RBSC - ECOLI - GREMLIN Contacts

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RBSC - Ribose transport system permease protein RbsC

UniProt:	P0AGI1	Sequences: MTTQTVSGRRYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVDNKKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10816
Length:	321 (267)
Sequences:	31325 (19569)
Seq/√Len:	1197.6

ECOLI - RBSC ARAH YPHD ALSC YTFT MGLC XYLH LSRD LSRC YJFF LIVM LIVH
BACSU - RBSC YUFP YUFQ
HALSA - Q9HR22 Q9HR23
SULSO - Q97UZ9 Q97UZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
105_L	229_L	3.863	1.00
109_A	225_S	3.572	1.00
109_A	229_L	3.068	1.00
86_V	107_L	2.964	1.00
113_A	225_S	2.923	1.00
206_E	220_K	2.768	1.00
90_I	103_A	2.688	1.00
57_A	179_M	2.542	1.00
64_T	278_T	2.514	1.00
199_I	223_V	2.477	1.00
215_N	218_K	2.444	1.00
121_K	217_N	2.442	1.00
218_K	222_I	2.344	1.00
187_W	191_H	2.305	1.00
189_M	195_L	2.296	1.00
108_G	232_S	2.269	1.00
188_Y	192_H	2.227	1.00
112_G	228_G	2.220	1.00
113_A	221_I	2.201	1.00
115_T	133_M	2.190	1.00
198_Y	219_I	2.161	1.00
256_D	289_N	2.125	1.00
195_L	222_I	2.118	1.00
117_V	121_K	2.102	1.00
185_A	189_M	2.027	1.00
96_N	99_V	1.986	1.00
105_L	233_L	1.955	1.00
59_M	257_A	1.948	1.00
81_A	141_T	1.935	1.00
87_A	104_A	1.916	1.00
98_L	102_A	1.865	1.00
101_V	236_I	1.787	1.00
87_A	236_I	1.780	1.00
108_G	228_G	1.780	1.00
53_T	286_G	1.757	1.00
60_A	278_T	1.751	1.00
184_L	188_Y	1.738	1.00
202_L	219_I	1.726	1.00
201_A	209_T	1.692	1.00
66_V	227_C	1.689	1.00
116_G	221_I	1.673	1.00
135_L	138_R	1.661	1.00
65_L	186_A	1.622	1.00
194_R	198_Y	1.577	1.00
53_T	283_L	1.568	1.00
68_L	200_Y	1.525	1.00
57_A	282_A	1.524	1.00
91_V	100_A	1.520	1.00
111_I	137_L	1.499	1.00
105_L	236_I	1.495	1.00
82_L	111_I	1.478	1.00
256_D	306_K	1.471	1.00
195_L	199_I	1.466	1.00
121_K	221_I	1.453	1.00
222_I	225_S	1.443	1.00
206_E	210_R	1.433	1.00
207_A	210_R	1.427	1.00
59_M	80_L	1.425	1.00
78_S	138_R	1.419	1.00
264_G	277_G	1.415	1.00
133_M	137_L	1.410	1.00
89_S	144_Y	1.397	1.00
183_F	279_L	1.392	1.00
198_Y	214_I	1.367	1.00
274_R	277_G	1.367	1.00
99_V	102_A	1.353	1.00
80_L	238_E	1.346	1.00
198_Y	209_T	1.332	1.00
69_T	223_V	1.331	1.00
90_I	95_V	1.327	1.00
62_G	230_L	1.307	1.00
58_I	234_A	1.300	1.00
117_V	221_I	1.286	1.00
95_V	99_V	1.275	1.00
