YXEN - BACSU - GREMLIN Contacts

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YXEN - Probable amino-acid permease protein YxeN

UniProt:	P54953	Sequences: MNTIDWEFMISAFPTLIQALPITLFMAIAAMIFAIIGGLILALITKNKIPVLHQLSKLYISFFRGVPTLVQLFLIYYGLPQLFPEMSKMTALTAAIIGLSLKNAAYLAEIFRAALNSVDDGQLEACLSVGMTKFQAYRRIILPQAIRNAIPATGNTFIGLLKETSLAFTLGVMEMFAQGKMYASGNLKYFETYLAVAIVYWVLTIIYSILQDLFERAMSKPYRT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	224 (202)
Sequences:	28392 (17210)
Seq/√Len:	1210.9

ECOLI - YECS GLNP HISM GLTJ GLTK ARTQ HISQ YHDY ARTM METI POTH YEHY POTB POTC CYST THIP POTI PSTC CYSW YDCV PSTA YDCU YCJP MODB YCJO YHDX TAUC YNJC UGPA YEHW SSUC UGPE PROW MALF PHNE MALG
BACSU - YXEN TCYL ARTQ TCYB GLNP YCKA TCYM GLNM METP ARAP YURN YTEP YQGI AMYD OPUCB OPUAB LPLB OPUBD GANP OPUBB GANQ YQGH AMYC MDXG SSUC OPUCD YURM MDXF YTLD YVGM YESQ YESP ARAQ YTCP LPLC
HALSA - Q9HML6 Q9HMT4 Q9HP02 Q9HR05 Q9HS11 Q9HPK3 Q9HP01 Q9HNI9 Q9HHQ7 Q9HHQ6 Q9HML7 Q9HS12
SULSO - Q97UZ0 Q97ZC1 Q97YY2 Q97UF3 Q97UF4 Q97UY9 Q97YY3 Q97ZC2 Q97Z98 Q97VC0 Q97ZT7 Q97ZT6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
126_C	136_A	3.610	1.00
33_F	100_S	3.333	1.00
21_P	25_F	3.243	1.00
132_T	135_Q	2.943	1.00
154_G	211_Q	2.907	1.00
95_A	167_A	2.898	1.00
188_K	191_E	2.791	1.00
29_A	96_I	2.721	1.00
134_F	138_R	2.593	1.00
44_I	56_S	2.331	1.00
127_L	136_A	2.301	1.00
209_I	213_L	2.200	1.00
66_V	71_Q	2.190	1.00
122_Q	144_Q	2.178	1.00
123_L	136_A	2.128	1.00
179_G	196_V	2.033	1.00
41_L	108_A	2.009	1.00
135_Q	139_R	1.965	1.00
42_A	111_F	1.944	1.00
51_V	55_L	1.925	1.00
123_L	127_L	1.899	1.00
41_L	104_A	1.882	1.00
51_V	54_Q	1.838	1.00
75_I	98_G	1.783	1.00
50_P	54_Q	1.756	1.00
22_I	25_F	1.755	1.00
31_M	157_F	1.731	1.00
177_A	181_M	1.726	1.00
25_F	92_L	1.720	1.00
17_I	21_P	1.677	1.00
39_L	111_F	1.672	1.00
131_M	135_Q	1.656	1.00
213_L	216_R	1.650	1.00
114_A	148_N	1.607	1.00
18_Q	21_P	1.583	1.00
37_G	104_A	1.577	1.00
180_K	183_A	1.576	1.00
50_P	53_H	1.571	1.00
205_I	209_I	1.552	1.00
112_R	116_N	1.540	1.00
178_Q	181_M	1.516	1.00
133_K	137_Y	1.508	1.00
127_L	133_K	1.497	1.00
177_A	180_K	1.488	1.00
126_C	131_M	1.487	1.00
175_M	178_Q	1.486	1.00
45_T	57_K	1.482	1.00
132_T	136_A	1.459	1.00
36_I	40_I	1.450	1.00
135_Q	138_R	1.444	1.00
179_G	183_A	1.437	1.00
90_T	93_T	1.433	1.00
107_L	156_T	1.432	1.00
123_L	141_I	1.432	1.00
27_A	157_F	1.429	1.00
209_I	212_D	1.420	1.00
201_W	205_I	1.415	1.00
210_L	213_L	1.405	1.00
15_T	18_Q	1.388	1.00
38_G	107_L	1.378	1.00
133_K	136_A	1.353	1.00
46_K	116_N	1.340	1.00
109_E	112_R	1.323	1.00
179_G	182_Y	1.321	1.00
33_F	96_I	1.319	1.00
49_I	54_Q	1.311	1.00
20_L	203_L	1.307	1.00
22_I	172_V	1.278	1.00
25_F	29_A	1.271	1.00
117_S	148_N	1.268	1.00
126_C	140_I	1.250	1.00
120_D	124_E	1.242	1.00
96_I	100_S	1.235	1.00
107_L	153_T	1.230	1.00
71_Q	102_K	1.218	1.00
