YBIB - ECOLI - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YBIB - Uncharacterized protein YbiB

UniProt:	P30177	Sequences: MDYRKIIKEIGRGKNHARDLDRDTARGLYAHMLNGEVPDLELGGVLIALRIKGEGEAEMLGFYEAMQNHTIKLTPPAGKPMPIVIPSYNGARKQANLTPLLAILLHKLGFPVVVHGVSEDPTRVLTETIFELMGITPTLHGGQAQAKLDEHQPVFMPVGAFCPPLEKQLAMRWRMGVRNSAHTLAKLATPFAEGEALRLSSVSHPEYIGRVAKFFSDIGGRALLMHGTEGEVYANPQRCPQINLIDREGMRVLYEKQDTAGSELLPQAKDPETTAQWIERCLAGSEPIPESLKIQMACCLVATGEAATISDGLARVNQAF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11580
Length:	320 (306)
Sequences:	4238 (2772)
Seq/√Len:	158.4

ECOLI - YBIB TRPGD
BACSU - TRPD
HALSA - TRPD Q9HNW7
SULSO - TRPD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
280_R	285_S	4.098	1.00
22_R	64_E	3.539	1.00
234_A	240_P	3.240	1.00
19_D	52_K	3.099	1.00
258_D	264_L	2.730	1.00
26_R	64_E	2.715	1.00
234_A	298_C	2.673	1.00
270_D	273_T	2.651	1.00
276_Q	280_R	2.632	1.00
209_G	252_V	2.573	1.00
146_A	150_E	2.497	1.00
38_P	174_R	2.485	1.00
100_L	278_I	2.471	1.00
148_L	154_V	2.429	1.00
208_I	243_N	2.416	1.00
26_R	68_N	2.413	1.00
44_G	47_I	2.399	1.00
13_G	24_T	2.379	1.00
30_A	69_H	2.368	1.00
60_L	217_D	2.309	1.00
28_L	45_V	2.171	1.00
293_K	317_N	2.167	1.00
21_D	24_T	2.140	1.00
104_L	292_L	2.111	1.00
144_A	154_V	2.084	1.00
244_L	253_L	2.043	1.00
268_A	274_T	2.041	1.00
308_T	311_D	2.015	1.00
108_L	300_L	2.001	1.00
38_P	41_E	2.001	1.00
236_P	265_L	1.981	1.00
223_L	302_A	1.968	1.00
205_P	241_Q	1.967	1.00
228_T	241_Q	1.963	1.00
216_S	245_I	1.960	1.00
132_L	272_E	1.954	1.00
110_F	300_L	1.915	1.00
30_A	68_N	1.911	1.00
25_A	62_F	1.901	1.00
140_H	143_Q	1.883	1.00
34_N	69_H	1.877	1.00
314_A	317_N	1.862	1.00
105_L	110_F	1.860	1.00
223_L	298_C	1.839	1.00
209_G	213_K	1.819	1.00
256_K	259_T	1.801	1.00
243_N	250_M	1.793	1.00
242_I	253_L	1.790	1.00
61_G	65_A	1.770	1.00
256_K	264_L	1.751	1.00
30_A	65_A	1.722	1.00
32_M	42_L	1.715	1.00
97_L	291_S	1.701	1.00
105_L	299_C	1.679	1.00
222_A	245_I	1.678	1.00
145_Q	149_D	1.659	1.00
196_A	220_G	1.645	1.00
66_M	188_A	1.632	1.00
31_H	36_E	1.622	1.00
47_I	177_V	1.618	1.00
269_K	274_T	1.610	1.00
22_R	61_G	1.609	1.00
221_R	246_D	1.585	1.00
86_P	198_R	1.579	1.00
239_C	254_Y	1.566	1.00
101_L	296_M	1.558	1.00
289_P	317_N	1.539	1.00
183_T	207_Y	1.535	1.00
279_E	283_A	1.521	1.00
306_A	312_G	1.520	1.00
139_L	143_Q	1.508	1.00
62_F	180_S	1.494	1.00