209_T	214_I	1.271	1.00
167_G	170_L	1.270	1.00
202_L	216_V	1.268	1.00
90_I	93_I	1.267	1.00
100_A	104_A	1.244	1.00
65_L	223_V	1.244	1.00
58_I	237_I	1.242	1.00
104_A	108_G	1.237	1.00
45_N	290_N	1.234	1.00
264_G	281_G	1.231	1.00
221_I	225_S	1.222	1.00
61_V	186_A	1.216	1.00
76_V	231_A	1.213	1.00
71_G	220_K	1.212	1.00
214_I	219_I	1.208	1.00
163_W	166_I	1.201	1.00
57_A	279_L	1.199	1.00
120_A	217_N	1.183	1.00
63_M	261_V	1.175	1.00
202_L	209_T	1.172	1.00
49_I	287_F	1.171	1.00
102_A	106_A	1.169	1.00
49_I	286_G	1.167	1.00
95_V	103_A	1.166	1.00
63_M	257_A	1.164	1.00
71_G	126_A	1.158	1.00
106_A	109_A	1.153	1.00
191_H	200_Y	1.145	1.00
79_L	111_I	1.119	1.00
225_S	229_L	1.117	1.00
60_A	260_A	1.112	1.00
78_S	137_L	1.106	1.00
92_G	96_N	1.103	1.00
89_S	145_T	1.099	1.00
86_V	90_I	1.097	1.00
187_W	192_H	1.095	1.00
290_N	293_N	1.093	1.00
166_I	169_P	1.091	1.00
182_V	230_L	1.091	1.00
71_G	224_Y	1.087	1.00
53_T	282_A	1.079	1.00
219_I	222_I	1.078	1.00
62_G	76_V	1.073	1.00
228_G	232_S	1.072	1.00
159_D	162_G	1.069	1.00
210_R	216_V	1.066	1.00
169_P	173_P	1.066	1.00
89_S	92_G	1.063	1.00
109_A	232_S	1.063	1.00
118_I	129_A	1.059	1.00
138_R	142_M	1.059	1.00
210_R	217_N	1.055	1.00
183_F	230_L	1.051	1.00
253_Y	256_D	1.039	1.00
60_A	261_V	1.038	1.00
68_L	273_G	1.038	1.00
222_I	226_L	1.036	1.00
87_A	240_A	1.036	1.00
289_N	306_K	1.036	1.00
85_A	141_T	1.034	1.00
110_A	113_A	1.029	1.00
186_A	226_L	1.027	1.00
301_Y	304_I	1.023	1.00
164_F	167_G	1.013	1.00
177_W	181_I	1.011	1.00
134_M	138_R	1.007	1.00
199_I	219_I	1.003	1.00
184_L	187_W	1.000	1.00
115_T	129_A	0.996	1.00
85_A	247_P	0.994	1.00
117_V	122_G	0.994	1.00
303_M	306_K	0.992	1.00
174_T	177_W	0.991	1.00
181_I	185_A	0.989	1.00
260_A	282_A	0.987	1.00
104_A	236_I	0.985	1.00
102_A	105_L	0.984	1.00
226_L	230_L	0.979	1.00
59_M	234_A	0.978	1.00
156_E	159_D	0.972	1.00
64_T	261_V	0.969	1.00
260_A	281_G	0.968	1.00
47_F	51_Q	0.963	1.00
235_G	239_V	0.944	1.00
120_A	130_T	0.943	1.00
82_L	86_V	0.943	1.00
195_L	219_I	0.939	1.00
291_G	295_L	0.936	1.00
67_I	261_V	0.936	1.00
83_T	108_G	0.930	1.00
158_A	161_F	0.928	1.00
276_V	280_I	0.923	1.00
170_L	177_W	0.923	1.00
54_S	176_V	0.923	1.00
77_G	254_E	0.920	1.00
55_V	234_A	0.905	1.00
44_N	47_F	0.905	1.00
52_Q	56_N	0.904	1.00
