YKFA - ECOLI - GREMLIN Contacts

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YKFA - Uncharacterized protein YkfA

UniProt:	P75678	Sequences: MNNSEGLKSFQQSLADLPQWVSERLLQQINQLTNYEPVIGIMGKTGVGKSSLCNALFAGDISPVSDVAACTREPLRFRLQVGDRYITLMDLPGVGESGARDTEYAALYREQLPRLDLVLWLIKADDRALTVDEHFYHQVIGEVYRHKVLFVISQSDKAEPTSGGGQLSTAQKQNISRKICLLHELFQPVHPVCAVSVRLQWGLKVMAERMIKCLPREATSPVVSQLHPSFRTTVVREQARSDFGETVGAVLDSISAFPLIPAPVRAVIQAVRTTVVSVARAVWDFFF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13339
Length:	287 (233)
Sequences:	7981 (5812)
Seq/√Len:	380.8

ECOLI - YKFA YFJP ERA DER MNME CRFC ENGB HFLX OBG FEOB
BACSU - ERA YPBR MNME DER ENGB HFLX OBG
HALSA - Q9HQ88 Q9HMD6 Q9HMC2 ENGB Y1111
SULSO - Q7LXR6 HFLX

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
191_P	209_R	3.579	1.00
55_A	203_L	2.972	1.00
55_A	200_Q	2.821	1.00
119_L	151_V	2.534	1.00
119_L	210_M	2.416	1.00
40_G	115_L	2.319	1.00
193_C	209_R	2.253	1.00
41_I	53_C	2.197	1.00
153_S	197_V	2.165	1.00
209_R	213_C	2.112	1.00
151_V	195_V	2.067	1.00
101_D	104_Y	2.046	1.00
243_F	247_V	1.941	1.00
209_R	212_K	1.930	1.00
241_S	245_E	1.912	1.00
124_A	152_I	1.905	1.00
130_T	134_H	1.900	1.00
133_E	137_H	1.892	1.00
51_S	197_V	1.864	1.00
237_E	240_R	1.816	1.00
202_G	205_V	1.814	1.00
44_K	132_D	1.811	1.00
121_L	153_S	1.807	1.00
172_K	194_A	1.796	1.00
259_L	262_A	1.766	1.00
219_T	223_V	1.747	1.00
233_T	237_E	1.741	1.00
154_Q	157_K	1.740	1.00
78_R	85_Y	1.721	1.00
41_I	119_L	1.698	1.00
224_S	228_P	1.686	1.00
80_Q	85_Y	1.651	1.00
52_L	121_L	1.645	1.00
180_C	183_H	1.639	1.00
122_I	150_F	1.623	1.00
152_I	194_A	1.608	1.00
220_S	224_S	1.596	1.00
224_S	227_H	1.575	1.00
133_E	178_K	1.542	1.00
227_H	231_R	1.516	1.00
173_Q	176_S	1.503	1.00
238_Q	242_D	1.502	1.00
123_K	126_D	1.498	1.00
103_E	106_A	1.481	1.00
128_A	132_D	1.451	1.00
221_P	225_Q	1.449	1.00
56_L	203_L	1.446	1.00
84_R	211_I	1.436	1.00
266_A	269_Q	1.429	1.00
213_C	217_E	1.416	1.00
250_V	253_S	1.412	1.00
244_G	248_G	1.409	1.00
242_D	246_T	1.408	1.00
239_A	243_F	1.401	1.00
39_I	86_I	1.387	1.00
223_V	226_L	1.386	1.00
51_S	64_V	1.363	1.00
233_T	236_R	1.362	1.00
265_R	269_Q	1.357	1.00
208_E	212_K	1.356	1.00
123_K	153_S	1.352	1.00
245_E	248_G	1.348	1.00
234_V	238_Q	1.345	1.00
235_V	239_A	1.326	1.00
226_L	230_F	1.324	1.00
38_V	87_T	1.316	1.00
222_V	227_H	1.315	1.00
249_A	253_S	1.303	1.00
