YFMC - BACSU - GREMLIN Contacts

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YFMC - Fe(3+)-citrate-binding protein YfmC

UniProt:	O34348	Sequences: MRTYSNKLIAIMSVLLLACLIVSGCSSSQNNNGSGKSESKDSRVIHDEEGKTTVSGTPKRVVVLELSFLDAVHNLGITPVGIADDNKKDMIKKLVGSSIDYTSVGTRSEPNLEVISSLKPDLIIADAERHKNIYKQLKKIAPTIELKSREATYDETIDSFTTIAKALNKEDEGKEKLAEHKKVINDLKAELPKDENRNIVLGVARADSFQLHTSSSYDGEIFKMLGFTHAVKSDNAYQEVSLEQLSKIDPDILFISANEGKTIVDEWKTNPLWKNLKAVKNGQVYDADRDTWTRFRGIKSSETSAKDVLKKVYNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	315 (283)
Sequences:	14161 (11154)
Seq/√Len:	663.0

ECOLI - FECB FEPB FHUD BTUF
BACSU - YFMC FHUD YCLQ FEUA YHFQ YFIY YVRC YXEB BTR
HALSA - BTUFA Q9HMF9 Q9HMG8 Q9HPB0 Q9HSB2
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
161_T	174_K	4.155	1.00
164_A	173_G	4.048	1.00
249_D	277_K	4.043	1.00
157_I	181_K	3.916	1.00
169_K	172_E	3.511	1.00
165_K	170_E	3.230	1.00
277_K	281_N	3.110	1.00
46_H	51_K	3.013	1.00
63_V	69_L	2.964	1.00
161_T	177_L	2.791	1.00
172_E	175_E	2.649	1.00
44_V	51_K	2.643	1.00
185_N	189_A	2.614	1.00
222_F	227_F	2.613	1.00
174_K	178_A	2.575	1.00
183_V	306_K	2.535	1.00
183_V	302_E	2.512	1.00
114_V	117_S	2.509	1.00
178_A	182_K	2.506	1.00
244_Q	247_K	2.368	1.00
47_D	52_T	2.251	1.00
62_V	115_I	2.248	1.00
198_N	228_T	2.157	1.00
72_V	167_L	2.147	1.00
61_V	167_L	2.113	1.00
219_G	223_K	2.085	1.00
181_K	185_N	2.081	1.00
77_I	167_L	2.024	1.00
182_K	186_D	2.015	1.00
251_D	277_K	1.984	1.00
136_Q	139_K	1.978	1.00
268_K	282_G	1.967	1.00
186_D	190_E	1.923	1.00
265_D	269_T	1.916	1.00
142_P	147_K	1.902	1.00
71_A	160_F	1.877	1.00
77_I	169_K	1.861	1.00
134_Y	138_K	1.846	1.00
175_E	179_E	1.836	1.00
252_I	285_Y	1.779	1.00
124_I	163_I	1.767	1.00
42_S	53_T	1.763	1.00
155_E	158_D	1.760	1.00
276_L	279_V	1.743	1.00
44_V	53_T	1.722	1.00
171_D	175_E	1.711	1.00
252_I	283_Q	1.681	1.00
264_V	268_K	1.656	1.00
179_E	183_V	1.637	1.00
185_N	188_K	1.607	1.00
277_K	280_K	1.607	1.00
43_R	165_K	1.601	1.00
158_D	161_T	1.583	1.00
110_P	115_I	1.549	1.00
102_T	114_V	1.549	1.00
275_N	280_K	1.548	1.00
135_K	139_K	1.534	1.00
62_V	118_L	1.523	1.00
172_E	176_K	1.520	1.00
111_N	114_V	1.469	1.00
158_D	162_T	1.456	1.00
199_I	227_F	1.433	1.00
265_D	268_K	1.432	1.00
307_D	310_K	1.430	1.00
131_K	135_K	1.419	1.00
116_S	140_I	1.414	1.00
273_W	279_V	1.393	1.00
197_R	252_I	1.392	1.00
196_N	228_T	1.378	1.00
261_K	265_D	1.373	1.00
170_E	174_K	1.361	1.00
189_A	192_P	1.357	1.00
157_I	177_L	1.354	1.00
63_V	72_V	1.351	1.00
242_L	270_N	1.345	1.00
113_E	243_E	1.341	1.00
143_T	147_K	1.336	1.00
253_L	278_A	1.310	1.00
161_T	181_K	1.297	1.00
176_K	179_E	1.294	1.00
244_Q	248_I	1.289	1.00
75_L	169_K	1.289	1.00
178_A	181_K	1.286	1.00
47_D	50_G	1.286	1.00
183_V	186_D	1.284	1.00
208_S	239_E	1.279	1.00
