YFMS - BACSU - GREMLIN Contacts

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YFMS - Putative sensory transducer protein YfmS

UniProt:	O06477	Sequences: MELTINTEKETADILDAFIKVAPYLNSLVQDDITIGIYDTEKLLVNIPAKTFSLNVKAGDPLQEGDIITDAIRSNQKKTSMVPKELFGFPLIARAIPLHDENGRVIGGVGLGTSLEESSKLHDVAESLSAVVEQTAAAISDISESINGFSTQMSGISSQAKKVSESAGEIADISVTVKGISDQSNLLGLNAAIEAARAGESGKGFSVVADEIRKLATHSKENVGQIDQITKKIHSLLKGLEESIESINQHTDGQAAAVEQISATMQEISGSAQHLAKMAEKALEEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	286 (270)
Sequences:	28789 (23037)
Seq/√Len:	1402.0

ECOLI - AER MCP3 MCP2 MCP1 MCP4
BACSU - YFMS MCPC TLPA MCPB MCPA TLPB YVAQ YOAH TLPC HEMAT
HALSA - Q9HQX8 Q9HS86 Q9HPQ5 Q9HRN6 HTR9 Q9HPA2 HMAT HTR4 HTR7 Q9HRA1 HTR2 HTR1 COST Q9HP10 Q9HR88 Q9HQT5 Q9HPW6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_S	35_I	2.436	1.00
27_S	32_D	2.367	1.00
53_S	56_V	2.310	1.00
41_E	46_N	2.173	1.00
169_E	172_D	2.064	1.00
22_A	47_I	2.028	1.00
166_S	236_L	1.968	1.00
36_G	60_D	1.963	1.00
114_S	117_E	1.927	1.00
165_E	168_G	1.878	1.00
151_T	155_G	1.852	1.00
166_S	232_K	1.835	1.00
175_V	179_G	1.804	1.00
43_L	46_N	1.781	1.00
162_K	236_L	1.758	1.00
161_K	165_E	1.745	1.00
22_A	51_T	1.740	1.00
28_L	56_V	1.721	1.00
137_A	141_D	1.718	1.00
144_E	148_G	1.696	1.00
21_V	49_A	1.687	1.00
141_D	144_E	1.678	1.00
164_S	168_G	1.669	1.00
166_S	169_E	1.644	1.00
25_L	55_N	1.638	1.00
134_Q	137_A	1.634	1.00
178_K	227_D	1.630	1.00
126_E	130_A	1.627	1.00
26_N	47_I	1.624	1.00
165_E	169_E	1.622	1.00
214_K	217_T	1.619	1.00
217_T	221_E	1.617	1.00
238_K	242_E	1.614	1.00
119_S	123_D	1.611	1.00
130_A	134_Q	1.592	1.00
227_D	231_K	1.584	1.00
158_S	162_K	1.580	1.00
162_K	165_E	1.579	1.00
25_L	52_F	1.569	1.00
252_D	256_A	1.567	1.00
53_S	57_K	1.563	1.00
260_Q	263_A	1.558	1.00
155_G	158_S	1.549	1.00
140_S	144_E	1.535	1.00
120_K	123_D	1.529	1.00
26_N	51_T	1.525	1.00
164_S	241_E	1.512	1.00
267_E	270_G	1.510	1.00
26_N	54_L	1.499	1.00
224_G	228_Q	1.492	1.00
147_N	151_T	1.488	1.00
148_G	151_T	1.486	1.00
239_G	242_E	1.485	1.00
127_S	130_A	1.484	1.00
133_E	137_A	1.483	1.00
172_D	175_V	1.472	1.00
61_P	64_E	1.469	1.00
221_E	225_Q	1.468	1.00
136_A	140_S	1.453	1.00
22_A	26_N	1.451	1.00
253_G	256_A	1.443	1.00
259_E	263_A	1.442	1.00
123_D	127_S	1.436	1.00
28_L	55_N	1.425	1.00
242_E	245_E	1.408	1.00
154_S	158_S	1.406	1.00
19_I	22_A	1.402	1.00
176_T	222_N	1.399	1.00
151_T	154_S	1.399	1.00
152_Q	246_S	1.393	1.00
159_Q	239_G	1.393	1.00
220_K	224_G	1.386	1.00
36_G	53_S	1.378	1.00
113_T	117_E	1.365	1.00
96_I	99_H	1.365	1.00
158_S	161_K	1.352	1.00
58_A	61_P	1.351	1.00
123_D	126_E	1.347	1.00
249_Q	253_G	1.346	1.00
