YWFM - BACSU - GREMLIN Contacts

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YWFM - Uncharacterized transporter YwfM

UniProt:	P39649	Sequences: MKGNIYSLFVLIAAFFWGTTGTVQALAPESATPLAFGAFRLLIGGSAMLLAVWISRELHVKNWAWPLVFLAAVCMACYQPLFFTAVKETGIAVGTVIAIGSAPIIAGTLEWAVLKKRPRNSWWIATVLALAGCWLLFSDSSNVRIDVAGVLMALGAGASFAGYTLISKAMMKTQPPRATSAVVFMISAILLTPLLWQLDISWILTPRGLGTSLYIGLIATCAAYFLFAKGLTGVPASAAVTLSLAEPLTASLLGVFFIGEMLSPSSWLGIALMMLGLLVISAAPRKQKTAEAAHMS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	296 (274)
Sequences:	38998 (28751)
Seq/√Len:	1736.9

ECOLI - YICL YIJE YDDG YHBE RHTA YTFF YEDA EAMA RARD YIGM
BACSU - YWFM YVBV YDFC YYAM YCBK YETK YBFH YDED YDEK YCXC YOAV YXXF YRDR YOJE
HALSA - Q9HHP6 Q9HQ34 Q9HPI0
SULSO - Q97UX3 Q97X73 Q97UE8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_A	153_A	3.326	1.00
9_F	229_K	2.969	1.00
93_V	150_V	2.856	1.00
229_K	233_G	2.745	1.00
254_G	260_E	2.681	1.00
38_A	192_T	2.530	1.00
84_T	152_M	2.495	1.00
45_G	185_M	2.482	1.00
23_V	214_Y	2.411	1.00
61_K	64_A	2.369	1.00
125_A	276_G	2.364	1.00
81_L	155_G	2.313	1.00
229_K	232_T	2.276	1.00
105_I	157_G	2.160	1.00
81_L	152_M	2.152	1.00
116_K	168_K	2.100	1.00
109_L	165_L	2.097	1.00
95_T	250_A	2.085	1.00
25_A	260_E	2.059	1.00
206_P	210_G	2.040	1.00
43_I	216_G	2.026	1.00
24_Q	83_F	1.980	1.00
42_L	188_A	1.949	1.00
10_V	230_G	1.935	1.00
111_W	118_P	1.910	1.00
18_G	249_T	1.907	1.00
49_L	181_A	1.846	1.00
107_G	126_T	1.836	1.00
110_E	116_K	1.799	1.00
119_R	122_W	1.786	1.00
89_T	150_V	1.780	1.00
77_C	159_S	1.770	1.00
189_I	193_P	1.734	1.00
88_E	148_A	1.734	1.00
101_S	105_I	1.730	1.00
205_T	208_G	1.725	1.00
175_P	178_A	1.714	1.00
106_A	240_V	1.705	1.00
151_L	155_G	1.699	1.00
89_T	149_G	1.697	1.00
278_L	282_A	1.672	1.00
18_G	253_L	1.668	1.00
193_P	196_W	1.658	1.00
216_G	221_C	1.639	1.00
50_L	53_W	1.633	1.00
235_P	238_A	1.629	1.00
19_T	214_Y	1.623	1.00
129_A	244_L	1.619	1.00
64_A	173_T	1.604	1.00
105_I	161_A	1.601	1.00
81_L	159_S	1.596	1.00
45_G	188_A	1.595	1.00
63_W	66_P	1.589	1.00
15_F	249_T	1.558	1.00
263_S	266_S	1.548	1.00
38_A	188_A	1.509	1.00
84_T	88_E	1.495	1.00
94_G	153_A	1.495	1.00
125_A	280_I	1.476	1.00
147_V	150_V	1.442	1.00
49_L	53_W	1.439	1.00
105_I	158_A	1.435	1.00
27_A	36_F	1.428	1.00
13_A	230_G	1.421	1.00
167_S	228_A	1.403	1.00
67_L	71_A	1.384	1.00
264_P	268_L	1.372	1.00
84_T	87_K	1.360	1.00
44_G	184_F	1.354	1.00
31_A	208_G	1.346	1.00
125_A	279_V	1.346	1.00
51_A	55_S	1.335	1.00
16_F	218_I	1.326	1.00
26_L	211_T	1.323	1.00
110_E	114_L	1.313	1.00
253_L	257_F	1.313	1.00
9_F	226_L	1.312	1.00
109_L	113_V	1.309	1.00
147_V	151_L	1.307	1.00
36_F	215_I	1.303	1.00
91_I	254_G	1.300	1.00
47_A	221_C	1.300	1.00