229_E	238_R	1.489	1.00
228_T	238_R	1.472	1.00
50_R	54_E	1.463	1.00
74_T	145_Q	1.457	1.00
72_K	192_A	1.451	1.00
297_A	301_V	1.447	1.00
83_I	299_C	1.438	1.00
44_G	175_M	1.433	1.00
129_I	278_I	1.426	1.00
29_Y	62_F	1.415	1.00
22_R	217_D	1.394	1.00
297_A	312_G	1.390	1.00
265_L	287_P	1.377	1.00
133_M	275_A	1.373	1.00
129_I	275_A	1.350	1.00
28_L	37_V	1.347	1.00
13_G	18_R	1.342	1.00
143_Q	146_A	1.341	1.00
47_I	51_I	1.340	1.00
57_A	217_D	1.338	1.00
215_F	222_A	1.338	1.00
241_Q	252_V	1.336	1.00
39_D	174_R	1.336	1.00
307_A	311_D	1.331	1.00
40_L	174_R	1.331	1.00
56_E	60_L	1.318	1.00
239_C	256_K	1.309	1.00
42_L	171_M	1.286	1.00
305_E	315_R	1.260	1.00
37_V	42_L	1.232	1.00
118_S	128_T	1.218	1.00
241_Q	254_Y	1.208	1.00
9_E	24_T	1.207	1.00
192_A	195_E	1.200	1.00
56_E	214_F	1.200	1.00
227_G	238_R	1.196	1.00
139_L	147_K	1.194	1.00
81_M	196_A	1.191	1.00
243_N	252_V	1.191	1.00
165_L	168_Q	1.184	1.00
213_K	216_S	1.178	1.00
293_K	313_L	1.165	1.00
110_F	303_T	1.165	1.00
221_R	244_L	1.164	1.00
297_A	313_L	1.163	1.00
40_L	43_G	1.163	1.00
135_I	153_P	1.162	1.00
269_K	273_T	1.157	1.00
65_A	69_H	1.155	1.00
26_R	65_A	1.150	1.00
310_S	314_A	1.145	1.00
25_A	61_G	1.144	1.00
110_F	305_E	1.138	1.00
281_C	288_I	1.116	1.00
216_S	250_M	1.114	1.00
101_L	105_L	1.108	1.00
66_M	165_L	1.094	0.99
30_A	34_N	1.091	0.99
82_P	195_E	1.088	0.99
45_V	62_F	1.084	0.99
228_T	239_C	1.080	0.99
234_A	255_E	1.078	0.99
237_Q	266_P	1.073	0.99
255_E	260_A	1.068	0.99
118_S	131_E	1.065	0.99
234_A	294_I	1.064	0.99
168_Q	171_M	1.059	0.99
41_E	174_R	1.058	0.99
15_N	177_V	1.055	0.99
144_A	161_F	1.044	0.99
23_D	26_R	1.041	0.99
236_P	291_S	1.039	0.99
256_K	260_A	1.037	0.99
13_G	17_A	1.029	0.99
127_E	157_P	1.024	0.99
276_Q	279_E	1.023	0.99
105_L	112_V	1.023	0.99
244_L	301_V	1.018	0.99
82_P	113_V	1.012	0.99
265_L	290_E	1.010	0.99
312_G	316_V	1.006	0.99
95_A	277_W	1.006	0.99
15_N	47_I	0.995	0.99
170_A	174_R	0.990	0.99
33_L	66_M	0.990	0.99
235_N	238_R	0.982	0.99
52_K	58_E	0.979	0.99
306_A	315_R	0.975	0.99
240_P	257_Q	0.966	0.99
315_R	318_Q	0.966	0.99
260_A	313_L	0.966	0.99
289_P	293_K	0.964	0.99
54_E	59_M	0.963	0.99
40_L	171_M	0.960	0.99
123_R	270_D	0.958	0.99
271_P	275_A	0.958	0.99
63_Y	218_I	0.955	0.99
120_D	159_G	0.952	0.99
105_L	111_P	0.948	0.99
245_I	250_M	0.939	0.98
197_L	221_R	0.929	0.98
262_S	294_I	0.928	0.98
