YXEB - BACSU - GREMLIN Contacts

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YXEB - Iron(3+)-hydroxamate-binding protein YxeB

UniProt:	P54941	Sequences: MKKNILLVGMLVLLLMFVSACSGTASKGSSSDSASEKTEMRTYKSPKGNVNIPAHPKRIVTDFYAGELLSVGANVVGSGSWSFDNPFLKSKLKNVKDVGDPISVEKVMELQPDLIVVMNEENVDKLKKIAPTVVIPYNTAKNVEDTVSMFGDIAGAKDQAKSFMADFNKKAEAAKKKIAGVIDKDATFGIYENTDKGEFWVFNDNGGRGGQAVYNALGLKAPEKIEQDVIKKGEMKQLSQEVIPEYAADYMFITDYNPKGESKTLDKLENSSIWKNLDAVKHNRVFINDFDSFYPYDPISVSKQVDIITDMLIKRAEENKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	321 (281)
Sequences:	13463 (10698)
Seq/√Len:	638.2

ECOLI - FECB FEPB FHUD BTUF
BACSU - YXEB YVRC FHUD YFIY YHFQ FEUA YFMC YCLQ BTR
HALSA - BTUFA Q9HMG8 Q9HMF9 Q9HPB0
SULSO - Q97ZU2 Q980Z0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
148_S	161_K	4.117	1.00
247_A	278_D	4.050	1.00
151_G	160_A	3.931	1.00
144_E	168_N	3.821	1.00
156_A	159_Q	3.375	1.00
170_K	306_D	3.180	1.00
152_D	157_K	3.152	1.00
278_D	282_H	3.110	1.00
44_K	49_N	3.059	1.00
61_T	65_A	2.873	1.00
159_Q	162_S	2.666	1.00
42_T	49_N	2.652	1.00
172_E	176_K	2.645	1.00
148_S	164_M	2.634	1.00
161_K	165_A	2.563	1.00
165_A	169_K	2.509	1.00
106_K	109_E	2.485	1.00
214_Y	219_L	2.477	1.00
242_V	245_E	2.351	1.00
45_S	50_V	2.192	1.00
60_V	107_V	2.144	1.00
170_K	302_S	2.104	1.00
168_N	172_E	2.090	1.00
59_I	154_A	2.053	1.00
187_T	220_K	2.050	1.00
68_L	154_A	2.037	1.00
269_E	283_N	2.015	1.00
169_K	173_A	2.010	1.00
58_R	76_V	1.987	1.00
211_Q	215_N	1.986	1.00
173_A	177_K	1.951	1.00
249_D	278_D	1.945	1.00
67_E	147_V	1.915	1.00
73_A	154_A	1.860	1.00
162_S	166_D	1.854	1.00
125_K	128_K	1.843	1.00
266_D	270_N	1.835	1.00
42_T	51_N	1.811	1.00
123_V	127_K	1.777	1.00
40_M	51_N	1.758	1.00
73_A	156_A	1.757	1.00
142_N	145_D	1.754	1.00
250_Y	286_F	1.744	1.00
116_V	150_F	1.742	1.00
250_Y	284_R	1.735	1.00
277_L	280_V	1.730	1.00
265_L	269_E	1.696	1.00
158_D	162_S	1.686	1.00
172_E	175_K	1.668	1.00
278_D	281_K	1.656	1.00
102_I	107_V	1.601	1.00
145_D	148_S	1.585	1.00
96_K	106_K	1.585	1.00
276_N	281_K	1.582	1.00
306_D	310_D	1.541	1.00
77_G	110_L	1.538	1.00
41_R	152_D	1.537	1.00
60_V	110_L	1.528	1.00
262_S	266_D	1.512	1.00
124_D	128_K	1.467	1.00
166_D	170_K	1.461	1.00
108_M	129_I	1.456	1.00
176_K	179_A	1.434	1.00
240_Q	271_S	1.432	1.00
274_W	280_V	1.430	1.00
251_M	279_A	1.429	1.00
145_D	149_M	1.427	1.00
159_Q	163_F	1.415	1.00
105_E	241_E	1.415	1.00
266_D	269_E	1.408	1.00
186_A	250_Y	1.408	1.00
188_F	219_L	1.400	1.00
120_E	124_D	1.399	1.00
103_S	106_K	1.387	1.00
174_A	305_V	1.367	1.00
76_V	110_L	1.360	1.00
174_A	309_T	1.355	1.00
60_V	77_G	1.341	1.00
144_E	164_M	1.326	1.00
169_K	172_E	1.307	1.00
45_S	48_G	1.306	1.00
165_A	168_N	1.302	1.00
61_T	68_L	1.294	1.00
71_V	156_A	1.291	1.00