274_H	277_K	1.344	1.00
36_G	57_K	1.341	1.00
249_Q	252_D	1.341	1.00
242_E	246_S	1.339	1.00
99_H	103_G	1.339	1.00
73_R	77_K	1.329	1.00
74_S	78_K	1.328	1.00
219_S	223_V	1.327	1.00
100_D	103_G	1.327	1.00
36_G	56_V	1.326	1.00
130_A	133_E	1.318	1.00
92_I	96_I	1.308	1.00
60_D	63_Q	1.302	1.00
143_S	147_N	1.289	1.00
66_D	70_D	1.283	1.00
76_Q	79_T	1.282	1.00
137_A	140_S	1.280	1.00
266_Q	270_G	1.275	1.00
221_E	224_G	1.275	1.00
148_G	250_H	1.274	1.00
129_S	133_E	1.272	1.00
70_D	74_S	1.272	1.00
256_A	260_Q	1.265	1.00
161_K	164_S	1.261	1.00
47_I	50_K	1.261	1.00
263_A	267_E	1.258	1.00
160_A	240_L	1.248	1.00
144_E	147_N	1.247	1.00
67_I	71_A	1.242	1.00
32_D	35_I	1.242	1.00
110_G	114_S	1.237	1.00
26_N	30_Q	1.230	1.00
56_V	60_D	1.227	1.00
240_L	244_I	1.224	1.00
235_S	239_G	1.210	1.00
169_E	225_Q	1.209	1.00
152_Q	155_G	1.208	1.00
225_Q	228_Q	1.204	1.00
89_F	93_A	1.200	1.00
269_S	273_Q	1.192	1.00
245_E	249_Q	1.192	1.00
179_G	218_H	1.184	1.00
169_E	229_I	1.177	1.00
171_A	234_H	1.169	1.00
232_K	236_L	1.159	1.00
210_D	213_R	1.157	1.00
96_I	100_D	1.153	1.00
150_S	154_S	1.151	1.00
67_I	70_D	1.148	1.00
59_G	62_L	1.142	1.00
182_D	193_I	1.141	1.00
82_V	86_L	1.135	1.00
24_Y	37_I	1.133	1.00
25_L	51_T	1.131	1.00
162_K	166_S	1.121	1.00
247_I	254_Q	1.113	1.00
262_S	266_Q	1.108	1.00
277_K	281_K	1.105	1.00
131_V	134_Q	1.100	1.00
106_I	110_G	1.098	1.00
141_D	257_A	1.093	1.00
85_E	89_F	1.092	1.00
246_S	249_Q	1.087	1.00
69_T	76_Q	1.085	1.00
117_E	120_K	1.074	1.00
148_G	152_Q	1.070	1.00
277_K	280_E	1.062	1.00
74_S	77_K	1.052	1.00
103_G	107_G	1.047	1.00
86_L	89_F	1.045	1.00
20_K	24_Y	1.042	1.00
39_D	49_A	1.040	1.00
157_S	161_K	1.039	1.00
218_H	221_E	1.035	1.00
228_Q	231_K	1.034	1.00
235_S	238_K	1.034	1.00
270_G	274_H	1.033	1.00
273_Q	277_K	1.028	1.00
107_G	110_G	1.026	1.00
23_P	27_S	1.025	1.00
263_A	266_Q	1.019	1.00
173_I	222_N	1.017	1.00
57_K	61_P	1.011	1.00
192_A	210_D	1.010	1.00
21_V	52_F	1.008	1.00
145_S	253_G	1.003	1.00
24_Y	35_I	0.999	1.00
103_G	106_I	0.997	1.00
64_E	67_I	0.997	1.00
63_Q	67_I	0.993	1.00
88_G	92_I	0.989	1.00
71_A	74_S	0.989	1.00
152_Q	250_H	0.988	1.00
232_K	235_S	0.987	1.00
178_K	182_D	0.980	1.00
20_K	38_Y	0.978	1.00
20_K	23_P	0.977	1.00
13_D	17_A	0.971	1.00
274_H	278_M	0.968	1.00
224_G	227_D	0.965	1.00
161_K	245_E	0.964	1.00
27_S	30_Q	0.960	1.00
248_N	252_D	0.960	1.00
159_Q	243_S	0.947	1.00
54_L	58_A	0.947	1.00
89_F	92_I	0.947	1.00
131_V	267_E	0.945	1.00
63_Q	66_D	0.938	1.00
259_E	262_S	0.931	1.00
256_A	259_E	0.928	1.00
93_A	96_I	0.927	1.00
15_L	19_I	0.927	1.00
46_N	50_K	0.927	1.00
37_I	53_S	0.925	1.00
155_G	159_Q	0.925	1.00
29_V	54_L	0.923	1.00
101_E	105_V	0.923	1.00