54_E	178_R	0.926	0.98
37_V	41_E	0.923	0.98
56_E	213_K	0.922	0.98
59_M	214_F	0.915	0.98
199_L	225_M	0.913	0.98
31_H	37_V	0.913	0.98
19_D	57_A	0.911	0.98
57_A	61_G	0.910	0.98
197_L	302_A	0.909	0.98
85_I	101_L	0.905	0.98
281_C	292_L	0.905	0.98
60_L	64_E	0.903	0.98
272_E	276_Q	0.900	0.98
147_K	151_H	0.899	0.98
262_S	313_L	0.897	0.98
111_P	149_D	0.895	0.98
275_A	279_E	0.893	0.98
223_L	301_V	0.892	0.98
81_M	197_L	0.887	0.98
105_L	108_L	0.884	0.98
280_R	286_E	0.882	0.98
202_V	211_V	0.882	0.98
228_T	254_Y	0.881	0.98
44_G	177_V	0.880	0.98
27_G	31_H	0.880	0.98
229_E	235_N	0.877	0.98
60_L	214_F	0.877	0.98
211_V	224_L	0.874	0.97
42_L	168_Q	0.871	0.97
144_A	148_L	0.871	0.97
32_M	168_Q	0.867	0.97
226_H	230_G	0.867	0.97
56_E	217_D	0.866	0.97
138_T	160_A	0.866	0.97
287_P	290_E	0.862	0.97
147_K	154_V	0.862	0.97
20_L	58_E	0.862	0.97
39_D	170_A	0.858	0.97
86_P	126_T	0.856	0.97
39_D	171_M	0.855	0.97
85_I	198_R	0.848	0.97
19_D	55_G	0.847	0.97
48_A	52_K	0.846	0.97
67_Q	192_A	0.839	0.97
85_I	102_A	0.839	0.97
26_R	61_G	0.836	0.97
76_P	149_D	0.833	0.97
94_Q	231_E	0.831	0.97
227_G	235_N	0.829	0.97
245_I	248_E	0.826	0.96
71_I	163_P	0.821	0.96
314_A	318_Q	0.819	0.96
66_M	184_L	0.817	0.96
99_P	130_F	0.816	0.96
103_I	107_K	0.815	0.96
209_G	243_N	0.813	0.96
301_V	306_A	0.811	0.96
197_L	220_G	0.807	0.96
86_P	101_L	0.807	0.96
263_E	290_E	0.804	0.96
146_A	149_D	0.803	0.96
22_R	60_L	0.803	0.96
207_Y	210_R	0.802	0.96
33_L	188_A	0.799	0.96
25_A	180_S	0.798	0.96
92_R	121_P	0.798	0.96
104_L	296_M	0.798	0.96
244_L	251_R	0.789	0.95
77_A	149_D	0.786	0.95
141_G	145_Q	0.784	0.95
83_I	112_V	0.783	0.95
304_G	312_G	0.782	0.95
103_I	153_P	0.782	0.95
132_L	271_P	0.781	0.95
301_V	308_T	0.779	0.95
91_A	94_Q	0.777	0.95
9_E	13_G	0.776	0.95
144_A	156_M	0.774	0.95
246_D	251_R	0.774	0.95
129_I	133_M	0.769	0.95
100_L	282_L	0.767	0.95
234_A	260_A	0.763	0.95
277_W	281_C	0.761	0.94
35_G	167_K	0.760	0.94
259_T	310_S	0.751	0.94
10_I	14_K	0.750	0.94
43_G	171_M	0.748	0.94
26_R	30_A	0.747	0.94
67_Q	218_I	0.747	0.94
75_P	148_L	0.737	0.93
203_S	207_Y	0.735	0.93
12_R	16_H	0.735	0.93
301_V	309_I	0.732	0.93
290_E	317_N	0.731	0.93
143_Q	147_K	0.730	0.93
28_L	32_M	0.730	0.93
105_L	296_M	0.728	0.93
200_S	211_V	0.728	0.93
10_I	13_G	0.725	0.93
39_D	167_K	0.724	0.93
33_L	167_K	0.721	0.93
297_A	309_I	0.721	0.93
59_M	183_T	0.720	0.93
