ARAQ - BACSU - GREMLIN Contacts

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ARAQ - L-arabinose transport system permease protein AraQ

UniProt:	P94530	Sequences: MLRHSPQFSVYRIALTLFFMMLSLLYLFPIFCLLLGSLKPSSELLRVGLNLDIDPKVMSFDNYTFLFNGGSIYFKWFFNSLVLGLFTTVLTLFFSSMIGYGLAVYDFKGRNIIFVLVLIIMMVPLEVMMLPLFKLTVGLHLIDSYTGVILPFIVSPVAVFFFRQYALGLPRDLLDSARMDGCTEFGIFFRIMAPLMKPAFGAMIILQSLNSWNNFLWPLIVLRSKEMFTLPIGLSSLLSPYGNNYDMLISGSVFAILPVIIIFLFFQKYFISGLTVGGVKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	281 (252)
Sequences:	68849 (45247)
Seq/√Len:	2850.3

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
186_G	190_R	3.981	1.00
78_F	82_V	3.268	1.00
178_R	187_I	3.185	1.00
163_R	167_L	3.034	1.00
76_W	233_G	2.701	1.00
75_K	78_F	2.665	1.00
37_S	63_Y	2.605	1.00
183_T	186_G	2.561	1.00
165_Y	199_A	2.548	1.00
104_V	174_L	2.542	1.00
177_A	187_I	2.514	1.00
228_F	236_S	2.495	1.00
64_T	68_N	2.474	1.00
74_F	78_F	2.420	1.00
174_L	192_M	2.387	1.00
61_D	64_T	2.350	1.00
184_E	187_I	2.343	1.00
88_T	204_I	2.287	1.00
90_L	153_I	2.252	1.00
185_F	189_F	2.230	1.00
162_F	200_F	2.210	1.00
244_N	247_M	2.169	1.00
61_D	65_F	2.136	1.00
107_F	110_R	2.122	1.00
182_C	186_G	2.060	1.00
186_G	189_F	2.034	1.00
158_A	203_M	1.983	1.00
96_S	188_F	1.947	1.00
35_L	39_K	1.942	1.00
103_A	167_L	1.939	1.00
173_L	195_L	1.914	1.00
177_A	182_C	1.912	1.00
166_A	196_M	1.910	1.00
31_F	35_L	1.901	1.00
114_F	163_R	1.882	1.00
96_S	196_M	1.852	1.00
92_L	204_I	1.826	1.00
75_K	79_N	1.768	1.00
178_R	184_E	1.756	1.00
87_T	211_S	1.735	1.00
86_F	149_I	1.721	1.00
225_K	228_F	1.719	1.00
174_L	187_I	1.718	1.00
82_V	86_F	1.709	1.00
84_G	208_S	1.683	1.00
95_S	158_A	1.646	1.00
96_S	162_F	1.631	1.00
174_L	178_R	1.616	1.00
65_F	247_M	1.599	1.00
98_I	159_V	1.598	1.00
171_R	174_L	1.555	1.00
16_T	20_M	1.552	1.00
233_G	237_L	1.501	1.00
102_L	159_V	1.492	1.00
65_F	68_N	1.491	1.00
109_G	112_I	1.468	1.00
264_L	268_K	1.463	1.00
158_A	207_Q	1.462	1.00
215_F	219_L	1.443	1.00
28_F	32_C	1.437	1.00
106_D	110_R	1.431	1.00
60_F	64_T	1.430	1.00
34_L	253_V	1.419	1.00
103_A	163_R	1.419	1.00
83_L	229_T	1.399	1.00
32_C	36_G	1.356	1.00
93_F	97_M	1.345	1.00
202_A	206_L	1.345	1.00
99_G	162_F	1.338	1.00
166_A	192_M	1.334	1.00
91_T	207_Q	1.332	1.00
193_A	200_F	1.327	1.00
217_W	221_V	1.322	1.00
162_F	203_M	1.309	1.00
171_R	175_D	1.307	1.00
59_S	62_N	1.305	1.00
104_V	171_R	1.302	1.00
96_S	200_F	1.277	1.00
215_F	235_S	1.261	1.00
228_F	233_G	1.252	1.00