222_V	225_Q	1.300	1.00
174_N	177_R	1.300	1.00
251_L	254_I	1.291	1.00
259_L	263_P	1.290	1.00
243_F	255_S	1.289	1.00
152_I	192_V	1.281	1.00
228_P	232_T	1.270	1.00
180_C	184_E	1.263	1.00
155_S	194_A	1.258	1.00
236_R	240_R	1.258	1.00
149_L	209_R	1.252	1.00
240_R	243_F	1.251	1.00
228_P	231_R	1.244	1.00
181_L	185_L	1.238	1.00
236_R	239_A	1.225	1.00
125_D	157_K	1.221	1.00
76_R	87_T	1.216	1.00
204_K	208_E	1.207	1.00
149_L	193_C	1.205	1.00
248_G	252_D	1.202	1.00
137_H	140_I	1.190	1.00
244_G	251_L	1.189	1.00
266_A	270_A	1.184	1.00
71_T	79_L	1.182	1.00
259_L	266_A	1.180	1.00
227_H	230_F	1.174	1.00
129_L	132_D	1.172	1.00
235_V	238_Q	1.172	1.00
223_V	230_F	1.168	1.00
219_T	222_V	1.164	1.00
109_R	138_Q	1.161	1.00
206_M	210_M	1.160	1.00
156_D	196_S	1.156	1.00
44_K	129_L	1.154	1.00
52_L	56_L	1.153	1.00
254_I	258_P	1.153	1.00
119_L	206_M	1.142	1.00
84_R	215_P	1.141	1.00
71_T	75_L	1.137	1.00
56_L	207_A	1.136	1.00
78_R	87_T	1.132	1.00
174_N	178_K	1.128	1.00
151_V	206_M	1.119	1.00
240_R	244_G	1.119	1.00
172_K	176_S	1.117	1.00
267_V	270_A	1.117	1.00
261_P	265_R	1.110	1.00
70_C	75_L	1.108	1.00
173_Q	177_R	1.106	1.00
221_P	226_L	1.098	1.00
199_L	202_G	1.094	1.00
182_L	186_F	1.085	1.00
203_L	207_A	1.079	1.00
234_V	237_E	1.078	1.00
223_V	227_H	1.075	1.00
117_L	149_L	1.071	1.00
264_V	270_A	1.062	1.00
260_I	264_V	1.060	1.00
106_A	110_E	1.052	1.00
53_C	88_L	1.049	1.00
40_G	91_L	1.046	1.00
221_P	227_H	1.038	1.00
172_K	185_L	1.036	1.00
234_V	239_A	1.031	1.00
224_S	230_F	1.028	1.00
238_Q	241_S	1.027	1.00
251_L	255_S	1.026	1.00
130_T	133_E	1.022	1.00
251_L	257_F	1.020	1.00
242_D	247_V	1.007	1.00
211_I	215_P	1.006	1.00
239_A	242_D	1.005	1.00
233_T	240_R	1.002	1.00
160_P	163_G	0.997	1.00
44_K	131_V	0.992	1.00
253_S	256_A	0.992	1.00
252_D	255_S	0.990	1.00
262_A	266_A	0.986	1.00
53_C	62_S	0.975	1.00
235_V	243_F	0.974	1.00
263_P	266_A	0.971	1.00
263_P	267_V	0.967	1.00
236_R	243_F	0.966	1.00
181_L	184_E	0.965	1.00
244_G	247_V	0.963	1.00
246_T	250_V	0.960	1.00
200_Q	203_L	0.957	1.00
136_Y	140_I	0.949	1.00
219_T	226_L	0.941	1.00
265_R	270_A	0.940	1.00
253_S	257_F	0.939	1.00
224_S	232_T	0.938	1.00
81_V	211_I	0.935	1.00
249_A	252_D	0.934	1.00
250_V	255_S	0.928	1.00
262_A	269_Q	0.921	1.00
158_A	163_G	0.911	1.00
120_W	136_Y	0.909	1.00
242_D	245_E	0.908	1.00
237_E	241_S	0.904	1.00
176_S	182_L	0.902	1.00