60_I	108_A	1.217	1.00
183_A	189_Y	1.216	1.00
114_A	149_A	1.194	1.00
29_A	100_S	1.191	1.00
111_F	149_A	1.182	1.00
57_K	112_R	1.179	1.00
131_M	139_R	1.177	1.00
34_A	103_N	1.155	1.00
213_L	217_A	1.155	1.00
27_A	161_L	1.153	1.00
174_E	178_Q	1.149	1.00
186_N	189_Y	1.142	1.00
55_L	59_Y	1.138	1.00
92_L	96_I	1.134	1.00
81_Q	84_P	1.130	1.00
49_I	52_L	1.122	1.00
93_T	96_I	1.110	1.00
35_I	153_T	1.083	1.00
40_I	44_I	1.070	1.00
15_T	178_Q	1.064	1.00
55_L	58_L	1.061	1.00
180_K	184_S	1.056	1.00
191_E	194_L	1.053	1.00
27_A	164_T	1.051	1.00
179_G	192_T	1.020	1.00
26_M	167_A	1.017	1.00
115_L	141_I	1.014	1.00
212_D	215_E	1.009	1.00
53_H	57_K	1.008	1.00
181_M	185_G	1.006	1.00
14_P	18_Q	1.003	1.00
89_M	93_T	0.996	1.00
110_I	152_A	0.990	1.00
173_M	177_A	0.989	1.00
18_Q	22_I	0.986	1.00
54_Q	58_L	0.979	1.00
63_F	101_L	0.978	1.00
66_V	102_K	0.974	1.00
206_I	210_L	0.963	1.00
29_A	33_F	0.960	1.00
193_Y	197_A	0.951	1.00
110_I	156_T	0.947	1.00
41_L	56_S	0.944	1.00
185_G	188_K	0.937	1.00
74_L	78_G	0.933	1.00
120_D	123_L	0.930	1.00
148_N	152_A	0.928	1.00
30_A	100_S	0.927	1.00
72_L	167_A	0.924	1.00
194_L	197_A	0.917	1.00
71_Q	75_I	0.912	1.00
42_A	115_L	0.911	1.00
107_L	111_F	0.902	1.00
193_Y	196_V	0.901	1.00
23_T	161_L	0.899	1.00
115_L	145_A	0.896	1.00
176_F	180_K	0.895	1.00
30_A	99_L	0.893	1.00
30_A	160_L	0.893	1.00
43_L	137_Y	0.884	1.00
49_I	53_H	0.883	1.00
183_A	193_Y	0.883	1.00
169_T	173_M	0.882	1.00
44_I	47_N	0.881	1.00
46_K	123_L	0.880	1.00
174_E	177_A	0.874	1.00
38_G	111_F	0.862	1.00
195_A	199_V	0.862	1.00
137_Y	142_L	0.861	1.00
72_L	98_G	0.857	1.00
32_I	36_I	0.856	1.00
121_G	124_E	0.853	1.00
197_A	200_Y	0.850	1.00
212_D	216_R	0.846	1.00
103_N	156_T	0.843	1.00
137_Y	141_I	0.842	1.00
31_M	160_L	0.822	1.00
61_S	205_I	0.818	1.00
204_T	208_S	0.816	1.00
118_V	145_A	0.816	1.00
159_G	163_E	0.815	1.00
92_L	172_V	0.813	1.00
190_F	194_L	0.785	1.00
91_A	94_A	0.783	1.00
176_F	179_G	0.783	1.00
91_A	171_G	0.778	1.00
28_I	32_I	0.778	1.00
71_Q	98_G	0.777	1.00
34_A	107_L	0.776	1.00
68_T	163_E	0.771	1.00
48_K	51_V	0.767	1.00
46_K	115_L	0.766	1.00
103_N	160_L	0.760	1.00
44_I	52_L	0.760	1.00
125_A	128_S	0.754	1.00
69_L	169_T	0.747	1.00
210_L	214_F	0.744	1.00
208_S	212_D	0.739	1.00
48_K	53_H	0.737	1.00
161_L	203_L	0.735	1.00
54_Q	57_K	0.734	1.00
56_S	108_A	0.734	1.00
72_L	170_L	0.727	1.00
26_M	30_A	0.727	1.00
118_V	148_N	0.726	1.00
111_F	115_L	0.725	1.00
58_L	61_S	0.722	1.00
38_G	108_A	0.721	1.00
27_A	31_M	0.718	1.00
17_I	20_L	0.716	1.00
194_L	198_I	0.714	1.00
52_L	55_L	0.710	1.00
37_G	100_S	0.707	1.00
29_A	32_I	0.707	1.00
63_F	105_A	0.706	1.00
45_T	48_K	0.705	1.00
174_E	179_G	0.703	1.00
99_L	160_L	0.702	1.00
45_T	109_E	0.693	1.00
93_T	97_I	0.692	1.00
41_L	44_I	0.692	1.00
59_Y	63_F	0.690	1.00
26_M	92_L	0.689	1.00
68_T	102_K	0.686	1.00
207_Y	211_Q	0.686	1.00
196_V	200_Y	0.683	1.00