112_I	115_V	1.246	1.00
172_D	175_D	1.241	1.00
222_L	227_M	1.236	1.00
177_A	191_I	1.225	1.00
80_S	230_L	1.225	1.00
10_V	14_A	1.225	1.00
145_Y	227_M	1.223	1.00
89_V	93_F	1.217	1.00
43_E	57_V	1.217	1.00
237_L	242_G	1.217	1.00
224_S	227_M	1.216	1.00
100_Y	166_A	1.211	1.00
237_L	244_N	1.208	1.00
92_L	200_F	1.202	1.00
169_L	195_L	1.200	1.00
136_T	147_G	1.189	1.00
79_N	82_V	1.180	1.00
86_F	89_V	1.177	1.00
71_S	75_K	1.176	1.00
65_F	69_G	1.169	1.00
11_Y	15_L	1.164	1.00
236_S	240_P	1.143	1.00
20_M	24_L	1.143	1.00
197_K	201_G	1.134	1.00
40_P	43_E	1.114	1.00
183_T	187_I	1.114	1.00
112_I	116_L	1.100	1.00
214_N	217_W	1.098	1.00
33_L	253_V	1.096	1.00
141_L	146_T	1.093	1.00
162_F	199_A	1.085	1.00
32_C	35_L	1.081	1.00
13_I	17_L	1.074	1.00
174_L	184_E	1.073	1.00
86_F	90_L	1.057	1.00
155_S	159_V	1.053	1.00
228_F	232_I	1.050	1.00
229_T	232_I	1.039	1.00
268_K	271_I	1.036	1.00
41_S	45_L	1.025	1.00
100_Y	188_F	1.023	1.00
87_T	91_T	1.016	1.00
134_K	138_G	1.011	1.00
103_A	166_A	1.010	1.00
81_L	85_L	1.010	1.00
13_I	16_T	1.005	1.00
100_Y	184_E	1.001	1.00
67_F	74_F	1.000	1.00
187_I	190_R	0.999	1.00
151_P	221_V	0.996	1.00
161_F	203_M	0.996	1.00
195_L	198_P	0.991	1.00
10_V	13_I	0.986	1.00
233_G	251_G	0.984	1.00
97_M	101_G	0.982	1.00
110_R	167_L	0.978	1.00
182_C	187_I	0.976	1.00
89_V	204_I	0.969	1.00
12_R	16_T	0.957	1.00
15_L	19_F	0.943	1.00
259_V	263_F	0.939	1.00
233_G	236_S	0.938	1.00
218_P	229_T	0.935	1.00
63_Y	253_V	0.934	1.00
265_F	269_Y	0.932	1.00
87_T	152_F	0.919	1.00
132_L	221_V	0.916	1.00
99_G	103_A	0.914	1.00
143_D	224_S	0.910	1.00
82_V	85_L	0.909	1.00
149_I	153_I	0.903	1.00
77_F	230_L	0.899	1.00
36_G	249_I	0.897	1.00
214_N	218_P	0.895	1.00
219_L	232_I	0.895	1.00
23_S	27_L	0.892	1.00
36_G	39_K	0.883	1.00
85_L	89_V	0.880	1.00
37_S	41_S	0.876	1.00
91_T	95_S	0.874	1.00
165_Y	196_M	0.873	1.00
238_L	248_L	0.867	1.00
42_S	45_L	0.866	1.00
62_N	246_D	0.861	1.00
197_K	200_F	0.858	1.00
95_S	159_V	0.855	1.00
67_F	70_G	0.854	1.00
133_F	137_V	0.850	1.00
187_I	192_M	0.849	1.00
196_M	199_A	0.848	1.00
102_L	114_F	0.847	1.00
111_N	114_F	0.846	1.00
66_L	254_F	0.845	1.00
38_L	58_M	0.844	1.00
90_L	93_F	0.843	1.00
118_L	160_F	0.840	1.00
99_G	159_V	0.837	1.00
73_Y	251_G	0.837	1.00
158_A	162_F	0.836	1.00
147_G	151_P	0.834	1.00
90_L	149_I	0.833	1.00
235_S	239_S	0.833	1.00
188_F	193_A	0.832	1.00
237_L	251_G	0.831	1.00
78_F	81_L	0.826	1.00
108_K	111_N	0.825	1.00
162_F	196_M	0.821	1.00