117_V	134_V	1.285	1.00
198_E	237_Q	1.279	1.00
79_G	82_S	1.278	1.00
157_K	161_K	1.270	1.00
158_D	161_K	1.269	1.00
133_V	153_I	1.266	1.00
68_L	73_A	1.248	1.00
307_I	310_D	1.248	1.00
124_D	127_K	1.242	1.00
14_L	17_F	1.236	1.00
173_A	176_K	1.229	1.00
170_K	173_A	1.217	1.00
52_I	55_H	1.214	1.00
263_K	266_D	1.196	1.00
149_M	152_D	1.194	1.00
187_T	249_D	1.194	1.00
13_L	16_M	1.190	1.00
148_S	168_N	1.186	1.00
286_F	311_M	1.186	1.00
57_K	113_D	1.184	1.00
147_V	160_A	1.179	1.00
163_F	166_D	1.178	1.00
96_K	99_G	1.175	1.00
58_R	111_Q	1.171	1.00
189_G	192_E	1.167	1.00
242_V	246_Y	1.164	1.00
204_D	215_N	1.161	1.00
166_D	169_K	1.158	1.00
104_V	125_K	1.150	1.00
86_P	89_K	1.148	1.00
164_M	168_N	1.127	1.00
133_V	149_M	1.123	1.00
56_P	113_D	1.118	1.00
45_S	123_V	1.107	1.00
175_K	216_A	1.095	1.00
177_K	309_T	1.090	1.00
70_S	163_F	1.086	1.00
59_I	114_L	1.077	1.00
40_M	54_A	1.075	1.00
222_P	246_Y	1.066	1.00
114_L	133_V	1.062	1.00
122_N	125_K	1.058	1.00
69_L	92_L	1.048	1.00
178_I	181_V	1.043	1.00
223_E	246_Y	1.040	1.00
190_I	214_Y	1.034	1.00
115_I	130_A	1.028	1.00
274_W	277_L	1.021	1.00
90_S	93_K	1.001	1.00
40_M	55_H	1.001	1.00
220_K	224_K	0.999	1.00
189_G	201_V	0.996	1.00
186_A	284_R	0.991	1.00
57_K	74_N	0.990	1.00
189_G	248_A	0.988	1.00
183_D	186_A	0.987	1.00
175_K	179_A	0.984	1.00
148_S	152_D	0.982	1.00
171_A	305_V	0.969	1.00
250_Y	312_L	0.966	1.00
222_P	225_I	0.959	1.00
280_V	285_V	0.959	1.00
47_K	127_K	0.956	1.00
272_S	275_K	0.944	1.00
278_D	284_R	0.943	1.00
219_L	312_L	0.940	1.00
75_V	95_V	0.937	1.00
11_L	15_L	0.936	1.00
39_E	54_A	0.934	1.00
252_F	308_I	0.932	1.00
149_M	153_I	0.932	1.00
188_F	214_Y	0.931	1.00
52_I	131_P	0.926	1.00
151_G	164_M	0.925	1.00
171_A	175_K	0.924	1.00
47_K	134_V	0.923	1.00
135_I	149_M	0.923	1.00
253_I	287_I	0.917	1.00
212_A	215_N	0.914	1.00
78_S	95_V	0.914	1.00
59_I	68_L	0.913	1.00
160_A	164_M	0.906	1.00
305_V	309_T	0.905	1.00
263_K	267_K	0.903	1.00
170_K	174_A	0.902	1.00
68_L	75_V	0.900	1.00
223_E	242_V	0.897	1.00
80_S	97_D	0.896	1.00
167_F	216_A	0.896	1.00
15_L	18_V	0.893	1.00
269_E	285_V	0.889	1.00
39_E	155_G	0.882	1.00
150_F	154_A	0.871	1.00
55_H	156_A	0.870	1.00
52_I	56_P	0.869	1.00
206_G	211_Q	0.868	1.00
40_M	53_P	0.867	1.00
68_L	116_V	0.865	1.00
202_F	206_G	0.858	1.00
225_I	246_Y	0.855	1.00
54_A	57_K	0.851	1.00
243_I	277_L	0.844	1.00
67_E	150_F	0.839	1.00
267_K	270_N	0.839	1.00
69_L	75_V	0.838	1.00
16_M	19_S	0.835	1.00
45_S	49_N	0.834	1.00
161_K	164_M	0.834	1.00
112_P	115_I	0.829	1.00
116_V	153_I	0.828	1.00
289_D	292_S	0.826	1.00
305_V	310_D	0.824	1.00
89_K	92_L	0.823	1.00
275_K	280_V	0.821	1.00
56_P	114_L	0.820	1.00
69_L	91_K	0.818	1.00
244_P	277_L	0.813	1.00
306_D	309_T	0.813	1.00
55_H	155_G	0.812	1.00
43_Y	133_V	0.811	1.00