85_I	126_T	0.720	0.93
216_S	249_G	0.717	0.93
236_P	266_P	0.717	0.93
213_K	250_M	0.710	0.92
197_L	303_T	0.709	0.92
93_K	123_R	0.705	0.92
46_L	165_L	0.704	0.92
220_G	247_R	0.702	0.92
258_D	263_E	0.702	0.92
223_L	253_L	0.702	0.92
95_A	288_I	0.701	0.92
93_K	267_Q	0.700	0.92
136_T	143_Q	0.700	0.92
140_H	160_A	0.698	0.91
28_L	31_H	0.697	0.91
70_T	188_A	0.695	0.91
49_L	54_E	0.695	0.91
8_K	12_R	0.695	0.91
58_E	61_G	0.694	0.91
229_E	237_Q	0.693	0.91
205_P	252_V	0.693	0.91
144_A	147_K	0.690	0.91
29_Y	180_S	0.690	0.91
83_I	110_F	0.684	0.91
102_A	153_P	0.684	0.91
100_L	281_C	0.682	0.91
165_L	188_A	0.681	0.90
236_P	262_S	0.681	0.90
91_A	122_T	0.680	0.90
311_D	315_R	0.679	0.90
15_N	51_I	0.673	0.90
253_L	301_V	0.667	0.90
236_P	290_E	0.666	0.89
43_G	47_I	0.663	0.89
85_I	299_C	0.662	0.89
304_G	315_R	0.661	0.89
309_I	312_G	0.660	0.89
71_I	141_G	0.660	0.89
105_L	300_L	0.660	0.89
236_P	287_P	0.660	0.89
281_C	286_E	0.659	0.89
268_A	277_W	0.659	0.89
113_V	156_M	0.658	0.89
22_R	57_A	0.654	0.89
213_K	217_D	0.654	0.89
48_A	51_I	0.650	0.88
179_N	182_H	0.648	0.88
73_L	144_A	0.647	0.88
208_I	252_V	0.645	0.88
62_F	184_L	0.643	0.88
126_T	129_I	0.643	0.88
136_T	139_L	0.642	0.88
127_E	131_E	0.641	0.88
56_E	210_R	0.640	0.88
65_A	68_N	0.639	0.87
132_L	275_A	0.632	0.87
55_G	58_E	0.630	0.87
278_I	282_L	0.628	0.87
273_T	276_Q	0.628	0.87
113_V	148_L	0.628	0.87
199_L	302_A	0.627	0.86
47_I	175_M	0.627	0.86
212_A	245_I	0.626	0.86
85_I	199_L	0.626	0.86
239_C	264_L	0.625	0.86
124_V	271_P	0.624	0.86
298_C	309_I	0.622	0.86
223_L	309_I	0.620	0.86
223_L	242_I	0.618	0.86
301_V	305_E	0.615	0.85
159_G	173_W	0.615	0.85
300_L	305_E	0.614	0.85
307_A	315_R	0.613	0.85
64_E	68_N	0.612	0.85
44_G	51_I	0.607	0.85
208_I	241_Q	0.604	0.84
221_R	304_G	0.604	0.84
63_Y	184_L	0.603	0.84
23_D	27_G	0.603	0.84
83_I	303_T	0.603	0.84
103_I	282_L	0.601	0.84
142_G	145_Q	0.599	0.84
103_I	135_I	0.597	0.84
205_P	228_T	0.595	0.84
276_Q	285_S	0.595	0.84
44_G	171_M	0.595	0.84
106_H	109_G	0.595	0.84
200_S	224_L	0.594	0.83
300_L	316_V	0.592	0.83
9_E	18_R	0.589	0.83
300_L	306_A	0.585	0.82
311_D	314_A	0.585	0.82
293_K	297_A	0.584	0.82
63_Y	67_Q	0.584	0.82
229_E	240_P	0.581	0.82
198_R	222_A	0.581	0.82
107_K	151_H	0.580	0.82
44_G	48_A	0.578	0.82
9_E	12_R	0.577	0.82
200_S	215_F	0.576	0.82
63_Y	66_M	0.576	0.82
89_N	185_A	0.575	0.81
