	111_Q	1.996	1.00
221_M	279_T	1.976	1.00
232_K	236_K	1.965	1.00
127_T	130_S	1.961	1.00
206_Q	285_T	1.949	1.00
240_R	290_E	1.932	1.00
28_Y	61_I	1.931	1.00
65_I	212_V	1.894	1.00
93_R	148_E	1.873	1.00
149_G	159_T	1.869	1.00
50_E	53_A	1.869	1.00
4_A	61_I	1.868	1.00
237_T	240_R	1.863	1.00
28_Y	45_V	1.840	1.00
6_T	66_N	1.837	1.00
2_N	28_Y	1.829	1.00
28_Y	43_T	1.828	1.00
164_F	208_I	1.781	1.00
230_D	233_Q	1.772	1.00
23_Q	209_R	1.764	1.00
278_I	283_R	1.736	1.00
26_H	43_T	1.730	1.00
162_A	211_A	1.727	1.00
47_W	53_A	1.718	1.00
202_E	295_Q	1.716	1.00
51_G	97_R	1.701	1.00
143_H	147_K	1.691	1.00
226_P	278_I	1.691	1.00
55_E	98_L	1.665	1.00
206_Q	210_Y	1.661	1.00
5_M	17_T	1.659	1.00
93_R	97_R	1.610	1.00
85_L	144_L	1.592	1.00
209_R	213_E	1.583	1.00
168_L	292_A	1.579	1.00
90_N	93_R	1.565	1.00
62_D	107_K	1.542	1.00
274_P	278_I	1.524	1.00
92_T	145_W	1.521	1.00
3_I	25_H	1.521	1.00
23_Q	213_E	1.520	1.00
51_G	55_E	1.513	1.00
16_L	65_I	1.507	1.00
49_S	86_S	1.499	1.00
200_H	295_Q	1.498	1.00
210_Y	214_N	1.491	1.00
179_L	183_F	1.482	1.00
19_V	22_R	1.467	1.00
237_T	241_V	1.461	1.00
16_L	67_L	1.455	1.00
108_T	160_V	1.443	1.00
82_Q	86_S	1.440	1.00
128_E	276_K	1.438	1.00
53_A	56_Q	1.428	1.00
16_L	205_A	1.423	1.00
164_F	204_A	1.389	1.00
19_V	205_A	1.376	1.00
12_L	167_M	1.364	1.00
64_W	99_I	1.360	1.00
56_Q	60_H	1.359	1.00
132_T	143_H	1.343	1.00
251_P	254_F	1.342	1.00
188_T	249_P	1.339	1.00
67_L	112_A	1.333	1.00
112_A	164_F	1.332	1.00
277_A	280_S	1.324	1.00
33_N	44_Y	1.322	1.00
100_Q	155_M	1.322	1.00
51_G	94_E	1.320	1.00
195_W	228_P	1.319	1.00
147_K	150_Q	1.314	1.00
180_P	185_A	1.307	1.00
59_P	102_Q	1.295	1.00
55_E	102_Q	1.294	1.00
17_T	29_I	1.260	1.00
150_Q	161_Y	1.257	1.00
113_S	117_I	1.256	1.00
96_Q	152_I	1.246	1.00
286_Y	295_Q	1.240	1.00
63_V	108_T	1.234	1.00
111_Q	145_W	1.233	1.00
165_G	272_A	1.229	1.00
25_H	213_E	1.226	1.00
8_G	17_T	1.210	1.00
233_Q	236_K	1.201	1.00
200_H	292_A	1.198	1.00
65_I	208_I	1.187	1.00
138_L	142_A	1.185	1.00
148_E	151_H	1.184	1.00
201_V	205_A	1.182	1.00
18_G	171_K	1.180	1.00
58_L	61_I	1.179	1.00
162_A	208_I	1.179	1.00
123_E	130_S	1.165	1.00
140_H	144_L	1.162	1.00
127_T	273_L	1.162	1.00
76_W	80_T	1.149	1.00
276_K	279_T	1.148	1.00
97_R	100_Q	1.145	1.00
88_R	141_T	1.137	1.00
3_I	63_V	1.137	1.00
4_A	30_L	1.136	1.00
66_N	92_T	1.132	1.00
56_Q	59_P	1.127	1.00
123_E	127_T	1.127	1.00
111_Q	149_G	1.121	1.00
291_F	294_S	1.114	1.00
199_I	204_A	1.113	1.00