179_M	183_F	0.904	1.00
78_S	134_M	0.903	1.00
85_A	145_T	0.903	1.00
167_G	171_G	0.902	1.00
83_T	104_A	0.900	1.00
197_R	200_Y	0.899	1.00
68_L	191_H	0.898	1.00
164_F	168_R	0.894	1.00
119_V	129_A	0.894	1.00
227_C	231_A	0.894	1.00
218_K	221_I	0.893	1.00
90_I	100_A	0.893	1.00
118_I	122_G	0.892	1.00
69_T	199_I	0.891	1.00
64_T	273_G	0.890	1.00
143_V	301_Y	0.886	1.00
180_G	184_L	0.882	1.00
123_R	206_E	0.881	1.00
73_D	76_V	0.880	1.00
60_A	282_A	0.879	1.00
57_A	183_F	0.870	1.00
187_W	276_V	0.870	1.00
87_A	91_V	0.869	1.00
292_L	305_V	0.868	1.00
168_R	172_V	0.862	1.00
58_I	179_M	0.861	1.00
79_L	231_A	0.860	1.00
63_M	76_V	0.860	1.00
84_G	239_V	0.858	1.00
80_L	253_Y	0.857	1.00
168_R	171_G	0.855	1.00
89_S	93_I	0.854	1.00
208_A	212_S	0.848	1.00
252_G	256_D	0.848	1.00
61_V	182_V	0.847	1.00
217_N	220_K	0.838	1.00
202_L	223_V	0.834	1.00
61_V	278_T	0.833	1.00
66_V	73_D	0.830	1.00
248_T	251_T	0.829	1.00
99_V	103_A	0.828	1.00
105_L	232_S	0.828	1.00
272_K	276_V	0.826	1.00
216_V	220_K	0.825	1.00
106_A	110_A	0.825	1.00
65_L	190_L	0.824	1.00
114_V	118_I	0.821	1.00
175_P	237_I	0.817	1.00
153_G	156_E	0.815	1.00
46_L	291_G	0.814	1.00
116_G	120_A	0.814	1.00
77_G	252_G	0.811	1.00
65_L	226_L	0.810	1.00
80_L	250_G	0.810	1.00
285_L	306_K	0.810	1.00
312_L	316_V	0.807	1.00
231_A	235_G	0.802	1.00
205_N	208_A	0.796	1.00
86_V	89_S	0.792	1.00
174_T	178_I	0.792	1.00
278_T	282_A	0.792	1.00
274_R	278_T	0.791	1.00
84_G	249_A	0.788	1.00
139_G	142_M	0.783	1.00
113_A	117_V	0.782	1.00
79_L	108_G	0.778	1.00
202_L	220_K	0.777	1.00
176_V	180_G	0.776	1.00
83_T	235_G	0.775	1.00
190_L	199_I	0.774	1.00
59_M	76_V	0.768	1.00
290_N	294_L	0.767	1.00
206_E	216_V	0.762	1.00
88_A	245_A	0.761	1.00
238_E	242_L	0.756	1.00
229_L	232_S	0.754	1.00
110_A	114_V	0.751	1.00
116_G	121_K	0.748	1.00
148_S	151_N	0.745	1.00
217_N	221_I	0.745	1.00
48_N	52_Q	0.744	1.00
158_A	162_G	0.741	1.00
155_T	158_A	0.737	1.00
84_G	245_A	0.737	1.00
149_P	152_T	0.736	1.00
229_L	233_L	0.735	1.00
59_M	62_G	0.729	1.00
198_Y	215_N	0.725	1.00
169_P	172_V	0.725	1.00
165_G	168_R	0.724	1.00
87_A	100_A	0.723	1.00
185_A	188_Y	0.716	1.00
169_P	177_W	0.715	1.00
136_L	140_V	0.714	1.00
306_K	310_I	0.713	1.00
308_V	312_L	0.713	1.00
58_I	182_V	0.711	1.00
105_L	109_A	0.710	1.00