60_R	80_V	1.266	1.00
231_V	248_I	1.259	1.00
233_S	248_I	1.258	1.00
88_K	91_I	1.254	1.00
135_K	138_K	1.252	1.00
54_V	57_T	1.248	1.00
182_K	185_N	1.227	1.00
171_D	174_K	1.225	1.00
59_K	121_D	1.218	1.00
59_K	80_V	1.211	1.00
18_A	21_I	1.210	1.00
186_D	189_A	1.208	1.00
130_H	133_I	1.208	1.00
187_L	305_A	1.196	1.00
72_V	77_I	1.196	1.00
58_P	121_D	1.177	1.00
230_A	248_I	1.173	1.00
162_T	165_K	1.168	1.00
200_V	203_V	1.166	1.00
142_P	145_E	1.158	1.00
160_F	173_G	1.153	1.00
112_L	136_Q	1.152	1.00
198_N	251_D	1.142	1.00
60_R	119_K	1.129	1.00
214_S	223_K	1.124	1.00
302_E	306_K	1.119	1.00
177_L	181_K	1.118	1.00
188_K	224_M	1.103	1.00
305_A	309_L	1.101	1.00
73_H	78_T	1.099	1.00
74_N	176_K	1.098	1.00
262_T	265_D	1.092	1.00
90_M	93_K	1.085	1.00
179_E	182_K	1.083	1.00
47_D	134_Y	1.074	1.00
188_K	192_P	1.069	1.00
42_S	55_S	1.056	1.00
61_V	122_L	1.055	1.00
187_L	309_L	1.046	1.00
200_V	250_P	1.043	1.00
81_G	84_D	1.036	1.00
201_L	222_F	1.035	1.00
42_S	56_G	1.032	1.00
197_R	283_Q	1.024	1.00
200_V	211_L	1.022	1.00
123_I	141_A	1.016	1.00
81_G	118_L	1.007	1.00
125_A	145_E	0.998	1.00
262_T	266_E	0.992	1.00
133_I	136_Q	0.990	1.00
306_K	310_K	0.989	1.00
184_I	188_K	0.987	1.00
89_D	92_K	0.985	1.00
72_V	124_I	0.983	1.00
273_W	276_L	0.975	1.00
255_I	286_D	0.971	1.00
42_S	57_T	0.968	1.00
228_T	232_K	0.964	1.00
144_I	166_A	0.961	1.00
190_E	309_L	0.960	1.00
60_R	82_I	0.959	1.00
161_T	165_K	0.945	1.00
285_Y	311_K	0.941	1.00
81_G	101_Y	0.938	1.00
254_F	308_V	0.936	1.00
91_I	94_L	0.935	1.00
80_V	169_K	0.931	1.00
164_A	177_L	0.930	1.00
41_D	168_N	0.927	1.00
61_V	72_V	0.926	1.00
271_P	274_K	0.926	1.00
183_V	187_L	0.924	1.00
49_E	138_K	0.916	1.00
85_D	88_K	0.916	1.00
151_A	154_D	0.911	1.00
162_T	166_A	0.910	1.00
277_K	283_Q	0.905	1.00
231_V	244_Q	0.905	1.00
199_I	222_F	0.904	1.00
266_E	269_T	0.904	1.00
305_A	310_K	0.897	1.00
220_E	223_K	0.893	1.00
180_H	224_M	0.893	1.00
279_V	284_V	0.890	1.00
75_L	176_K	0.889	1.00
71_A	163_I	0.883	1.00
57_T	169_K	0.881	1.00
263_I	266_E	0.878	1.00
47_D	51_K	0.878	1.00
41_D	56_G	0.876	1.00
288_D	291_T	0.876	1.00
173_G	177_L	0.876	1.00
20_L	23_S	0.872	1.00
72_V	81_G	0.861	1.00
84_D	103_S	0.860	1.00
54_V	58_P	0.858	1.00
77_I	80_V	0.857	1.00
65_E	126_D	0.856	1.00
300_S	303_T	0.849	1.00
25_C	28_S	0.848	1.00
211_L	231_V	0.843	1.00
56_G	59_K	0.840	1.00
73_H	94_L	0.837	1.00
245_L	276_L	0.836	1.00
58_P	122_L	0.831	1.00
18_A	22_V	0.831	1.00
214_S	232_K	0.826	1.00
299_K	303_T	0.826	1.00
163_I	167_L	0.826	1.00
122_L	166_A	0.823	1.00
43_R	54_V	0.823	1.00
202_G	270_N	0.821	1.00
124_I	166_A	0.818	1.00
88_K	92_K	0.816	1.00
159_S	162_T	0.816	1.00
220_E	224_M	0.814	1.00
70_D	299_K	0.813	1.00
175_E	178_A	0.808	1.00
80_V	83_A	0.807	1.00
180_H	184_I	0.806	1.00
