YYAM - BACSU - GREMLIN Contacts

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YYAM - Uncharacterized transporter YyaM

UniProt:	P37511	Sequences: MKHLNIYIMLLGFSIFTGATFNLAKYTVGYFSPSSSAAWRFGLAAAVMLIILIFTEGIKKSQLRKNAVSYIVLGIIGIFGFNALFFVGLKYTSPVNGALIMGLNPLLTAILARIILKDNMTKKQVLGIFFAFIGVLLVITQGSIETIKTLSISGGDLIIFTGNVCWALYGVLGRRFVKDGTPLSTTTYTMVIGAVSLIVVSLFTSKPVSLSNIPIGVWGAIAFMAFFTSVLGYLWWNQGIKEIGASKTSLFFNLVPVVTMIISFAVGTPIKVFQVIGAVLVILGVLTASGVIRIPKYNTKEQSAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	305 (276)
Sequences:	38723 (28214)
Seq/√Len:	1698.3

ECOLI - YICL YTFF YHBE YIJE EAMA YEDA YDDG RARD RHTA YIGM
BACSU - YYAM YETK YRDR YWFM YDFC YVBV YCXC YBFH YCBK YXXF YDED YOAV YDEK 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
88_G	159_I	3.439	1.00
9_M	238_Q	2.886	1.00
96_N	156_D	2.769	1.00
263_S	268_T	2.618	1.00
238_Q	242_E	2.602	1.00
45_A	191_V	2.526	1.00
87_V	158_I	2.516	1.00
127_G	284_G	2.512	1.00
38_A	198_I	2.493	1.00
84_L	161_T	2.434	1.00
23_L	223_F	2.345	1.00
107_L	163_N	2.226	1.00
118_D	174_R	2.190	1.00
238_Q	241_K	2.182	1.00
63_L	66_N	2.182	1.00
111_L	171_V	2.096	1.00
84_L	158_I	2.066	1.00
25_K	268_T	2.026	1.00
113_R	120_M	1.959	1.00
18_G	258_V	1.956	1.00
43_L	225_A	1.916	1.00
42_G	194_A	1.909	1.00
98_A	259_T	1.904	1.00
80_G	165_C	1.902	1.00
24_A	86_F	1.898	1.00
157_L	161_T	1.893	1.00
10_L	239_G	1.882	1.00
92_T	156_D	1.869	1.00
215_I	219_G	1.867	1.00
49_L	187_T	1.842	1.00
112_A	118_D	1.829	1.00
108_T	249_S	1.806	1.00
109_A	128_I	1.797	1.00
50_I	53_I	1.789	1.00
225_A	230_V	1.767	1.00
103_L	107_L	1.766	1.00
92_T	155_G	1.701	1.00
91_Y	154_G	1.654	1.00
286_L	290_G	1.652	1.00
195_V	199_V	1.648	1.00
121_T	124_Q	1.645	1.00
45_A	194_A	1.644	1.00
18_G	262_I	1.640	1.00
66_N	179_D	1.629	1.00
84_L	165_C	1.610	1.00
181_T	184_S	1.589	1.00
19_A	223_F	1.573	1.00
244_G	247_K	1.573	1.00
107_L	167_A	1.555	1.00
15_I	258_V	1.551	1.00
214_P	217_V	1.550	1.00
131_A	253_N	1.544	1.00
199_V	202_L	1.539	1.00
38_A	194_A	1.531	1.00
111_L	115_I	1.495	1.00
65_K	69_S	1.494	1.00
127_G	288_A	1.485	1.00
271_K	274_Q	1.481	1.00
13_F	239_G	1.476	1.00
272_V	276_I	1.426	1.00
97_G	159_I	1.426	1.00
153_S	156_D	1.418	1.00
31_F	217_V	1.409	1.00
49_L	53_I	1.401	1.00
68_V	72_V	1.384	1.00
107_L	164_V	1.376	1.00
94_P	263_S	1.372	1.00
92_T	96_N	1.370	1.00
65_K	68_V	1.362	1.00
275_V	279_V	1.359	1.00
87_V	91_Y	1.354	1.00
137_L	280_L	1.351	1.00
112_A	116_L	1.328	1.00
173_G	237_N	1.328	1.00
16_F	227_F	1.323	1.00
51_I	55_T	1.318	1.00
64_R	68_V	1.317	1.00
47_V	230_V	1.315	1.00
71_I	192_I	1.299	1.00
46_A	50_I	1.298	1.00
22_N	262_I	1.297	1.00
27_T	36_S	1.290	1.00
9_M	235_W	1.289	1.00
36_S	224_M	1.287	1.00