23_P	26_N	0.919	1.00
17_A	41_E	0.918	1.00
234_H	238_K	0.913	1.00
168_G	172_D	0.912	1.00
167_A	237_L	0.911	1.00
87_F	91_L	0.910	1.00
250_H	253_G	0.910	1.00
24_Y	27_S	0.909	1.00
146_I	149_F	0.904	1.00
65_G	69_T	0.900	1.00
127_S	131_V	0.900	1.00
93_A	97_P	0.898	1.00
90_P	94_R	0.898	1.00
253_G	257_A	0.897	1.00
178_K	224_G	0.891	1.00
178_K	223_V	0.890	1.00
133_E	136_A	0.888	1.00
18_F	45_V	0.886	1.00
100_D	104_R	0.886	1.00
97_P	100_D	0.883	1.00
75_N	78_K	0.878	1.00
82_V	85_E	0.878	1.00
141_D	145_S	0.878	1.00
257_A	260_Q	0.878	1.00
143_S	262_S	0.873	1.00
138_A	141_D	0.871	1.00
149_F	254_Q	0.868	1.00
154_S	248_N	0.867	1.00
164_S	238_K	0.866	1.00
173_I	176_T	0.866	1.00
73_R	76_Q	0.863	1.00
231_K	235_S	0.859	1.00
101_E	108_G	0.851	1.00
69_T	72_I	0.848	1.00
122_H	126_E	0.845	1.00
182_D	220_K	0.843	1.00
185_N	213_R	0.843	1.00
267_E	271_S	0.837	1.00
104_R	107_G	0.834	1.00
168_G	171_A	0.834	1.00
145_S	148_G	0.832	1.00
146_I	254_Q	0.830	1.00
87_F	90_P	0.824	1.00
21_V	48_P	0.818	1.00
94_R	108_G	0.816	1.00
54_L	57_K	0.816	1.00
189_L	197_R	0.811	1.00
45_V	49_A	0.809	1.00
39_D	50_K	0.809	1.00
22_A	48_P	0.804	1.00
25_L	48_P	0.804	1.00
145_S	250_H	0.801	1.00
110_G	113_T	0.800	1.00
150_S	255_A	0.800	1.00
21_V	25_L	0.800	1.00
174_S	178_K	0.799	1.00
132_V	135_T	0.798	1.00
192_A	213_R	0.794	1.00
157_S	245_E	0.789	1.00
15_L	45_V	0.789	1.00
39_D	53_S	0.789	1.00
271_S	275_L	0.788	1.00
14_I	17_A	0.786	1.00
157_S	248_N	0.784	1.00
49_A	53_S	0.784	1.00
24_Y	52_F	0.784	1.00
68_I	71_A	0.783	1.00
19_I	23_P	0.783	1.00
240_L	247_I	0.780	1.00
134_Q	138_A	0.780	1.00
37_I	49_A	0.779	1.00
121_L	279_A	0.777	1.00
38_Y	53_S	0.776	1.00
270_G	273_Q	0.775	1.00
71_A	75_N	0.766	1.00
75_N	79_T	0.764	1.00
64_E	68_I	0.763	1.00
167_A	233_I	0.760	1.00
136_A	266_Q	0.755	1.00
94_R	101_E	0.755	1.00
24_Y	28_L	0.752	1.00
55_N	59_G	0.751	1.00
159_Q	240_L	0.750	1.00
18_F	48_P	0.750	1.00
236_L	239_G	0.750	1.00
86_L	90_P	0.746	1.00
138_A	260_Q	0.746	1.00
155_G	243_S	0.742	1.00
94_R	98_L	0.742	1.00
234_H	237_L	0.735	1.00
15_L	18_F	0.734	1.00
169_E	232_K	0.732	1.00
233_I	236_L	0.728	1.00
255_A	259_E	0.726	1.00
50_K	53_S	0.725	1.00
124_V	127_S	0.722	1.00
153_M	156_I	0.721	1.00
216_A	219_S	0.720	1.00
65_G	68_I	0.719	1.00
29_V	51_T	0.718	1.00
174_S	227_D	0.713	1.00
251_T	254_Q	0.709	1.00
170_I	230_T	0.706	1.00
153_M	247_I	0.702	1.00
243_S	246_S	0.696	1.00
147_N	150_S	0.696	1.00
128_L	251_T	0.693	1.00
179_G	182_D	0.691	1.00
46_N	49_A	0.688	1.00
261_I	265_M	0.688	1.00
175_V	178_K	0.688	1.00
173_I	229_I	0.687	1.00
39_D	46_N	0.680	1.00
213_R	217_T	0.680	1.00
24_Y	56_V	0.678	1.00
87_F	101_E	0.677	1.00