68_F	124_I	0.803	1.00
201_L	256_S	0.803	1.00
246_S	276_L	0.799	1.00
64_L	123_I	0.795	1.00
268_K	284_V	0.794	1.00
274_K	279_V	0.787	1.00
255_I	284_V	0.787	1.00
122_L	144_I	0.784	1.00
120_P	123_I	0.775	1.00
154_D	158_D	0.775	1.00
191_L	194_D	0.775	1.00
161_T	164_A	0.772	1.00
41_D	57_T	0.772	1.00
74_N	299_K	0.770	1.00
19_C	22_V	0.769	1.00
176_K	180_H	0.768	1.00
123_I	140_I	0.768	1.00
49_E	145_E	0.767	1.00
174_K	177_L	0.766	1.00
19_C	23_S	0.766	1.00
57_T	168_N	0.764	1.00
246_S	275_N	0.761	1.00
184_I	305_A	0.760	1.00
200_V	245_L	0.759	1.00
163_I	166_A	0.758	1.00
144_I	162_T	0.757	1.00
254_F	285_Y	0.754	1.00
73_H	93_K	0.754	1.00
25_C	29_Q	0.751	1.00
83_A	118_L	0.747	1.00
98_S	101_Y	0.745	1.00
187_L	191_L	0.744	1.00
240_V	248_I	0.742	1.00
205_R	208_S	0.739	1.00
199_I	203_V	0.738	1.00
84_D	101_Y	0.734	1.00
63_V	81_G	0.730	1.00
74_N	160_F	0.725	1.00
86_N	103_S	0.723	1.00
157_I	161_T	0.720	1.00
75_L	172_E	0.717	1.00
297_G	300_S	0.717	1.00
200_V	204_A	0.716	1.00
76_G	172_E	0.714	1.00
106_T	109_E	0.713	1.00
75_L	167_L	0.713	1.00
303_T	310_K	0.711	1.00
152_T	155_E	0.711	1.00
78_T	81_G	0.711	1.00
256_S	287_A	0.708	1.00
154_D	157_I	0.708	1.00
216_S	219_G	0.704	1.00
79_P	83_A	0.703	1.00
160_F	176_K	0.700	1.00
296_R	299_K	0.700	1.00
304_S	308_V	0.697	1.00
23_S	26_S	0.696	1.00
132_N	135_K	0.696	1.00
212_H	237_Y	0.696	1.00
212_H	216_S	0.695	1.00
75_L	164_A	0.692	1.00
156_T	180_H	0.691	1.00
202_G	253_L	0.690	1.00
62_V	120_P	0.689	1.00
102_T	105_G	0.688	1.00
270_N	274_K	0.687	1.00
183_V	309_L	0.684	1.00
199_I	202_G	0.682	1.00
142_P	146_L	0.680	1.00
82_I	118_L	0.679	1.00
88_K	94_L	0.676	1.00
184_I	224_M	0.676	1.00
303_T	306_K	0.675	1.00
199_I	254_F	0.674	1.00
190_E	193_K	0.673	1.00
261_K	264_V	0.669	1.00
241_S	244_Q	0.668	1.00
75_L	160_F	0.667	1.00
197_R	227_F	0.666	1.00
204_A	207_D	0.666	1.00
127_A	147_K	0.664	1.00
157_I	184_I	0.664	1.00
297_G	301_S	0.660	1.00
264_V	286_D	0.660	1.00
25_C	30_N	0.660	1.00
76_G	169_K	0.659	1.00
90_M	94_L	0.655	1.00
78_T	100_D	0.655	1.00
76_G	79_P	0.653	1.00
70_D	297_G	0.652	1.00
62_V	83_A	0.652	1.00
62_V	104_V	0.650	1.00
167_L	170_E	0.649	1.00
60_R	121_D	0.645	1.00
246_S	250_P	0.644	1.00
69_L	94_L	0.642	1.00
263_I	267_W	0.642	1.00
131_K	134_Y	0.641	1.00
94_L	98_S	0.641	1.00
89_D	93_K	0.637	1.00
138_K	143_T	0.633	1.00
143_T	146_L	0.632	1.00
54_V	142_P	0.632	1.00
21_I	24_G	0.631	1.00
102_T	118_L	0.631	1.00
250_P	253_L	0.629	1.00
112_L	115_I	0.629	1.00
115_I	137_L	0.628	1.00
222_F	225_L	0.628	1.00
63_V	68_F	0.627	1.00
75_L	173_G	0.621	1.00
28_S	31_N	0.621	1.00
252_I	256_S	0.619	1.00
73_H	81_G	0.617	1.00
215_S	219_G	0.616	1.00
113_E	116_S	0.608	1.00
62_V	123_I	0.607	1.00
48_E	162_T	0.607	1.00
41_D	55_S	0.605	1.00
180_H	183_V	0.605	1.00
270_N	273_W	0.604	1.00