50_I	54_F	1.282	1.00
122_K	126_L	1.267	1.00
95_V	260_M	1.266	1.00
44_A	190_M	1.266	1.00
93_S	96_N	1.265	1.00
91_Y	158_I	1.264	1.00
125_V	129_F	1.263	1.00
17_T	232_G	1.255	1.00
127_G	287_T	1.249	1.00
279_V	283_L	1.248	1.00
26_Y	220_A	1.247	1.00
72_V	172_L	1.244	1.00
137_L	273_F	1.244	1.00
131_A	284_G	1.239	1.00
87_V	90_K	1.235	1.00
258_V	262_I	1.230	1.00
216_G	219_G	1.227	1.00
134_G	277_G	1.221	1.00
99_L	278_A	1.220	1.00
111_L	168_L	1.217	1.00
30_Y	217_V	1.214	1.00
215_I	218_W	1.214	1.00
69_S	172_L	1.211	1.00
64_R	67_A	1.207	1.00
254_L	258_V	1.205	1.00
167_A	171_V	1.194	1.00
210_L	213_I	1.192	1.00
129_F	133_I	1.190	1.00
270_I	275_V	1.189	1.00
138_V	277_G	1.174	1.00
219_G	223_F	1.170	1.00
196_S	199_V	1.161	1.00
153_S	157_L	1.160	1.00
38_A	42_G	1.160	1.00
75_I	196_S	1.149	1.00
174_R	244_G	1.147	1.00
175_R	178_K	1.144	1.00
45_A	187_T	1.143	1.00
38_A	201_S	1.143	1.00
123_K	287_T	1.136	1.00
108_T	245_A	1.126	1.00
7_Y	251_F	1.123	1.00
32_S	35_S	1.110	1.00
116_L	171_V	1.106	1.00
25_K	29_G	1.104	1.00
109_A	120_M	1.095	1.00
8_I	12_G	1.091	1.00
120_M	125_V	1.090	1.00
91_Y	155_G	1.089	1.00
79_F	196_S	1.085	1.00
89_L	97_G	1.075	1.00
154_G	158_I	1.073	1.00
40_R	229_S	1.071	1.00
174_R	178_K	1.071	1.00
100_I	163_N	1.059	1.00
34_S	200_V	1.055	1.00
111_L	167_A	1.053	1.00
13_F	17_T	1.052	1.00
111_L	164_V	1.052	1.00
19_A	262_I	1.050	1.00
79_F	197_L	1.050	1.00
23_L	220_A	1.046	1.00
240_I	248_T	1.040	1.00
24_A	89_L	1.034	1.00
12_G	235_W	1.030	1.00
174_R	245_A	1.028	1.00
91_Y	152_I	1.027	1.00
94_P	266_V	1.024	1.00
74_G	192_I	1.020	1.00
17_T	236_W	1.020	1.00
13_F	235_W	1.013	1.00
66_N	180_G	1.004	1.00
240_I	244_G	1.004	1.00
113_R	119_N	1.003	1.00
30_Y	214_P	1.002	1.00
118_D	124_Q	0.999	1.00
16_F	235_W	0.997	1.00
108_T	170_G	0.994	1.00
134_G	281_V	0.990	1.00
123_K	291_V	0.986	1.00
122_K	125_V	0.985	1.00
27_T	217_V	0.983	1.00
216_G	220_A	0.983	1.00
37_A	86_F	0.982	1.00
33_P	37_A	0.979	1.00
219_G	222_A	0.977	1.00
114_I	117_K	0.977	1.00
123_K	290_G	0.972	1.00
119_N	123_K	0.968	1.00
100_I	156_D	0.965	1.00
222_A	225_A	0.964	1.00
92_T	159_I	0.962	1.00
121_T	125_V	0.960	1.00
103_L	135_V	0.954	1.00
35_S	201_S	0.954	1.00
154_G	157_L	0.954	1.00
133_I	137_L	0.953	1.00
218_W	222_A	0.948	1.00
94_P	268_T	0.944	1.00
100_I	159_I	0.943	1.00
69_S	73_L	0.940	1.00
155_G	159_I	0.940	1.00
34_S	83_A	0.938	1.00
244_G	248_T	0.937	1.00
163_N	167_A	0.937	1.00
85_F	89_L	0.929	1.00
68_V	71_I	0.924	1.00
130_F	284_G	0.920	1.00
47_V	226_F	0.918	1.00
111_L	114_I	0.907	1.00
99_L	136_L	0.906	1.00
27_T	220_A	0.902	1.00
69_S	176_F	0.902	1.00
200_V	204_T	0.902	1.00
140_T	271_K	0.901	1.00
136_L	140_T	0.898	1.00
243_I	248_T	0.895	1.00
