YIBA - ECOLI - GREMLIN Contacts

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YIBA - Protein YibA

UniProt:	P0ADK6	Sequences: MSNTYQKRKASKEYGLYNQCKKLNDDELFRLLDDHNSLKRISSARVLQLRGGQDAVRLAIEFCSDKNYIRRDIGAFILGQIKICKKCEDNVFNILNNMALNDKSACVRATAIESTAQRCKKNPIYSPKIVEQSQITAFDKSTNVRRATAFAISVINDKATIPLLINLLKDPNGDVRNWAAFAININKYDNSDIRDCFVEMLQDKNEEVRIEAIIGLSYRKDKRVLSVLCDELKKNTVYDDIIEAAGELGDKTLLPVLDTMLYKFDDNEIITSAIDKLKRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11187
Length:	280 (233)
Sequences:	13210 (10474)
Seq/√Len:	686.2

ECOLI - YIBA
HALSA - Q9HQX3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_D	39_K	3.018	1.00
145_R	170_D	2.843	1.00
176_R	203_D	2.506	1.00
197_F	215_G	2.412	1.00
203_D	208_V	2.364	1.00
226_S	230_D	2.267	1.00
31_L	43_S	2.244	1.00
65_D	70_R	2.067	1.00
252_T	258_D	2.055	1.00
108_R	139_D	2.025	1.00
139_D	144_V	1.986	1.00
196_C	199_E	1.980	1.00
227_V	230_D	1.962	1.00
40_R	65_D	1.909	1.00
252_T	256_V	1.903	1.00
62_F	74_G	1.880	1.00
42_S	46_V	1.828	1.00
185_I	190_N	1.816	1.00
102_D	107_V	1.805	1.00
58_L	62_F	1.788	1.00
217_S	220_K	1.777	1.00
40_R	43_S	1.775	1.00
237_V	240_D	1.775	1.00
240_D	243_E	1.758	1.00
214_I	218_Y	1.755	1.00
211_E	214_I	1.749	1.00
240_D	247_E	1.734	1.00
170_D	175_V	1.733	1.00
246_G	249_G	1.729	1.00
48_Q	51_G	1.720	1.00
210_I	214_I	1.677	1.00
132_Q	136_T	1.672	1.00
202_Q	227_V	1.671	1.00
61_E	64_S	1.651	1.00
58_L	61_E	1.649	1.00
70_R	73_I	1.620	1.00
253_L	256_V	1.619	1.00
199_E	202_Q	1.610	1.00
251_K	255_P	1.559	1.00
163_L	166_N	1.555	1.00
131_E	135_I	1.550	1.00
178_W	181_F	1.534	1.00
92_F	96_N	1.524	1.00
167_L	179_A	1.520	1.00
90_N	93_N	1.517	1.00
136_T	139_D	1.517	1.00
184_N	215_G	1.503	1.00
223_R	227_V	1.493	1.00
200_M	208_V	1.491	1.00
37_S	67_N	1.479	1.00
177_N	181_F	1.474	1.00
240_D	244_A	1.473	1.00
214_I	217_S	1.464	1.00
231_E	237_V	1.453	1.00
239_D	243_E	1.446	1.00
209_R	212_A	1.443	1.00
142_T	172_N	1.435	1.00
41_I	73_I	1.430	1.00
73_I	76_F	1.426	1.00
142_T	146_R	1.423	1.00
150_F	178_W	1.408	1.00
252_T	255_P	1.403	1.00
195_D	199_E	1.387	1.00
31_L	34_D	1.366	1.00
27_E	30_R	1.362	1.00
146_R	178_W	1.348	1.00
83_I	117_Q	1.334	1.00
253_L	258_D	1.327	1.00
134_Q	138_F	1.324	1.00
95_L	114_S	1.316	1.00
79_G	83_I	1.307	1.00
255_P	258_D	1.301	1.00