120_N	124_I	1.290	1.00
46_S	50_L	1.288	1.00
129_A	276_G	1.280	1.00
62_N	66_P	1.279	1.00
89_T	93_V	1.273	1.00
249_T	253_L	1.273	1.00
267_W	271_A	1.264	1.00
161_A	165_L	1.261	1.00
207_R	210_G	1.260	1.00
90_G	93_V	1.255	1.00
135_L	265_S	1.245	1.00
17_W	223_A	1.243	1.00
135_L	272_L	1.239	1.00
132_G	269_G	1.237	1.00
206_P	209_L	1.231	1.00
271_A	275_L	1.230	1.00
92_A	251_S	1.230	1.00
22_T	253_L	1.230	1.00
121_S	279_V	1.222	1.00
245_A	249_T	1.220	1.00
50_L	54_I	1.219	1.00
262_L	267_W	1.202	1.00
88_E	152_M	1.202	1.00
210_G	214_Y	1.191	1.00
32_T	35_A	1.185	1.00
30_S	208_G	1.184	1.00
123_W	127_V	1.178	1.00
7_S	242_L	1.176	1.00
148_A	152_M	1.171	1.00
207_R	211_T	1.165	1.00
96_V	270_I	1.162	1.00
86_V	94_G	1.162	1.00
169_A	173_T	1.157	1.00
168_K	172_K	1.154	1.00
25_A	29_E	1.152	1.00
34_L	194_L	1.152	1.00
112_A	115_K	1.148	1.00
132_G	273_M	1.139	1.00
8_L	12_I	1.133	1.00
168_K	235_P	1.129	1.00
109_L	162_G	1.127	1.00
169_A	172_K	1.127	1.00
190_L	193_P	1.120	1.00
106_A	236_A	1.116	1.00
120_N	123_W	1.115	1.00
127_V	131_A	1.113	1.00
40_R	220_T	1.111	1.00
74_C	162_G	1.109	1.00
45_G	181_A	1.104	1.00
30_S	205_T	1.103	1.00
38_A	195_L	1.101	1.00
88_E	149_G	1.097	1.00
136_L	269_G	1.095	1.00
89_T	153_A	1.095	1.00
23_V	211_T	1.091	1.00
82_F	86_V	1.087	1.00
13_A	226_L	1.082	1.00
194_L	198_L	1.073	1.00
121_S	282_A	1.071	1.00
62_N	65_W	1.071	1.00
76_A	190_L	1.068	1.00
38_A	42_L	1.068	1.00
148_A	151_L	1.068	1.00
168_K	236_A	1.060	1.00
114_L	165_L	1.049	1.00
88_E	146_D	1.043	1.00
109_L	161_A	1.040	1.00
118_P	123_W	1.038	1.00
231_L	239_A	1.035	1.00
111_W	117_R	1.031	1.00
57_E	175_P	1.028	1.00
71_A	74_C	1.024	1.00
13_A	17_W	1.024	1.00
12_I	226_L	1.023	1.00
121_S	283_A	1.019	1.00
24_Q	86_V	1.017	1.00
37_G	83_F	1.016	1.00
97_I	150_V	1.011	1.00
116_K	122_W	1.009	1.00
19_T	253_L	1.008	1.00
16_F	226_L	1.007	1.00
193_P	197_Q	1.003	1.00
107_G	118_P	1.002	1.00
17_W	227_F	0.997	1.00
76_A	191_L	0.993	1.00
91_I	258_I	0.988	1.00
106_A	164_T	0.988	1.00
210_G	213_L	0.986	1.00
134_W	138_S	0.978	1.00
97_I	157_G	0.976	1.00
33_P	37_G	0.976	1.00
149_G	153_A	0.969	1.00
41_L	187_S	0.956	1.00
264_P	267_W	0.956	1.00
101_S	133_C	0.954	1.00
213_L	216_G	0.949	1.00
34_L	80_P	0.944	1.00
27_A	211_T	0.938	1.00
106_A	161_A	0.938	1.00
42_L	192_T	0.933	1.00
128_L	276_G	0.932	1.00
14_A	18_G	0.931	1.00
157_G	161_A	0.929	1.00
234_V	239_A	0.929	1.00
119_R	123_W	0.919	1.00
35_A	195_L	0.915	1.00
109_L	158_A	0.914	1.00
138_S	263_S	0.913	1.00
231_L	235_P	0.906	1.00
27_A	208_G	0.904	1.00
72_A	190_L	0.904	1.00
75_M	163_Y	0.902	1.00
209_L	213_L	0.901	1.00
53_W	57_E	0.898	1.00
22_T	257_F	0.895	1.00
97_I	153_A	0.890	1.00
235_P	239_A	0.885	1.00