167_F	171_A	0.810	1.00
66_G	297_D	0.809	1.00
189_G	193_N	0.808	1.00
78_S	97_D	0.808	1.00
150_F	153_I	0.804	1.00
71_V	163_F	0.803	1.00
183_D	220_K	0.802	1.00
74_N	156_A	0.800	1.00
71_V	154_A	0.797	1.00
289_D	307_I	0.796	1.00
14_L	18_V	0.794	1.00
115_I	129_I	0.793	1.00
212_A	216_A	0.792	1.00
41_R	52_I	0.792	1.00
302_S	306_D	0.791	1.00
39_E	55_H	0.791	1.00
21_C	24_T	0.788	1.00
162_S	165_A	0.788	1.00
265_L	287_I	0.786	1.00
114_L	153_I	0.785	1.00
12_V	16_M	0.780	1.00
264_T	267_K	0.778	1.00
64_Y	116_V	0.773	1.00
70_S	147_V	0.771	1.00
86_P	90_S	0.770	1.00
248_A	251_M	0.768	1.00
190_I	254_T	0.761	1.00
148_S	151_G	0.750	1.00
177_K	180_G	0.749	1.00
221_A	225_I	0.744	1.00
77_G	99_G	0.743	1.00
307_I	311_M	0.742	1.00
71_V	159_Q	0.741	1.00
201_V	223_E	0.739	1.00
127_K	132_T	0.738	1.00
252_F	286_F	0.736	1.00
9_G	13_L	0.734	1.00
71_V	151_G	0.731	1.00
146_T	149_M	0.728	1.00
19_S	22_S	0.724	1.00
256_Y	290_F	0.720	1.00
244_P	276_N	0.718	1.00
147_V	163_F	0.717	1.00
144_E	148_S	0.712	1.00
202_F	235_M	0.712	1.00
171_A	216_A	0.710	1.00
191_Y	251_M	0.709	1.00
186_A	219_L	0.708	1.00
262_S	265_L	0.706	1.00
163_F	167_F	0.706	1.00
10_M	14_L	0.705	1.00
178_I	309_T	0.702	1.00
144_E	171_A	0.701	1.00
271_S	275_K	0.701	1.00
189_G	243_I	0.701	1.00
191_Y	194_T	0.701	1.00
98_V	110_L	0.697	1.00
213_V	305_V	0.696	1.00
61_T	75_V	0.695	1.00
66_G	299_I	0.694	1.00
11_L	17_F	0.694	1.00
119_N	136_P	0.688	1.00
92_L	95_V	0.688	1.00
299_I	302_S	0.682	1.00
253_I	285_V	0.682	1.00
60_V	112_P	0.682	1.00
10_M	13_L	0.680	1.00
297_D	300_S	0.680	1.00
190_I	210_G	0.680	1.00
17_F	20_A	0.677	1.00
309_T	312_L	0.674	1.00
175_K	217_L	0.673	1.00
107_V	126_L	0.668	1.00
15_L	19_S	0.668	1.00
304_Q	308_I	0.667	1.00
11_L	14_L	0.665	1.00
121_E	124_D	0.663	1.00
304_Q	307_I	0.658	1.00
238_L	246_Y	0.655	1.00
72_G	156_A	0.655	1.00
12_V	15_L	0.655	1.00
91_K	94_N	0.652	1.00
123_V	134_V	0.651	1.00
188_F	252_F	0.650	1.00
88_L	92_L	0.650	1.00
174_A	178_I	0.647	1.00
104_V	122_N	0.646	1.00
298_P	302_S	0.646	1.00
70_S	299_I	0.644	1.00
170_K	309_T	0.644	1.00
148_S	157_K	0.643	1.00
295_P	300_S	0.642	1.00
105_E	108_M	0.642	1.00
43_Y	52_I	0.641	1.00
58_R	113_D	0.640	1.00
72_G	159_Q	0.638	1.00
104_V	129_I	0.638	1.00
247_A	251_M	0.637	1.00
46_P	149_M	0.635	1.00
200_W	237_Q	0.631	1.00
244_P	248_A	0.630	1.00
20_A	24_T	0.628	1.00
71_V	147_V	0.627	1.00
143_V	167_F	0.626	1.00
52_I	114_L	0.626	1.00
64_Y	150_F	0.625	1.00
264_T	268_L	0.624	1.00
75_V	78_S	0.624	1.00
96_K	110_L	0.622	1.00
120_E	123_V	0.616	1.00
250_Y	254_T	0.616	1.00
88_L	91_K	0.616	1.00
174_A	177_K	0.614	1.00
18_V	21_C	0.610	1.00
39_E	53_P	0.609	1.00
308_I	312_L	0.607	1.00
255_D	287_I	0.606	1.00
191_Y	271_S	0.606	1.00
21_C	25_A	0.605	1.00
52_I	153_I	0.600	1.00
154_A	157_K	0.600	1.00