20_L	209_R	1.109	1.00
19_V	202_E	1.102	1.00
45_V	60_H	1.100	1.00
3_I	20_L	1.092	1.00
126_F	130_S	1.088	1.00
193_R	230_D	1.088	1.00
193_R	232_K	1.083	1.00
29_I	42_M	1.076	1.00
210_Y	280_S	1.075	1.00
207_M	277_A	1.073	1.00
291_F	295_Q	1.072	1.00
173_A	177_M	1.072	1.00
129_D	276_K	1.067	1.00
239_A	245_P	1.066	1.00
118_Y	222_N	1.065	1.00
98_L	101_K	1.062	1.00
219_G	279_T	1.061	1.00
15_H	202_E	1.052	1.00
111_Q	161_Y	1.051	1.00
110_I	162_A	1.050	1.00
9_T	31_S	1.047	1.00
55_E	59_P	1.043	1.00
239_A	246_H	1.040	1.00
90_N	94_E	1.039	1.00
163_R	220_P	1.039	1.00
94_E	97_R	1.035	1.00
99_I	109_L	1.028	1.00
95_V	109_L	1.025	1.00
224_T	272_A	1.021	1.00
87_S	91_A	1.020	1.00
150_Q	159_T	1.020	1.00
18_G	22_R	1.019	1.00
229_V	289_L	1.018	1.00
229_V	233_Q	1.016	1.00
96_Q	109_L	1.016	1.00
15_H	201_V	1.016	1.00
97_R	101_K	1.011	1.00
236_K	239_A	1.010	1.00
6_T	95_V	1.008	1.00
150_Q	220_P	1.006	1.00
54_P	98_L	1.002	1.00
197_S	226_P	0.998	1.00
186_G	249_P	0.990	1.00
228_P	271_R	0.989	1.00
70_K	87_S	0.989	1.00
274_P	284_F	0.988	1.00
98_L	102_Q	0.987	1.00
206_Q	282_F	0.987	1.00
146_E	163_R	0.984	1.00
21_T	42_M	0.984	1.00
290_E	294_S	0.981	1.00
89_I	144_L	0.979	1.00
34_A	46_Q	0.971	1.00
85_L	90_N	0.966	1.00
228_P	269_G	0.963	1.00
33_N	36_E	0.962	1.00
11_F	169_G	0.959	1.00
85_L	89_I	0.959	1.00
21_T	41_N	0.956	1.00
195_W	230_D	0.955	1.00
58_L	98_L	0.940	1.00
176_L	180_P	0.939	1.00
15_H	18_G	0.935	1.00
200_H	286_Y	0.927	1.00
195_W	269_G	0.923	1.00
210_Y	213_E	0.923	1.00
100_Q	157_I	0.921	1.00
167_M	204_A	0.919	1.00
31_S	44_Y	0.919	1.00
30_L	57_E	0.919	1.00
286_Y	291_F	0.917	1.00
250_V	253_F	0.917	1.00
250_V	254_F	0.915	1.00
58_L	64_W	0.914	1.00
176_L	179_L	0.913	1.00
67_L	208_I	0.911	1.00
84_I	141_T	0.908	1.00
11_F	201_V	0.907	1.00
2_N	62_D	0.906	1.00
51_G	101_K	0.905	1.00
109_L	149_G	0.892	1.00
206_Q	209_R	0.887	1.00
14_Q	171_K	0.884	1.00
162_A	223_V	0.882	1.00
96_Q	149_G	0.882	1.00
2_N	25_H	0.880	1.00
144_L	147_K	0.880	1.00
241_V	290_E	0.874	1.00
15_H	19_V	0.872	1.00
52_A	55_E	0.868	1.00
221_M	276_K	0.866	1.00
239_A	244_R	0.859	1.00
160_V	211_A	0.852	1.00
94_E	98_L	0.850	1.00
233_Q	237_T	0.850	1.00
45_V	57_E	0.849	1.00
64_W	95_V	0.848	1.00
207_M	282_F	0.846	1.00
52_A	56_Q	0.838	1.00
200_H	203_D	0.835	1.00
92_T	149_G	0.835	1.00
30_L	53_A	0.833	1.00
202_E	286_Y	0.833	1.00
17_T	27_V	0.830	1.00
70_K	83_H	0.829	1.00
206_Q	286_Y	0.828	1.00
203_D	225_A	0.824	1.00