242_I	246_G	1.299	1.00
141_S	144_V	1.298	1.00
44_A	77_I	1.292	1.00
241_I	250_D	1.292	1.00
166_N	169_K	1.282	1.00
76_F	80_Q	1.278	1.00
181_F	211_E	1.276	1.00
90_N	94_I	1.273	1.00
164_L	182_A	1.272	1.00
209_R	213_I	1.269	1.00
94_I	97_N	1.267	1.00
26_D	30_R	1.259	1.00
121_K	124_I	1.257	1.00
113_E	117_Q	1.255	1.00
213_I	244_A	1.253	1.00
138_F	166_N	1.252	1.00
181_F	185_I	1.244	1.00
238_Y	242_I	1.239	1.00
177_N	211_E	1.216	1.00
136_T	148_T	1.216	1.00
132_Q	135_I	1.211	1.00
251_K	256_V	1.208	1.00
246_G	250_D	1.202	1.00
74_G	77_I	1.200	1.00
146_R	172_N	1.187	1.00
49_L	52_G	1.171	1.00
147_A	151_A	1.169	1.00
227_V	231_E	1.165	1.00
213_I	217_S	1.163	1.00
119_C	154_V	1.162	1.00
244_A	248_L	1.158	1.00
42_S	45_R	1.152	1.00
210_I	240_D	1.150	1.00
41_I	45_R	1.145	1.00
109_A	113_E	1.140	1.00
45_R	48_Q	1.139	1.00
107_V	110_T	1.136	1.00
243_E	247_E	1.134	1.00
239_D	242_I	1.132	1.00
230_D	233_K	1.130	1.00
72_D	76_F	1.121	1.00
206_E	210_I	1.118	1.00
62_F	70_R	1.102	1.00
67_N	71_R	1.100	1.00
228_L	244_A	1.088	1.00
244_A	247_E	1.086	1.00
39_K	46_V	1.086	1.00
125_Y	128_K	1.086	1.00
207_E	211_E	1.076	1.00
241_I	244_A	1.075	1.00
54_D	57_R	1.072	1.00
48_Q	52_G	1.069	1.00
180_A	184_N	1.064	1.00
135_I	138_F	1.063	1.00
234_K	237_V	1.056	1.00
80_Q	84_C	1.053	1.00
254_L	258_D	1.046	1.00
177_N	207_E	1.039	1.00
185_I	189_D	1.039	1.00
45_R	49_L	1.036	1.00
247_E	250_D	1.035	1.00
36_N	39_K	1.030	1.00
153_S	182_A	1.030	1.00
71_R	74_G	1.027	1.00
209_R	234_K	1.016	1.00
251_K	254_L	1.014	1.00
93_N	97_N	1.011	1.00
31_L	39_K	1.009	1.00
238_Y	241_I	1.006	1.00
59_A	77_I	0.990	1.00
146_R	150_F	0.989	1.00
44_A	48_Q	0.981	1.00
251_K	258_D	0.980	1.00
200_M	203_D	0.979	1.00
39_K	42_S	0.975	1.00
181_F	184_N	0.964	1.00
35_H	39_K	0.963	1.00
179_A	182_A	0.962	1.00
61_E	65_D	0.954	1.00
175_V	178_W	0.948	1.00
73_I	77_I	0.947	1.00
145_R	148_T	0.944	1.00
38_L	42_S	0.941	1.00
176_R	179_A	0.936	1.00
107_V	111_A	0.934	1.00
54_D	58_L	0.930	1.00
243_E	246_G	0.929	1.00
167_L	170_D	0.929	1.00
125_Y	129_I	0.927	1.00
40_R	44_A	0.921	1.00
45_R	73_I	0.921	1.00
62_F	65_D	0.917	1.00
110_T	113_E	0.916	1.00
201_L	216_L	0.911	1.00
253_L	257_L	0.910	1.00
196_C	200_M	0.909	1.00
170_D	176_R	0.906	1.00
79_G	82_K	0.903	1.00
59_A	74_G	0.902	1.00
149_A	167_L	0.899	1.00
212_A	216_L	0.898	1.00