165_S	168_F	0.683	1.00
72_L	166_L	0.675	1.00
192_T	195_A	0.674	1.00
75_I	94_A	0.661	1.00
49_I	55_L	0.658	1.00
190_F	197_A	0.658	1.00
20_L	199_V	0.652	1.00
185_G	189_Y	0.652	1.00
25_F	93_T	0.652	1.00
205_I	208_S	0.650	1.00
141_I	144_Q	0.649	1.00
21_P	24_L	0.648	1.00
33_F	36_I	0.648	1.00
59_Y	104_A	0.647	1.00
42_A	46_K	0.641	1.00
29_A	92_L	0.636	1.00
118_V	144_Q	0.635	1.00
47_N	133_K	0.631	1.00
102_K	163_E	0.629	1.00
181_M	184_S	0.629	1.00
99_L	167_A	0.628	1.00
45_T	108_A	0.622	1.00
152_A	155_N	0.621	1.00
167_A	172_V	0.619	1.00
118_V	141_I	0.615	1.00
75_I	78_G	0.612	1.00
91_A	172_V	0.609	1.00
123_L	133_K	0.606	1.00
14_P	17_I	0.601	1.00
24_L	28_I	0.600	1.00
73_F	77_Y	0.597	1.00
202_V	206_I	0.594	1.00
57_K	61_S	0.592	1.00
175_M	179_G	0.592	1.00
179_G	185_G	0.590	1.00
74_L	194_L	0.589	1.00
27_A	30_A	0.585	1.00
61_S	109_E	0.584	1.00
100_S	104_A	0.584	1.00
47_N	56_S	0.583	1.00
180_K	185_G	0.583	1.00
62_F	66_V	0.583	1.00
47_N	123_L	0.582	1.00
36_I	39_L	0.581	1.00
31_M	153_T	0.580	1.00
19_A	178_Q	0.580	1.00
176_F	181_M	0.580	1.00
31_M	35_I	0.577	1.00
206_I	209_I	0.576	1.00
192_T	196_V	0.576	1.00
90_T	94_A	0.571	1.00
25_F	28_I	0.568	1.00
39_L	142_L	0.565	1.00
61_S	201_W	0.563	1.00
165_S	200_Y	0.560	1.00
121_G	125_A	0.559	1.00
95_A	172_V	0.558	1.00
26_M	95_A	0.555	1.00
131_M	136_A	0.554	1.00
76_Y	94_A	0.554	1.00
182_Y	185_G	0.552	1.00
182_Y	192_T	0.552	1.00
43_L	142_L	0.551	1.00
35_I	111_F	0.550	1.00
63_F	71_Q	0.549	1.00
173_M	178_Q	0.549	1.00
47_N	50_P	0.547	1.00
151_P	215_E	0.545	1.00
183_A	186_N	0.540	1.00
120_D	127_L	0.538	1.00
157_F	207_Y	0.537	1.00
203_L	207_Y	0.537	1.00
214_F	218_M	0.535	1.00
38_G	42_A	0.535	1.00
22_I	92_L	0.534	1.00
80_P	89_M	0.533	1.00
31_M	107_L	0.532	1.00
182_Y	186_N	0.531	1.00
122_Q	140_I	0.531	1.00
111_F	145_A	0.529	1.00
95_A	99_L	0.524	1.00
161_L	207_Y	0.522	1.00
104_A	108_A	0.520	1.00
184_S	187_L	0.518	1.00
79_L	89_M	0.517	1.00
166_L	171_G	0.516	1.00
42_A	108_A	0.515	1.00
59_Y	105_A	0.514	1.00
48_K	52_L	0.514	1.00
99_L	164_T	0.514	1.00
156_T	159_G	0.512	1.00
89_M	94_A	0.511	1.00
198_I	202_V	0.508	1.00
126_C	129_V	0.508	1.00
201_W	208_S	0.506	1.00
45_T	53_H	0.506	1.00
45_T	60_I	0.505	1.00
200_Y	204_T	0.504	1.00
20_L	175_M	0.503	1.00
190_F	193_Y	0.502	1.00
211_Q	214_F	0.502	1.00
167_A	174_E	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
4ymuD	2	0.9598	100	0.354	Contact Map
2onkC	2	0.9598	100	0.36	Contact Map
3d31C	2	0.942	100	0.381	Contact Map
3rlfF	1	0.933	100	0.382	Contact Map
4tquM	1	0.9732	100	0.391	Contact Map
3tuiA	2	0.933	100	0.416	Contact Map
3rlfG	1	0.9955	99.9	0.433	Contact Map
4tquN	1	0.9286	99.9	0.467	Contact Map
2l2tA	2	0.1875	14.8	0.939	Contact Map
4mt1A	3	0.7946	12.1	0.941	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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