91_I	260_E	0.880	1.00
146_D	150_V	0.876	1.00
14_A	249_T	0.871	1.00
194_L	197_Q	0.871	1.00
24_Q	28_P	0.870	1.00
109_L	112_A	0.869	1.00
80_P	84_T	0.863	1.00
66_P	69_F	0.856	1.00
64_A	174_Q	0.852	1.00
185_M	189_I	0.851	1.00
96_V	134_W	0.848	1.00
234_V	238_A	0.847	1.00
255_V	262_L	0.847	1.00
212_S	216_G	0.842	1.00
117_R	121_S	0.841	1.00
74_C	163_Y	0.833	1.00
49_L	185_M	0.831	1.00
47_A	217_L	0.831	1.00
47_A	50_L	0.829	1.00
117_R	120_N	0.823	1.00
251_S	262_L	0.823	1.00
230_G	239_A	0.819	1.00
196_W	199_D	0.813	1.00
53_W	56_R	0.810	1.00
131_A	135_L	0.803	1.00
162_G	166_I	0.799	1.00
205_T	209_L	0.799	1.00
131_A	272_L	0.794	1.00
133_C	137_F	0.790	1.00
248_L	270_I	0.789	1.00
251_S	270_I	0.787	1.00
153_A	157_G	0.786	1.00
197_Q	200_I	0.784	1.00
72_A	186_I	0.783	1.00
89_T	94_G	0.781	1.00
270_I	274_M	0.778	1.00
74_C	159_S	0.772	1.00
186_I	189_I	0.771	1.00
22_T	254_G	0.771	1.00
245_A	248_L	0.764	1.00
74_C	166_I	0.763	1.00
265_S	268_L	0.763	1.00
181_A	185_M	0.762	1.00
132_G	276_G	0.760	1.00
78_Y	163_Y	0.758	1.00
48_M	221_C	0.755	1.00
144_R	147_V	0.755	1.00
213_L	217_L	0.751	1.00
204_L	209_L	0.743	1.00
54_I	57_E	0.743	1.00
10_V	242_L	0.738	1.00
135_L	268_L	0.735	1.00
35_A	39_F	0.734	1.00
45_G	49_L	0.734	1.00
111_W	115_K	0.732	1.00
104_I	129_A	0.732	1.00
78_Y	159_S	0.731	1.00
11_L	249_T	0.727	1.00
268_L	272_L	0.723	1.00
76_A	80_P	0.723	1.00
118_P	122_W	0.722	1.00
39_F	43_I	0.719	1.00
21_G	82_F	0.719	1.00
222_A	226_L	0.718	1.00
218_I	222_A	0.715	1.00
22_T	91_I	0.711	1.00
124_I	128_L	0.711	1.00
255_V	261_M	0.710	1.00
14_A	245_A	0.703	1.00
37_G	191_L	0.703	1.00
72_A	76_A	0.703	1.00
67_L	72_A	0.703	1.00
160_F	164_T	0.702	1.00
72_A	75_M	0.702	1.00
42_L	46_S	0.701	1.00
186_I	190_L	0.699	1.00
275_L	279_V	0.699	1.00
51_A	177_R	0.696	1.00
116_K	237_S	0.691	1.00
241_T	280_I	0.687	1.00
101_S	104_I	0.686	1.00
211_T	214_Y	0.685	1.00
70_L	74_C	0.683	1.00
52_V	181_A	0.682	1.00
108_T	112_A	0.681	1.00
68_V	186_I	0.678	1.00
254_G	258_I	0.675	1.00
188_A	192_T	0.675	1.00
106_A	165_L	0.674	1.00
182_V	186_I	0.674	1.00
10_V	234_V	0.674	1.00
276_G	280_I	0.673	1.00
107_G	122_W	0.671	1.00
189_I	192_T	0.669	1.00
225_F	229_K	0.667	1.00
262_L	266_S	0.660	1.00
67_L	166_I	0.658	1.00
195_L	199_D	0.657	1.00
85_A	149_G	0.654	1.00
47_A	216_G	0.652	1.00
97_I	154_L	0.650	1.00
100_G	103_P	0.648	1.00
43_I	47_A	0.644	1.00
26_L	258_I	0.643	1.00
77_C	81_L	0.642	1.00
174_Q	179_T	0.642	1.00
60_V	64_A	0.641	1.00
160_F	227_F	0.641	1.00
44_G	221_C	0.641	1.00
75_M	224_Y	0.637	1.00
251_S	255_V	0.636	1.00
100_G	133_C	0.634	1.00
128_L	279_V	0.634	1.00
114_L	169_A	0.632	1.00
180_S	228_A	0.631	1.00
61_K	65_W	0.630	1.00
214_Y	218_I	0.629	1.00