229_S	232_T	0.899	1.00
80_Q	83_D	0.897	1.00
50_S	62_S	0.894	1.00
222_V	229_S	0.892	1.00
56_L	79_L	0.888	1.00
117_L	210_M	0.887	1.00
51_S	195_V	0.886	1.00
262_A	270_A	0.886	1.00
260_I	267_V	0.882	1.00
262_A	268_I	0.882	1.00
138_Q	141_G	0.882	1.00
261_P	264_V	0.881	1.00
108_Y	112_L	0.877	1.00
105_A	108_Y	0.873	1.00
257_F	260_I	0.870	1.00
265_R	268_I	0.866	1.00
207_A	211_I	0.862	1.00
260_I	263_P	0.861	1.00
149_L	210_M	0.860	1.00
155_S	201_W	0.859	1.00
55_A	197_V	0.853	1.00
220_S	227_H	0.849	1.00
100_R	104_Y	0.849	1.00
150_F	189_V	0.847	1.00
62_S	77_F	0.832	1.00
117_L	213_C	0.831	1.00
179_I	183_H	0.831	1.00
128_A	133_E	0.829	1.00
256_A	259_L	0.823	1.00
52_L	203_L	0.817	1.00
246_T	249_A	0.813	1.00
235_V	262_A	0.811	1.00
183_H	192_V	0.810	1.00
205_V	209_R	0.807	1.00
103_E	107_L	0.804	1.00
131_V	134_H	0.800	1.00
240_R	246_T	0.797	1.00
178_K	182_L	0.796	1.00
225_Q	229_S	0.796	1.00
264_V	267_V	0.796	1.00
71_T	77_F	0.792	1.00
177_R	180_C	0.792	1.00
133_E	185_L	0.791	1.00
191_P	213_C	0.790	1.00
221_P	228_P	0.789	1.00
58_A	200_Q	0.788	1.00
264_V	268_I	0.787	1.00
123_K	154_Q	0.783	1.00
233_T	239_A	0.781	1.00
234_V	240_R	0.773	1.00
205_V	208_E	0.771	1.00
262_A	265_R	0.770	1.00
247_V	258_P	0.770	1.00
107_L	111_Q	0.767	1.00
268_I	271_V	0.765	1.00
263_P	270_A	0.764	1.00
193_C	202_G	0.760	1.00
91_L	108_Y	0.757	1.00
229_S	233_T	0.756	1.00
257_F	261_P	0.753	1.00
219_T	224_S	0.752	1.00
39_I	210_M	0.740	1.00
225_Q	230_F	0.740	1.00
82_G	211_I	0.734	1.00
44_K	47_V	0.731	1.00
226_L	229_S	0.722	1.00
89_M	111_Q	0.720	1.00
201_W	205_V	0.718	1.00
161_T	173_Q	0.717	1.00
176_S	179_I	0.708	1.00
107_L	110_E	0.706	1.00
45_T	68_A	0.703	1.00
176_S	180_C	0.700	0.99
247_V	254_I	0.700	0.99
222_V	226_L	0.698	0.99
137_H	141_G	0.697	0.99
71_T	80_Q	0.692	0.99
248_G	251_L	0.689	0.99
52_L	195_V	0.688	0.99
248_G	254_I	0.686	0.99
260_I	266_A	0.685	0.99
247_V	251_L	0.677	0.99
264_V	271_V	0.676	0.99
244_G	253_S	0.676	0.99
97_S	101_D	0.671	0.99
244_G	250_V	0.670	0.99
254_I	257_F	0.670	0.99
230_F	233_T	0.669	0.99
219_T	225_Q	0.667	0.99
196_S	199_L	0.665	0.99
258_P	262_A	0.659	0.99
81_V	207_A	0.658	0.99
225_Q	228_P	0.656	0.99
151_V	193_C	0.656	0.99
57_F	79_L	0.654	0.99
259_L	264_V	0.648	0.99
223_V	229_S	0.645	0.99
39_I	117_L	0.645	0.99
163_G	194_A	0.645	0.99
220_S	223_V	0.644	0.99
221_P	224_S	0.644	0.99
182_L	187_Q	0.637	0.99