240_Q	274_W	0.598	1.00
50_V	133_V	0.596	1.00
251_M	274_W	0.596	1.00
61_T	64_Y	0.595	1.00
65_A	78_S	0.594	1.00
239_S	242_V	0.594	1.00
41_R	54_A	0.591	1.00
10_M	17_F	0.591	1.00
188_F	191_Y	0.585	1.00
55_H	113_D	0.585	1.00
274_W	285_V	0.584	1.00
104_V	107_V	0.582	1.00
296_Y	304_Q	0.581	1.00
167_F	170_K	0.579	1.00
304_Q	310_D	0.578	1.00
71_V	150_F	0.576	1.00
87_F	90_S	0.575	1.00
167_F	301_V	0.573	1.00
135_I	139_T	0.572	1.00
166_D	302_S	0.568	1.00
204_D	224_K	0.567	1.00
131_P	134_V	0.567	1.00
144_E	167_F	0.566	1.00
105_E	239_S	0.564	1.00
164_M	167_F	0.564	1.00
12_V	17_F	0.563	1.00
211_Q	221_A	0.561	1.00
254_T	288_N	0.560	1.00
56_P	154_A	0.560	1.00
135_I	150_F	0.560	1.00
292_S	307_I	0.559	1.00
71_V	160_A	0.559	1.00
192_E	196_K	0.558	1.00
62_D	118_M	0.557	1.00
95_V	99_G	0.556	1.00
102_I	122_N	0.556	1.00
231_K	236_K	0.552	1.00
53_P	131_P	0.550	1.00
60_V	76_V	0.549	1.00
20_A	23_G	0.548	1.00
214_Y	217_L	0.546	1.00
176_K	180_G	0.545	1.00
106_K	110_L	0.544	1.00
188_F	192_E	0.544	1.00
68_L	150_F	0.544	1.00
37_K	40_M	0.540	1.00
217_L	305_V	0.540	1.00
238_L	243_I	0.537	0.99
60_V	115_I	0.536	0.99
93_K	96_K	0.535	0.99
36_E	39_E	0.534	0.99
147_V	164_M	0.533	0.99
268_L	271_S	0.532	0.99
115_I	126_L	0.531	0.99
168_N	171_A	0.530	0.99
173_A	306_D	0.530	0.99
191_Y	201_V	0.529	0.99
264_T	269_E	0.529	0.99
271_S	274_W	0.529	0.99
143_V	147_V	0.529	0.99
50_V	131_P	0.529	0.99
69_L	95_V	0.529	0.99
223_E	238_L	0.527	0.99
58_R	110_L	0.526	0.99
189_G	222_P	0.526	0.99
186_A	249_D	0.525	0.99
47_K	123_V	0.525	0.99
64_Y	135_I	0.525	0.99
75_V	79_G	0.524	0.99
221_A	224_K	0.524	0.99
13_L	17_F	0.522	0.99
244_P	273_I	0.520	0.99
41_R	55_H	0.520	0.99
87_F	91_K	0.519	0.99
77_G	98_V	0.519	0.99
108_M	241_E	0.518	0.99
293_F	304_Q	0.518	0.99
144_E	216_A	0.517	0.99
174_A	217_L	0.516	0.99
187_T	222_P	0.516	0.99
171_A	174_A	0.515	0.99
277_L	281_K	0.515	0.99
56_P	59_I	0.515	0.99
148_S	160_A	0.514	0.99
47_K	120_E	0.512	0.99
301_V	304_Q	0.512	0.99
121_E	125_K	0.511	0.99
67_E	298_P	0.509	0.99
67_E	70_S	0.507	0.99
115_I	132_T	0.506	0.99
247_A	277_L	0.504	0.99
217_L	309_T	0.503	0.99
65_A	82_S	0.502	0.99
137_Y	146_T	0.502	0.99
206_G	235_M	0.502	0.99
219_L	250_Y	0.501	0.99
99_G	102_I	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
4n01A	1	0.8505	100	0.245	Contact Map
4mlzA	1	0.8411	100	0.267	Contact Map
4hn9A	1	0.866	100	0.293	Contact Map
4mo9A	1	0.8442	100	0.298	Contact Map
4ovkA	1	0.8474	100	0.3	Contact Map
3tlkA	1	0.8411	100	0.306	Contact Map
3lhsA	1	0.8567	100	0.309	Contact Map
4ljsA	1	0.8785	100	0.319	Contact Map
3tnyA	1	0.8287	100	0.322	Contact Map
4pagA	2	0.838	100	0.322	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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