67_A	192_I	0.892	1.00
272_V	275_V	0.883	1.00
108_T	167_A	0.877	1.00
41_F	193_G	0.866	1.00
78_I	169_Y	0.866	1.00
200_V	203_F	0.864	1.00
22_N	263_S	0.856	1.00
199_V	203_F	0.855	1.00
119_N	122_K	0.851	1.00
14_S	18_G	0.851	1.00
76_I	168_L	0.849	1.00
72_V	75_I	0.840	1.00
14_S	258_V	0.836	1.00
66_N	69_S	0.832	1.00
76_I	165_C	0.830	1.00
42_G	198_I	0.830	1.00
56_E	59_K	0.829	1.00
53_I	56_E	0.829	1.00
49_L	191_V	0.826	1.00
276_I	280_L	0.824	1.00
11_L	258_V	0.823	1.00
47_V	50_I	0.823	1.00
243_I	247_K	0.821	1.00
239_G	248_T	0.821	1.00
107_L	160_F	0.818	1.00
227_F	231_L	0.812	1.00
254_L	257_V	0.812	1.00
37_A	197_L	0.806	1.00
257_V	278_A	0.804	1.00
70_Y	180_G	0.804	1.00
79_F	83_A	0.803	1.00
192_I	195_V	0.797	1.00
83_A	87_V	0.795	1.00
175_R	179_D	0.793	1.00
222_A	226_F	0.793	1.00
106_L	131_A	0.793	1.00
126_L	130_F	0.793	1.00
260_M	270_I	0.789	1.00
191_V	195_V	0.784	1.00
214_P	218_W	0.783	1.00
133_I	280_L	0.783	1.00
137_L	276_I	0.782	1.00
110_I	114_I	0.777	1.00
168_L	172_L	0.777	1.00
69_S	175_R	0.773	1.00
63_L	67_A	0.773	1.00
202_L	205_S	0.769	1.00
284_G	288_A	0.768	1.00
187_T	191_V	0.767	1.00
135_V	139_I	0.763	1.00
48_M	230_V	0.760	1.00
278_A	282_I	0.754	1.00
166_W	170_G	0.752	1.00
88_G	97_G	0.750	1.00
260_M	278_A	0.750	1.00
273_F	276_I	0.745	1.00
45_A	49_L	0.744	1.00
100_I	160_F	0.743	1.00
220_A	223_F	0.742	1.00
140_T	143_S	0.739	1.00
152_I	156_D	0.738	1.00
113_R	117_K	0.738	1.00
10_L	251_F	0.730	1.00
283_L	287_T	0.729	1.00
52_L	187_T	0.727	1.00
14_S	254_L	0.723	1.00
159_I	163_N	0.721	1.00
71_I	74_G	0.721	1.00
81_F	165_C	0.719	1.00
109_A	124_Q	0.717	1.00
70_Y	74_G	0.710	1.00
203_F	206_K	0.708	1.00
51_I	183_L	0.707	1.00
270_I	274_Q	0.705	1.00
47_V	225_A	0.702	1.00
217_V	220_A	0.701	1.00
22_N	94_P	0.701	1.00
69_S	72_V	0.700	1.00
108_T	171_V	0.699	1.00
192_I	196_S	0.695	1.00
209_S	212_N	0.694	1.00
186_T	237_N	0.690	1.00
151_S	154_G	0.687	1.00
103_L	106_L	0.682	1.00
130_F	287_T	0.681	1.00
76_I	172_L	0.680	1.00
231_L	235_W	0.678	1.00
79_F	200_V	0.676	1.00
166_W	236_W	0.676	1.00
221_I	225_A	0.675	1.00
10_L	243_I	0.675	1.00
120_M	124_Q	0.674	1.00
43_L	47_V	0.674	1.00
62_Q	66_N	0.674	1.00
78_I	233_Y	0.673	1.00
21_F	85_F	0.672	1.00
20_T	228_T	0.667	1.00
42_G	46_A	0.666	1.00
31_F	36_S	0.666	1.00
74_G	79_F	0.665	1.00
223_F	227_F	0.659	1.00
26_Y	266_V	0.659	1.00
35_S	39_W	0.659	1.00
51_I	54_F	0.657	1.00
81_F	169_Y	0.657	1.00
92_T	97_G	0.655	1.00
115_I	168_L	0.655	1.00
24_A	28_V	0.652	1.00
80_G	84_L	0.652	1.00
85_F	97_G	0.650	1.00
105_P	253_N	0.650	1.00
118_D	246_S	0.648	1.00
39_W	43_L	0.647	1.00
191_V	194_A	0.641	1.00
102_G	135_V	0.640	1.00
188_Y	192_I	0.638	1.00
16_F	232_G	0.636	1.00
134_G	284_G	0.635	1.00