39_K	43_E	0.819	1.00
189_F	193_A	0.819	1.00
151_P	217_W	0.819	1.00
237_L	247_M	0.818	1.00
101_G	107_F	0.816	1.00
207_Q	211_S	0.809	1.00
197_K	269_Y	0.808	1.00
77_F	81_L	0.808	1.00
36_G	40_P	0.804	1.00
255_A	259_V	0.802	1.00
152_F	211_S	0.799	1.00
182_C	190_R	0.795	1.00
184_E	188_F	0.794	1.00
261_I	265_F	0.790	1.00
141_L	144_S	0.784	1.00
151_P	154_V	0.781	1.00
137_V	142_I	0.757	1.00
173_L	191_I	0.756	1.00
139_L	142_I	0.755	1.00
91_T	158_A	0.755	1.00
91_T	211_S	0.753	1.00
76_W	79_N	0.753	1.00
58_M	61_D	0.753	1.00
232_I	236_S	0.751	1.00
148_V	218_P	0.751	1.00
33_L	249_I	0.748	1.00
129_M	216_L	0.745	1.00
266_F	269_Y	0.742	1.00
99_G	166_A	0.742	1.00
39_K	55_P	0.740	1.00
102_L	163_R	0.740	1.00
38_L	59_S	0.739	1.00
64_T	67_F	0.735	1.00
125_L	216_L	0.731	1.00
83_L	152_F	0.731	1.00
88_T	208_S	0.729	1.00
59_S	63_Y	0.728	1.00
200_F	203_M	0.728	1.00
129_M	220_I	0.726	1.00
28_F	31_F	0.723	1.00
265_F	268_K	0.722	1.00
84_G	88_T	0.718	1.00
60_F	63_Y	0.715	1.00
43_E	46_R	0.713	1.00
14_A	17_L	0.709	1.00
188_F	192_M	0.709	1.00
95_S	162_F	0.709	1.00
118_L	121_M	0.708	1.00
87_T	149_I	0.706	1.00
92_L	162_F	0.701	1.00
74_F	77_F	0.699	1.00
230_L	255_A	0.698	1.00
40_P	57_V	0.698	1.00
98_I	155_S	0.698	1.00
214_N	229_T	0.697	1.00
249_I	253_V	0.694	1.00
62_N	65_F	0.691	1.00
88_T	92_L	0.690	1.00
169_L	196_M	0.686	1.00
22_L	26_Y	0.686	1.00
176_S	180_D	0.683	1.00
176_S	179_M	0.683	1.00
171_R	178_R	0.681	1.00
65_F	244_N	0.680	1.00
102_L	113_I	0.678	1.00
222_L	228_F	0.678	1.00
148_V	152_F	0.677	1.00
82_V	145_Y	0.675	1.00
247_M	251_G	0.674	1.00
86_F	153_I	0.671	1.00
234_L	251_G	0.670	1.00
162_F	166_A	0.665	1.00
141_L	145_Y	0.664	1.00
23_S	26_Y	0.662	1.00
76_W	230_L	0.660	1.00
192_M	195_L	0.659	1.00
18_F	22_L	0.658	1.00
231_P	255_A	0.656	1.00
19_F	23_S	0.656	1.00
14_A	18_F	0.653	1.00
134_K	137_V	0.653	1.00
33_L	252_S	0.651	1.00
98_I	117_V	0.651	1.00
24_L	28_F	0.651	1.00
260_I	264_L	0.648	1.00
200_F	204_I	0.644	1.00
199_A	203_M	0.644	1.00
40_P	56_K	0.642	1.00
17_L	20_M	0.642	1.00
80_S	231_P	0.638	1.00
263_F	267_Q	0.636	1.00
107_F	113_I	0.631	1.00
70_G	75_K	0.623	1.00
108_K	112_I	0.623	1.00
111_N	115_V	0.617	1.00
109_G	113_I	0.616	1.00
114_F	160_F	0.614	1.00
42_S	46_R	0.611	1.00
70_G	74_F	0.608	1.00
57_V	61_D	0.605	1.00
43_E	56_K	0.604	1.00
210_N	213_N	0.604	1.00
83_L	87_T	0.601	1.00
71_S	225_K	0.600	1.00
101_G	105_Y	0.599	1.00
12_R	15_L	0.597	1.00
246_D	249_I	0.595	1.00