287_A	292_W	0.604	1.00
97_S	100_D	0.603	1.00
129_R	133_I	0.603	1.00
189_A	193_K	0.603	1.00
157_I	180_H	0.601	1.00
43_R	56_G	0.596	1.00
45_I	54_V	0.596	1.00
25_C	31_N	0.594	1.00
54_V	122_L	0.590	1.00
72_V	163_I	0.588	1.00
58_P	167_L	0.587	1.00
225_L	309_L	0.584	1.00
219_G	232_K	0.584	1.00
304_S	310_K	0.584	1.00
191_L	309_L	0.580	1.00
177_L	180_H	0.578	1.00
73_H	101_Y	0.578	1.00
257_A	286_D	0.577	1.00
300_S	304_S	0.576	1.00
258_N	289_R	0.574	1.00
188_K	225_L	0.573	1.00
92_K	99_I	0.573	1.00
242_L	273_W	0.572	1.00
80_V	167_L	0.572	1.00
214_S	233_S	0.571	1.00
161_T	170_E	0.570	1.00
146_L	162_T	0.570	1.00
263_I	268_K	0.569	1.00
160_F	177_L	0.568	1.00
215_S	235_N	0.566	1.00
133_I	137_L	0.566	1.00
104_V	118_L	0.566	1.00
299_K	302_E	0.563	1.00
134_Y	137_L	0.563	1.00
43_R	57_T	0.560	1.00
307_D	311_K	0.560	1.00
213_T	219_G	0.558	1.00
214_S	219_G	0.558	1.00
62_V	81_G	0.557	1.00
68_F	163_I	0.557	1.00
176_K	298_I	0.554	1.00
219_G	229_H	0.554	1.00
231_V	240_V	0.554	1.00
227_F	252_I	0.553	1.00
94_L	97_S	0.553	1.00
296_R	300_S	0.553	1.00
157_I	224_M	0.552	1.00
89_D	94_L	0.551	1.00
57_T	121_D	0.550	1.00
200_V	230_A	0.549	1.00
181_K	184_I	0.549	1.00
234_D	238_Q	0.549	1.00
112_L	133_I	0.549	1.00
201_L	218_D	0.547	1.00
180_H	301_S	0.544	1.00
253_L	273_W	0.543	1.00
114_V	118_L	0.542	1.00
116_S	243_E	0.542	1.00
132_N	136_Q	0.541	1.00
212_H	218_D	0.540	1.00
230_A	233_S	0.539	1.00
216_S	237_Y	0.534	1.00
198_N	252_I	0.534	1.00
184_I	301_S	0.530	1.00
240_V	245_L	0.530	1.00
46_H	49_E	0.529	1.00
24_G	28_S	0.529	1.00
298_I	302_E	0.528	0.99
267_W	270_N	0.528	0.99
49_E	131_K	0.528	0.99
187_L	190_E	0.528	0.99
305_A	311_K	0.526	0.99
71_A	74_N	0.526	0.99
303_T	307_D	0.523	0.99
69_L	82_I	0.523	0.99
302_E	305_A	0.521	0.99
52_T	144_I	0.519	0.99
210_Q	237_Y	0.517	0.99
113_E	241_S	0.517	0.99
276_L	280_K	0.515	0.99
197_R	201_L	0.515	0.99
105_G	110_P	0.514	0.99
41_D	58_P	0.514	0.99
198_N	230_A	0.512	0.99
112_L	140_I	0.511	0.99
54_V	166_A	0.510	0.99
301_S	305_A	0.508	0.99
68_F	71_A	0.507	0.99
42_S	54_V	0.506	0.99
184_I	187_L	0.506	0.99
246_S	272_L	0.506	0.99
295_F	300_S	0.505	0.99
264_V	267_W	0.504	0.99
273_W	284_V	0.503	0.99
188_K	191_L	0.501	0.99
216_S	236_A	0.500	0.99
210_Q	239_E	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	0.873	100	0.199	Contact Map
3tnyA	1	0.8508	100	0.259	Contact Map
3lhsA	1	0.8698	100	0.263	Contact Map
4mlzA	1	0.873	100	0.263	Contact Map
3tlkA	1	0.8571	100	0.271	Contact Map
4hn9A	1	0.8794	100	0.274	Contact Map
3gfvA	1	0.8635	100	0.28	Contact Map
4mx8A	1	0.8698	100	0.281	Contact Map
3mwfA	1	0.8476	100	0.282	Contact Map
4mo9A	1	0.8698	100	0.284	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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