252_L	256_F	0.629	1.00
31_A	36_F	0.627	1.00
107_G	111_W	0.625	1.00
61_K	66_P	0.624	1.00
20_T	219_A	0.620	1.00
182_V	185_M	0.620	1.00
21_G	95_T	0.617	1.00
16_F	223_A	0.614	1.00
12_I	16_F	0.614	1.00
196_W	200_I	0.609	1.00
208_G	211_T	0.604	1.00
85_A	94_G	0.602	1.00
152_M	155_G	0.602	1.00
277_L	280_I	0.600	1.00
178_A	182_V	0.599	1.00
75_M	183_V	0.598	1.00
7_S	238_A	0.597	1.00
266_S	270_I	0.595	1.00
180_S	183_V	0.594	1.00
261_M	265_S	0.594	1.00
56_R	59_H	0.593	1.00
263_S	267_W	0.591	1.00
103_P	244_L	0.590	1.00
105_I	154_L	0.589	1.00
101_S	157_G	0.588	1.00
83_F	87_K	0.587	1.00
82_F	94_G	0.582	1.00
185_M	188_A	0.581	1.00
82_F	156_A	0.578	1.00
16_F	219_A	0.578	1.00
176_P	180_S	0.576	1.00
163_Y	228_A	0.574	1.00
74_C	78_Y	0.573	1.00
122_W	235_P	0.572	1.00
205_T	210_G	0.571	1.00
32_T	198_L	0.570	1.00
34_L	198_L	0.569	1.00
55_S	175_P	0.568	1.00
253_L	256_F	0.568	1.00
53_W	58_L	0.565	1.00
150_V	154_L	0.563	1.00
244_L	277_L	0.561	1.00
137_F	150_V	0.560	1.00
243_S	246_E	0.557	1.00
76_A	194_L	0.556	1.00
187_S	191_L	0.556	1.00
204_L	208_G	0.555	1.00
144_R	148_A	0.553	1.00
39_F	212_S	0.553	1.00
52_V	178_A	0.553	1.00
70_L	166_I	0.552	1.00
56_R	175_P	0.550	1.00
145_I	148_A	0.549	1.00
14_A	246_E	0.545	1.00
7_S	11_L	0.542	1.00
96_V	136_L	0.538	1.00
43_I	46_S	0.534	1.00
252_L	255_V	0.534	1.00
11_L	14_A	0.534	1.00
100_G	157_G	0.533	1.00
10_V	227_F	0.532	1.00
65_W	68_V	0.532	1.00
164_T	240_V	0.531	1.00
139_D	265_S	0.531	1.00
31_A	35_A	0.528	1.00
214_Y	217_L	0.527	1.00
114_L	168_K	0.527	1.00
95_T	100_G	0.527	1.00
110_E	237_S	0.527	1.00
190_L	194_L	0.524	1.00
55_S	177_R	0.520	1.00
230_G	234_V	0.520	1.00
51_A	54_I	0.518	1.00
163_Y	167_S	0.517	1.00
255_V	267_W	0.517	1.00
21_G	25_A	0.516	1.00
113_V	162_G	0.516	1.00
255_V	259_G	0.510	1.00
158_A	162_G	0.510	1.00
63_W	173_T	0.510	1.00
164_T	227_F	0.510	1.00
25_A	258_I	0.509	1.00
37_G	80_P	0.509	1.00
81_L	156_A	0.508	1.00
42_L	45_G	0.507	1.00
11_L	15_F	0.507	1.00
132_G	272_L	0.507	1.00
32_T	199_D	0.506	1.00
108_T	126_T	0.505	1.00
46_S	49_L	0.505	1.00
28_P	86_V	0.503	1.00
85_A	89_T	0.503	1.00
69_F	72_A	0.502	1.00
130_L	244_L	0.500	1.00
192_T	196_W	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
2i68A	2	0.2601	98.8	0.758	Contact Map
3b5dA	2	0.3412	98.3	0.793	Contact Map
1pw4A	1	0.9764	44.4	0.924	Contact Map
4pypA	1	0.9493	37.3	0.927	Contact Map
4he8J	1	0.5135	29.5	0.931	Contact Map
1u7gA	3	0.7872	24.5	0.933	Contact Map
4j05A	3	0.9628	21.7	0.935	Contact Map
2kluA	1	0.152	20.2	0.936	Contact Map
3b9wA	3	0.8074	18.9	0.937	Contact Map
2cfqA	1	0.6047	18.8	0.937	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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