100_L	292_L	0.575	0.81
81_M	305_E	0.575	0.81
11_G	14_K	0.574	0.81
256_K	294_I	0.573	0.81
32_M	45_V	0.572	0.81
284_G	289_P	0.571	0.81
73_L	156_M	0.569	0.81
191_F	195_E	0.568	0.81
262_S	293_K	0.567	0.81
103_I	278_I	0.567	0.81
107_K	282_L	0.567	0.81
89_N	186_K	0.566	0.80
199_L	299_C	0.565	0.80
133_M	279_E	0.563	0.80
268_A	288_I	0.562	0.80
313_L	317_N	0.560	0.80
83_I	197_L	0.559	0.80
286_E	290_E	0.557	0.79
38_P	171_M	0.556	0.79
40_L	47_I	0.555	0.79
147_K	153_P	0.555	0.79
304_G	307_A	0.554	0.79
63_Y	187_L	0.554	0.79
260_A	309_I	0.553	0.79
262_S	265_L	0.552	0.79
8_K	11_G	0.549	0.78
297_A	308_T	0.548	0.78
75_P	145_Q	0.548	0.78
25_A	29_Y	0.546	0.78
120_D	203_S	0.545	0.78
299_C	302_A	0.544	0.78
100_L	124_V	0.543	0.78
24_T	61_G	0.543	0.78
277_W	288_I	0.538	0.77
11_G	177_V	0.537	0.77
111_P	152_Q	0.537	0.77
242_I	255_E	0.536	0.77
101_L	104_L	0.536	0.77
54_E	58_E	0.536	0.77
63_Y	70_T	0.533	0.76
216_S	248_E	0.533	0.76
210_R	213_K	0.533	0.76
135_I	147_K	0.532	0.76
300_L	315_R	0.531	0.76
46_L	168_Q	0.530	0.76
220_G	304_G	0.529	0.76
221_R	301_V	0.528	0.76
286_E	289_P	0.527	0.76
202_V	208_I	0.526	0.75
15_N	50_R	0.525	0.75
50_R	176_G	0.525	0.75
96_N	114_V	0.524	0.75
83_I	195_E	0.522	0.75
63_Y	188_A	0.519	0.74
225_M	234_A	0.518	0.74
101_L	292_L	0.518	0.74
228_T	235_N	0.515	0.74
94_Q	97_L	0.515	0.74
89_N	96_N	0.514	0.74
29_Y	168_Q	0.514	0.74
223_L	244_L	0.514	0.74
83_I	302_A	0.513	0.74
260_A	294_I	0.513	0.74
142_G	146_A	0.512	0.73
268_A	275_A	0.511	0.73
25_A	58_E	0.510	0.73
59_M	210_R	0.510	0.73
82_P	111_P	0.509	0.73
17_A	51_I	0.509	0.73
10_I	48_A	0.508	0.73
246_D	249_G	0.508	0.73
131_E	137_P	0.508	0.73
81_M	111_P	0.506	0.73
22_R	26_R	0.506	0.73
77_A	145_Q	0.502	0.72
60_L	63_Y	0.502	0.72
67_Q	195_E	0.502	0.72
178_R	207_Y	0.501	0.72
168_Q	181_A	0.501	0.72
289_P	292_L	0.500	0.72

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
4muoA	2	0.9688	100	0.079	Contact Map
4giuA	2	0.9812	100	0.087	Contact Map
1vquA	2	0.9625	100	0.094	Contact Map
1khdA	2	0.9563	100	0.096	Contact Map
1o17A	2	0.9656	100	0.112	Contact Map
4gtnA	2	0.9406	100	0.114	Contact Map
4hkmA	2	0.95	100	0.115	Contact Map
2elcA	4	0.95	100	0.124	Contact Map
3h5qA	2	0.875	100	0.315	Contact Map
4eadA	2	0.8531	100	0.324	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.

Page generated in 0.0108 seconds.