67_A	188_Y	0.634	1.00
116_L	174_R	0.631	1.00
84_L	162_G	0.630	1.00
7_Y	247_K	0.624	1.00
78_I	193_G	0.622	1.00
85_F	162_G	0.619	1.00
67_A	71_I	0.616	1.00
193_G	197_L	0.614	1.00
99_L	139_I	0.614	1.00
262_I	265_A	0.614	1.00
250_L	288_A	0.613	1.00
186_T	189_T	0.611	1.00
21_F	98_A	0.611	1.00
184_S	188_Y	0.610	1.00
158_I	161_T	0.609	1.00
71_I	75_I	0.608	1.00
194_A	198_I	0.608	1.00
182_P	186_T	0.607	1.00
274_Q	278_A	0.607	1.00
234_L	238_Q	0.604	1.00
208_V	211_S	0.603	1.00
170_G	236_W	0.602	1.00
180_G	185_T	0.599	1.00
52_L	56_E	0.598	1.00
44_A	230_V	0.593	1.00
12_G	16_F	0.591	1.00
109_A	113_R	0.586	1.00
139_I	156_D	0.584	1.00
71_I	196_S	0.584	1.00
103_L	163_N	0.584	1.00
34_S	197_L	0.583	1.00
195_V	198_I	0.573	1.00
14_S	255_V	0.573	1.00
63_L	68_V	0.573	1.00
70_Y	185_T	0.572	1.00
169_Y	237_N	0.572	1.00
16_F	228_T	0.571	1.00
67_A	70_Y	0.571	1.00
102_G	105_P	0.569	1.00
263_S	266_V	0.569	1.00
88_G	155_G	0.567	1.00
78_I	189_T	0.567	1.00
269_P	273_F	0.566	1.00
55_T	181_T	0.565	1.00
28_V	89_L	0.562	1.00
282_I	286_L	0.562	1.00
170_G	249_S	0.560	1.00
22_N	259_T	0.560	1.00
214_P	219_G	0.559	1.00
124_Q	244_G	0.559	1.00
21_F	25_K	0.558	1.00
102_G	163_N	0.557	1.00
18_G	255_V	0.555	1.00
99_L	138_V	0.555	1.00
112_A	246_S	0.555	1.00
253_N	285_V	0.554	1.00
116_L	175_R	0.553	1.00
271_K	275_V	0.552	1.00
188_Y	191_V	0.551	1.00
110_I	128_I	0.548	1.00
66_N	70_Y	0.547	1.00
269_P	274_Q	0.546	1.00
7_Y	11_L	0.543	1.00
81_F	166_W	0.541	1.00
285_V	288_A	0.540	1.00
20_T	86_F	0.534	1.00
34_S	204_T	0.534	1.00
164_V	168_L	0.532	1.00
239_G	243_I	0.532	1.00
202_L	206_K	0.531	1.00
126_L	133_I	0.526	1.00
52_L	184_S	0.526	1.00
103_L	131_A	0.524	1.00
86_F	90_K	0.522	1.00
78_I	82_N	0.522	1.00
37_A	83_A	0.518	1.00
39_W	221_I	0.518	1.00
11_L	14_S	0.518	1.00
132_F	136_L	0.516	1.00
32_S	205_S	0.516	1.00
235_W	238_Q	0.514	1.00
50_I	55_T	0.513	1.00
141_Q	273_F	0.511	1.00
46_A	49_L	0.511	1.00
31_F	35_S	0.511	1.00
201_S	205_S	0.510	1.00
169_Y	189_T	0.509	1.00
252_F	255_V	0.507	1.00
121_T	291_V	0.505	1.00
106_L	132_F	0.505	1.00
19_A	228_T	0.505	1.00
55_T	59_K	0.504	1.00
40_R	82_N	0.503	1.00
81_F	85_F	0.500	1.00
17_T	255_V	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	0.2492	98.4	0.787	Contact Map
3b5dA	2	0.3311	98.3	0.792	Contact Map
1pw4A	1	0.9705	57	0.917	Contact Map
4j05A	3	0.9377	52	0.92	Contact Map
4tphA	2	0.8885	41.6	0.924	Contact Map
3wdoA	1	0.9443	38.8	0.926	Contact Map
4pypA	1	0.918	38.3	0.926	Contact Map
4he8J	1	0.5082	35.3	0.928	Contact Map
1u7gA	3	0.7672	28.2	0.931	Contact Map
4ldsA	2	0.5607	23.8	0.933	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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