70_R	74_G	0.894	1.00
133_S	151_A	0.893	1.00
168_L	183_I	0.891	1.00
46_V	50_R	0.888	1.00
180_A	215_G	0.881	1.00
180_A	200_M	0.877	1.00
45_R	52_G	0.872	1.00
80_Q	83_I	0.869	1.00
224_V	229_C	0.869	1.00
153_S	181_F	0.868	1.00
165_I	169_K	0.853	1.00
72_D	75_A	0.850	1.00
32_L	43_S	0.843	1.00
128_K	131_E	0.841	1.00
169_K	199_E	0.836	1.00
79_G	85_K	0.833	1.00
34_D	40_R	0.829	1.00
60_I	63_C	0.829	1.00
237_V	242_I	0.814	1.00
46_V	49_L	0.808	1.00
26_D	31_L	0.807	1.00
211_E	218_Y	0.805	1.00
180_A	212_A	0.805	1.00
43_S	46_V	0.796	1.00
106_C	109_A	0.793	1.00
116_A	119_C	0.791	1.00
173_G	176_R	0.791	1.00
65_D	74_G	0.784	1.00
28_L	46_V	0.782	1.00
26_D	29_F	0.780	1.00
240_D	246_G	0.777	1.00
231_E	241_I	0.771	1.00
31_L	42_S	0.771	1.00
142_T	149_A	0.771	1.00
201_L	213_I	0.771	1.00
207_E	210_I	0.770	1.00
110_T	117_Q	0.769	1.00
142_T	145_R	0.768	1.00
135_I	139_D	0.768	1.00
184_N	218_Y	0.765	1.00
79_G	114_S	0.764	1.00
185_I	188_Y	0.759	1.00
117_Q	120_K	0.758	1.00
71_R	102_D	0.757	1.00
134_Q	159_A	0.755	1.00
125_Y	134_Q	0.754	1.00
52_G	80_Q	0.753	1.00
79_G	117_Q	0.751	1.00
173_G	205_N	0.745	1.00
224_V	230_D	0.745	1.00
204_K	208_V	0.744	1.00
72_D	110_T	0.744	1.00
69_I	73_I	0.740	1.00
89_D	93_N	0.739	1.00
105_A	108_R	0.739	1.00
44_A	53_Q	0.736	1.00
153_S	178_W	0.735	1.00
48_Q	53_Q	0.727	1.00
148_T	151_A	0.722	1.00
89_D	96_N	0.719	1.00
202_Q	230_D	0.718	1.00
149_A	179_A	0.713	1.00
229_C	232_L	0.712	1.00
191_S	195_D	0.709	1.00
93_N	96_N	0.709	1.00
187_K	190_N	0.709	1.00
95_L	111_A	0.706	1.00
25_D	29_F	0.704	1.00
238_Y	250_D	0.703	1.00
77_I	80_Q	0.701	1.00
75_A	79_G	0.697	1.00
234_K	241_I	0.697	1.00
164_L	167_L	0.697	1.00
39_K	51_G	0.696	1.00
178_W	182_A	0.696	1.00
149_A	178_W	0.695	1.00
220_K	247_E	0.693	1.00
79_G	113_E	0.688	1.00
149_A	182_A	0.687	1.00
75_A	111_A	0.686	1.00
76_F	110_T	0.685	1.00
37_S	40_R	0.682	1.00
70_R	76_F	0.677	1.00
136_T	144_V	0.677	1.00
223_R	226_S	0.672	1.00
231_E	234_K	0.670	1.00
41_I	44_A	0.669	1.00
91_V	96_N	0.666	1.00
30_R	34_D	0.660	1.00
217_S	221_D	0.659	1.00
225_L	245_A	0.659	1.00
108_R	111_A	0.658	1.00
242_I	245_A	0.649	1.00
159_A	162_P	0.647	1.00
180_A	197_F	0.646	1.00
150_F	153_S	0.639	1.00
67_N	70_R	0.638	1.00
88_E	91_V	0.637	1.00
113_E	147_A	0.637	1.00
131_E	134_Q	0.635	1.00