210_D	214_K	0.675	1.00
33_I	59_G	0.675	1.00
252_D	255_A	0.671	1.00
233_I	237_L	0.668	1.00
21_V	24_Y	0.667	1.00
41_E	49_A	0.664	1.00
159_Q	236_L	0.663	1.00
228_Q	232_K	0.662	1.00
35_I	56_V	0.660	1.00
218_H	225_Q	0.657	1.00
87_F	98_L	0.656	1.00
183_Q	218_H	0.656	1.00
254_Q	275_L	0.654	1.00
50_K	54_L	0.651	1.00
52_F	56_V	0.650	1.00
35_I	39_D	0.645	1.00
178_K	220_K	0.642	1.00
244_I	247_I	0.642	1.00
15_L	22_A	0.638	1.00
136_A	269_S	0.638	1.00
183_Q	211_E	0.635	1.00
160_A	244_I	0.634	1.00
153_M	251_T	0.632	1.00
172_D	225_Q	0.632	1.00
239_G	243_S	0.627	1.00
70_D	73_R	0.626	1.00
42_K	46_N	0.624	1.00
159_Q	162_K	0.620	1.00
16_D	20_K	0.609	1.00
71_A	76_Q	0.608	1.00
62_L	65_G	0.607	1.00
69_T	73_R	0.603	1.00
172_D	176_T	0.598	1.00
101_E	104_R	0.597	1.00
30_Q	54_L	0.595	1.00
241_E	245_E	0.595	1.00
254_Q	257_A	0.595	1.00
132_V	269_S	0.593	1.00
14_I	18_F	0.592	1.00
41_E	45_V	0.584	1.00
26_N	29_V	0.583	1.00
28_L	52_F	0.583	1.00
22_A	25_L	0.582	1.00
145_S	257_A	0.579	1.00
111_L	114_S	0.577	1.00
16_D	19_I	0.574	1.00
17_A	45_V	0.574	1.00
154_S	252_D	0.574	1.00
72_I	76_Q	0.573	1.00
266_Q	269_S	0.571	1.00
254_Q	268_I	0.567	1.00
250_H	254_Q	0.566	1.00
13_D	16_D	0.562	1.00
90_P	93_A	0.561	1.00
126_E	129_S	0.560	1.00
95_A	99_H	0.559	1.00
275_L	278_M	0.558	1.00
81_M	85_E	0.554	1.00
135_T	265_M	0.554	1.00
149_F	251_T	0.553	1.00
114_S	118_S	0.550	1.00
154_S	157_S	0.549	1.00
128_L	135_T	0.549	1.00
19_I	47_I	0.548	1.00
77_K	82_V	0.548	1.00
134_Q	264_T	0.543	1.00
139_I	143_S	0.543	1.00
254_Q	261_I	0.543	1.00
27_S	55_N	0.542	1.00
180_I	219_S	0.542	1.00
129_S	276_A	0.541	1.00
25_L	28_L	0.539	1.00
147_N	255_A	0.538	1.00
141_D	253_G	0.538	1.00
20_K	39_D	0.537	1.00
109_V	113_T	0.537	1.00
135_T	149_F	0.535	1.00
139_I	142_I	0.535	1.00
120_K	278_M	0.532	1.00
233_I	240_L	0.529	1.00
72_I	79_T	0.526	1.00
140_S	262_S	0.525	1.00
21_V	45_V	0.523	1.00
140_S	143_S	0.519	1.00
163_V	240_L	0.518	1.00
78_K	82_V	0.514	1.00
200_E	203_K	0.513	1.00
168_G	234_H	0.510	1.00
174_S	226_I	0.507	1.00
142_I	258_V	0.505	1.00
150_S	252_D	0.504	1.00
91_L	94_R	0.503	1.00
28_L	33_I	0.500	1.00

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
3zx6A	2	0.9126	100	0.154	Contact Map
1qu7A	2	0.6434	100	0.337	Contact Map
2ch7A	2	0.8427	100	0.348	Contact Map
3g67A	2	0.6818	100	0.368	Contact Map
4i3mA	2	0.5245	99.7	0.674	Contact Map
3zccA	2	0.3811	98.1	0.832	Contact Map
4cq4A	4	0.2483	97.7	0.847	Contact Map
2f95B	2	0.0245	97.6	0.849	Contact Map
4gycB	2	0.0385	97.5	0.853	Contact Map
2rm8A	1	0.2343	95.8	0.88	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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