260_I	268_I	0.636	0.99
212_K	216_R	0.635	0.99
183_H	186_F	0.633	0.99
260_I	270_A	0.631	0.99
148_V	190_H	0.624	0.99
232_T	236_R	0.623	0.99
96_E	101_D	0.622	0.99
150_F	192_V	0.618	0.99
136_Y	139_V	0.614	0.99
63_P	75_L	0.611	0.99
204_K	207_A	0.610	0.99
124_A	158_A	0.607	0.99
243_F	248_G	0.605	0.99
259_L	267_V	0.604	0.99
238_Q	243_F	0.603	0.98
241_S	250_V	0.600	0.98
219_T	231_R	0.600	0.98
239_A	246_T	0.596	0.98
267_V	271_V	0.594	0.98
71_T	78_R	0.593	0.98
252_D	257_F	0.591	0.98
74_P	89_M	0.589	0.98
62_S	75_L	0.589	0.98
237_E	242_D	0.586	0.98
243_F	257_F	0.583	0.98
80_Q	219_T	0.582	0.98
72_R	77_F	0.580	0.98
184_E	187_Q	0.580	0.98
62_S	65_S	0.579	0.98
239_A	257_F	0.579	0.98
227_H	232_T	0.577	0.98
86_I	211_I	0.572	0.98
237_E	243_F	0.571	0.98
134_H	138_Q	0.570	0.98
172_K	179_I	0.569	0.98
264_V	269_Q	0.568	0.98
30_N	33_T	0.567	0.98
51_S	55_A	0.562	0.98
60_D	63_P	0.560	0.98
150_F	190_H	0.559	0.98
89_M	114_R	0.556	0.97
52_L	151_V	0.553	0.97
172_K	175_I	0.551	0.97
224_S	231_R	0.550	0.97
40_G	118_V	0.545	0.97
107_L	112_L	0.545	0.97
243_F	246_T	0.543	0.97
155_S	158_A	0.536	0.97
63_P	70_C	0.536	0.97
259_L	270_A	0.535	0.97
245_E	251_L	0.535	0.97
234_V	246_T	0.534	0.97
250_V	254_I	0.534	0.97
38_V	116_D	0.534	0.97
81_V	84_R	0.533	0.97
125_D	152_I	0.532	0.97
119_L	149_L	0.529	0.97
179_I	182_L	0.526	0.96
252_D	256_A	0.526	0.96
118_V	148_V	0.526	0.96
135_F	138_Q	0.525	0.96
101_D	105_A	0.523	0.96
71_T	76_R	0.521	0.96
261_P	269_Q	0.521	0.96
261_P	267_V	0.517	0.96
246_T	254_I	0.516	0.96
36_E	87_T	0.515	0.96
177_R	181_L	0.513	0.96
247_V	250_V	0.513	0.96
261_P	266_A	0.510	0.96
124_A	155_S	0.505	0.96
36_E	78_R	0.505	0.96
29_I	33_T	0.505	0.96
258_P	264_V	0.503	0.95
47_V	123_K	0.502	0.95
96_E	131_V	0.501	0.95
226_L	231_R	0.501	0.95
263_P	269_Q	0.500	0.95
176_S	194_A	0.500	0.95

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
2j69A	1	0.9686	100	0.437	Contact Map
3ievA	1	0.8432	100	0.443	Contact Map
1egaA	2	0.8397	100	0.46	Contact Map
1xzpA	4	0.9129	100	0.466	Contact Map
1wf3A	1	0.8397	100	0.468	Contact Map
4aurA	1	0.9826	100	0.469	Contact Map
3gehA	2	0.8467	100	0.475	Contact Map
1mkyA	1	0.8711	100	0.476	Contact Map
3geeA	2	0.784	100	0.48	Contact Map
4dcuA	1	0.9129	100	0.488	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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