224_T	274_P	0.823	1.00
16_L	20_L	0.820	1.00
168_L	200_H	0.820	1.00
2_N	61_I	0.819	1.00
124_K	130_S	0.818	1.00
163_R	222_N	0.817	1.00
100_Q	156_G	0.810	1.00
53_A	57_E	0.808	1.00
58_L	102_Q	0.805	1.00
33_N	46_Q	0.804	1.00
30_L	54_P	0.795	1.00
21_T	27_V	0.794	1.00
6_T	68_A	0.794	1.00
147_K	151_H	0.793	1.00
177_M	180_P	0.789	1.00
28_Y	60_H	0.787	1.00
150_Q	153_E	0.785	1.00
179_L	182_K	0.784	1.00
167_M	199_I	0.781	1.00
96_Q	148_E	0.779	1.00
26_H	41_N	0.778	1.00
102_Q	105_K	0.773	1.00
3_I	65_I	0.771	1.00
192_G	232_K	0.770	1.00
172_G	175_P	0.769	1.00
249_P	252_E	0.767	1.00
115_V	272_A	0.763	1.00
97_R	152_I	0.761	1.00
226_P	274_P	0.760	1.00
115_V	165_G	0.759	1.00
66_N	95_V	0.754	1.00
186_G	247_W	0.752	1.00
83_H	86_S	0.749	1.00
3_I	212_V	0.749	1.00
81_K	140_H	0.747	1.00
161_Y	220_P	0.746	1.00
151_H	154_A	0.743	1.00
113_S	146_E	0.742	1.00
85_L	141_T	0.737	1.00
136_D	139_S	0.737	1.00
210_Y	282_F	0.735	1.00
107_K	158_R	0.735	1.00
49_S	87_S	0.734	1.00
275_K	278_I	0.733	1.00
241_V	293_L	0.733	1.00
203_D	206_Q	0.730	1.00
32_R	48_L	0.728	1.00
144_L	148_E	0.725	1.00
50_E	54_P	0.725	1.00
152_I	155_M	0.723	1.00
182_K	185_A	0.722	1.00
100_Q	152_I	0.720	1.00
181_Y	239_A	0.715	1.00
64_W	109_L	0.715	1.00
92_T	96_Q	0.715	1.00
91_A	94_E	0.713	1.00
248_L	251_P	0.712	1.00
15_H	205_A	0.707	1.00
33_N	38_E	0.704	1.00
286_Y	292_A	0.702	1.00
102_Q	106_P	0.701	1.00
70_K	84_I	0.701	1.00
99_I	105_K	0.700	1.00
54_P	94_E	0.696	1.00
137_F	140_H	0.696	1.00
54_P	58_L	0.693	1.00
174_L	177_M	0.691	1.00
99_I	106_P	0.690	1.00
39_Q	42_M	0.687	1.00
119_G	133_S	0.684	1.00
148_E	152_I	0.683	1.00
243_H	246_H	0.677	1.00
25_H	62_D	0.675	1.00
249_P	254_F	0.675	1.00
211_A	280_S	0.674	1.00
16_L	208_I	0.674	1.00
195_W	271_R	0.673	1.00
236_K	240_R	0.672	1.00
125_T	271_R	0.672	1.00
232_K	250_V	0.671	1.00
117_I	132_T	0.668	1.00
229_V	234_F	0.668	1.00
164_F	167_M	0.667	1.00
83_H	87_S	0.663	1.00
170_E	200_H	0.663	1.00
210_Y	281_G	0.663	1.00
125_T	273_L	0.663	1.00
237_T	289_L	0.662	1.00
77_T	84_I	0.658	1.00
106_P	158_R	0.654	1.00
278_I	284_F	0.654	1.00
140_H	147_K	0.653	1.00
188_T	251_P	0.651	1.00
121_S	126_F	0.650	1.00
159_T	218_S	0.648	1.00
211_A	277_A	0.648	1.00
223_V	277_A	0.645	1.00
128_E	277_A	0.644	1.00
51_G	98_L	0.642	1.00
134_D	139_S	0.639	1.00
58_L	99_I	0.636	1.00
127_T	275_K	0.632	1.00
14_Q	18_G	0.628	1.00
170_E	295_Q	0.627	1.00
175_P	179_L	0.624	1.00
145_W	149_G	0.624	1.00