126_S	129_I	0.634	1.00
211_E	220_K	0.633	1.00
193_I	197_F	0.631	1.00
241_I	246_G	0.629	1.00
205_N	209_R	0.627	1.00
59_A	79_G	0.626	1.00
116_A	150_F	0.626	1.00
68_Y	72_D	0.625	1.00
145_R	149_A	0.621	1.00
112_I	136_T	0.618	1.00
233_K	239_D	0.616	1.00
228_L	241_I	0.614	1.00
55_A	59_A	0.611	1.00
111_A	114_S	0.611	1.00
212_A	215_G	0.610	1.00
165_I	196_C	0.607	1.00
113_E	116_A	0.605	1.00
57_R	61_E	0.604	1.00
69_I	80_Q	0.600	1.00
35_H	40_R	0.600	1.00
173_G	177_N	0.598	1.00
107_V	114_S	0.596	1.00
150_F	154_V	0.596	1.00
44_A	52_G	0.594	1.00
243_E	248_L	0.594	1.00
106_C	110_T	0.591	1.00
216_L	220_K	0.589	1.00
76_F	79_G	0.588	1.00
192_D	195_D	0.586	1.00
217_S	244_A	0.585	1.00
94_I	99_A	0.584	1.00
192_D	200_M	0.582	1.00
126_S	135_I	0.579	1.00
26_D	50_R	0.576	1.00
127_P	131_E	0.576	1.00
116_A	151_A	0.576	1.00
48_Q	76_F	0.573	1.00
55_A	61_E	0.571	1.00
88_E	92_F	0.567	1.00
215_G	219_R	0.566	1.00
213_I	240_D	0.565	1.00
29_F	34_D	0.563	1.00
48_Q	73_I	0.562	1.00
242_I	249_G	0.562	1.00
40_R	48_Q	0.556	1.00
237_V	241_I	0.555	1.00
112_I	148_T	0.554	1.00
162_P	166_N	0.551	1.00
220_K	249_G	0.551	1.00
213_I	228_L	0.550	1.00
130_V	134_Q	0.549	1.00
41_I	46_V	0.548	1.00
49_L	53_Q	0.548	1.00
175_V	182_A	0.547	1.00
46_V	51_G	0.546	1.00
65_D	71_R	0.544	1.00
176_R	180_A	0.544	1.00
27_E	31_L	0.542	1.00
92_F	95_L	0.540	1.00
100_L	108_R	0.528	1.00
149_A	153_S	0.525	1.00
57_R	60_I	0.523	1.00
210_I	237_V	0.521	1.00
44_A	73_I	0.519	0.99
243_E	249_G	0.518	0.99
112_I	117_Q	0.518	0.99
238_Y	249_G	0.518	0.99
239_D	246_G	0.513	0.99
240_D	245_A	0.512	0.99
63_C	66_K	0.511	0.99
217_S	247_E	0.510	0.99
233_K	256_V	0.510	0.99
69_I	72_D	0.507	0.99
229_C	239_D	0.506	0.99
44_A	59_A	0.502	0.99
30_R	33_D	0.501	0.99
74_G	78_L	0.500	0.99

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
1oyzA	1	0.975	100	0.279	Contact Map
4d4zA	1	0.9	99.9	0.411	Contact Map
1wa5B	1	0.9143	99.9	0.414	Contact Map
1b3uA	1	0.9929	99.9	0.429	Contact Map
3tpoA	1	0.9393	99.8	0.438	Contact Map
4rv1A	1	0.9929	99.8	0.446	Contact Map
4lacA	1	0.7179	99.8	0.456	Contact Map
4rxhB	1	0.9893	99.8	0.468	Contact Map
4uafB	1	0.9286	99.8	0.47	Contact Map
3nowA	3	0.9964	99.8	0.47	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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