132_L	135_L	0.595	1.00
27_L	31_F	0.595	1.00
189_F	192_M	0.592	1.00
249_I	252_S	0.592	1.00
161_F	199_A	0.591	1.00
142_I	145_Y	0.591	1.00
106_D	111_N	0.590	1.00
245_Y	249_I	0.590	1.00
100_Y	192_M	0.589	1.00
149_I	152_F	0.587	1.00
126_E	220_I	0.585	1.00
204_I	207_Q	0.585	1.00
201_G	204_I	0.584	1.00
187_I	191_I	0.584	1.00
63_Y	250_S	0.584	1.00
84_G	211_S	0.582	1.00
115_V	119_I	0.582	1.00
211_S	214_N	0.580	1.00
92_L	96_S	0.580	1.00
66_L	251_G	0.579	1.00
261_I	264_L	0.577	1.00
139_L	144_S	0.576	1.00
55_P	58_M	0.576	1.00
39_K	57_V	0.575	1.00
94_F	155_S	0.574	1.00
216_L	219_L	0.573	1.00
209_L	213_N	0.572	1.00
16_T	19_F	0.572	1.00
117_V	156_P	0.571	1.00
71_S	74_F	0.571	1.00
36_G	41_S	0.570	1.00
143_D	146_T	0.570	1.00
125_L	129_M	0.567	1.00
68_N	71_S	0.566	1.00
57_V	60_F	0.566	1.00
80_S	212_W	0.563	1.00
140_H	143_D	0.563	1.00
120_I	156_P	0.560	1.00
99_G	163_R	0.560	1.00
264_L	267_Q	0.556	1.00
66_L	247_M	0.555	1.00
237_L	240_P	0.553	1.00
37_S	250_S	0.553	1.00
136_T	142_I	0.552	1.00
121_M	157_V	0.550	1.00
79_N	227_M	0.548	1.00
114_F	167_L	0.547	1.00
84_G	212_W	0.543	1.00
98_I	101_G	0.543	1.00
83_L	149_I	0.542	1.00
121_M	156_P	0.541	1.00
245_Y	248_L	0.541	1.00
95_S	155_S	0.539	1.00
69_G	74_F	0.533	1.00
87_T	153_I	0.532	1.00
147_G	221_V	0.530	1.00
107_F	111_N	0.529	1.00
38_L	60_F	0.528	1.00
247_M	250_S	0.527	1.00
110_R	114_F	0.525	1.00
116_L	120_I	0.525	1.00
132_L	151_P	0.524	1.00
106_D	171_R	0.522	1.00
113_I	117_V	0.520	1.00
218_P	222_L	0.519	1.00
225_K	236_S	0.516	1.00
105_Y	184_E	0.514	1.00
39_K	56_K	0.514	1.00
218_P	232_I	0.510	1.00
192_M	196_M	0.510	1.00
100_Y	104_V	0.510	1.00
169_L	174_L	0.509	1.00
183_T	189_F	0.507	1.00
88_T	93_F	0.507	1.00
114_F	159_V	0.505	1.00
232_I	235_S	0.504	1.00
64_T	69_G	0.503	1.00
96_S	193_A	0.503	1.00
79_N	229_T	0.502	1.00
75_K	82_V	0.502	1.00
258_P	261_I	0.501	1.00
175_D	178_R	0.501	1.00
106_D	109_G	0.501	1.00
129_M	133_F	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
4tquN	1	0.9502	100	0.245	Contact Map
3rlfG	1	0.9502	100	0.249	Contact Map
2onkC	2	0.8541	100	0.314	Contact Map
4tquM	1	0.9075	100	0.327	Contact Map
3d31C	2	0.8363	100	0.337	Contact Map
3rlfF	1	0.9253	100	0.389	Contact Map
4ymuD	2	0.7544	99.9	0.498	Contact Map
3tuiA	2	0.7331	99.9	0.527	Contact Map
2cfqA	1	0.9181	4.5	0.955	Contact Map
2k1eA	3	0.3665	4.2	0.955	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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