12_L	204_A	0.623	1.00
175_P	180_P	0.623	1.00
205_A	209_R	0.619	1.00
165_G	224_T	0.617	1.00
122_L	130_S	0.616	1.00
177_M	181_Y	0.615	1.00
81_K	137_F	0.612	1.00
25_H	63_V	0.612	1.00
173_A	181_Y	0.610	1.00
78_E	137_F	0.608	1.00
20_L	212_V	0.608	1.00
23_Q	210_Y	0.607	1.00
63_V	110_I	0.606	1.00
99_I	102_Q	0.606	1.00
11_F	15_H	0.603	1.00
178_I	182_K	0.600	1.00
239_A	242_K	0.599	1.00
24_G	27_V	0.598	1.00
85_L	140_H	0.598	1.00
43_T	60_H	0.598	1.00
152_I	157_I	0.595	1.00
17_T	21_T	0.588	1.00
234_F	289_L	0.588	1.00
15_H	171_K	0.587	1.00
4_A	47_W	0.587	1.00
158_R	217_I	0.586	1.00
89_I	93_R	0.583	1.00
102_Q	107_K	0.581	1.00
4_A	58_L	0.581	1.00
235_G	239_A	0.581	1.00
184_L	244_R	0.580	1.00
229_V	237_T	0.577	1.00
66_N	109_L	0.576	1.00
194_Q	231_M	0.573	1.00
110_I	212_V	0.571	1.00
116_G	139_S	0.571	1.00
204_A	208_I	0.570	1.00
141_T	145_W	0.570	1.00
63_V	107_K	0.569	1.00
5_M	20_L	0.567	1.00
124_K	269_G	0.564	1.00
69_G	88_R	0.561	1.00
23_Q	206_Q	0.560	1.00
110_I	208_I	0.560	1.00
4_A	64_W	0.551	1.00
29_I	44_Y	0.550	1.00
172_G	176_L	0.550	1.00
96_Q	100_Q	0.549	1.00
117_I	146_E	0.547	1.00
184_L	187_G	0.544	1.00
132_T	147_K	0.543	1.00
9_T	33_N	0.541	1.00
183_F	186_G	0.539	1.00
31_S	35_R	0.538	1.00
197_S	228_P	0.535	1.00
285_T	291_F	0.534	1.00
4_A	57_E	0.529	1.00
121_S	124_K	0.525	1.00
173_A	180_P	0.524	1.00
45_V	53_A	0.524	1.00
99_I	107_K	0.523	1.00
216_G	279_T	0.523	1.00
57_E	60_H	0.521	1.00
70_K	88_R	0.520	1.00
162_A	207_M	0.519	1.00
35_R	38_E	0.516	1.00
277_A	284_F	0.514	1.00
140_H	151_H	0.514	1.00
110_I	211_A	0.514	1.00
151_H	155_M	0.513	1.00
93_R	144_L	0.512	1.00
180_P	188_T	0.512	1.00
93_R	151_H	0.511	1.00
92_T	111_Q	0.509	1.00
128_E	222_N	0.509	1.00
146_E	161_Y	0.508	1.00
166_V	196_L	0.507	1.00
173_A	176_L	0.506	1.00
160_V	221_M	0.506	1.00
237_T	293_L	0.506	1.00
267_V	270_Q	0.504	1.00
161_Y	218_S	0.503	1.00
58_L	95_V	0.503	1.00
54_P	57_E	0.500	1.00
31_S	34_A	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	0.9472	100	0.218	Contact Map
3m2pA	2	0.934	100	0.222	Contact Map
1sb8A	2	0.9703	100	0.225	Contact Map
3rufA	2	0.9571	100	0.228	Contact Map
1rpnA	4	0.9604	100	0.238	Contact Map
3slgA	4	0.9604	100	0.238	Contact Map
2c20A	2	0.9604	100	0.241	Contact Map
1orrA	3	0.9604	100	0.241	Contact Map
2pk3A	2	0.9538	100	0.242	Contact Map
2pzmA	2	0.9373	100	0.242	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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