83_T	107_L	0.709	1.00
80_L	234_A	0.708	1.00
62_G	231_A	0.706	1.00
53_T	57_A	0.705	1.00
282_A	286_G	0.698	1.00
82_L	108_G	0.694	1.00
74_L	258_I	0.693	1.00
283_L	287_F	0.692	1.00
300_Y	303_M	0.686	1.00
56_N	256_D	0.680	1.00
66_V	224_Y	0.679	1.00
56_N	260_A	0.674	1.00
259_A	310_I	0.670	1.00
67_I	258_I	0.669	1.00
126_A	224_Y	0.665	1.00
189_M	192_H	0.664	1.00
101_V	105_L	0.660	1.00
163_W	168_R	0.660	1.00
64_T	275_I	0.658	1.00
299_S	302_Q	0.658	1.00
64_T	68_L	0.656	1.00
45_N	294_L	0.654	1.00
289_N	302_Q	0.652	1.00
49_I	53_T	0.646	1.00
120_A	221_I	0.646	1.00
91_V	240_A	0.646	1.00
49_I	290_N	0.645	1.00
71_G	206_E	0.644	1.00
182_V	233_L	0.641	1.00
216_V	219_I	0.640	1.00
79_L	228_G	0.637	1.00
186_A	190_L	0.636	1.00
79_L	83_T	0.635	1.00
50_L	54_S	0.633	1.00
79_L	115_T	0.632	1.00
188_Y	191_H	0.631	1.00
112_G	225_S	0.631	1.00
82_L	137_L	0.630	1.00
56_N	282_A	0.629	1.00
183_F	187_W	0.627	1.00
232_S	236_I	0.617	1.00
51_Q	241_R	0.615	1.00
173_P	177_W	0.614	1.00
54_S	179_M	0.612	1.00
90_I	107_L	0.612	1.00
108_G	112_G	0.612	1.00
263_L	281_G	0.611	1.00
226_L	229_L	0.608	1.00
109_A	112_G	0.603	1.00
48_N	290_N	0.603	1.00
95_V	98_L	0.599	1.00
69_T	202_L	0.595	1.00
69_T	220_K	0.595	1.00
138_R	251_T	0.595	1.00
119_V	224_Y	0.594	1.00
163_W	167_G	0.594	1.00
83_T	231_A	0.592	1.00
79_L	112_G	0.589	1.00
195_L	226_L	0.588	1.00
97_A	240_A	0.588	1.00
105_L	108_G	0.586	1.00
79_L	137_L	0.581	1.00
62_G	66_V	0.581	1.00
88_A	150_V	0.579	1.00
138_R	254_E	0.579	1.00
186_A	230_L	0.578	1.00
75_S	115_T	0.577	1.00
181_I	184_L	0.577	1.00
51_Q	176_V	0.575	1.00
187_W	274_R	0.575	1.00
238_E	253_Y	0.575	1.00
55_V	238_E	0.574	1.00
189_M	222_I	0.574	1.00
135_L	139_G	0.573	1.00
56_N	253_Y	0.572	1.00
86_V	103_A	0.572	1.00
260_A	278_T	0.564	1.00
170_L	173_P	0.564	1.00
228_G	231_A	0.563	1.00
119_V	126_A	0.560	1.00
123_R	217_N	0.560	1.00
65_L	189_M	0.559	1.00
55_V	241_R	0.558	1.00
87_A	235_G	0.557	1.00
225_S	228_G	0.557	1.00
50_L	53_T	0.553	1.00
189_M	193_T	0.548	1.00
209_T	216_V	0.547	1.00
66_V	71_G	0.544	1.00
220_K	223_V	0.544	1.00
207_A	211_L	0.543	1.00
61_V	183_F	0.543	1.00
81_A	249_A	0.542	1.00
251_T	254_E	0.539	1.00
178_I	182_V	0.538	1.00
147_G	150_V	0.538	1.00
131_L	135_L	0.536	1.00
264_G	278_T	0.535	1.00
86_V	104_A	0.535	1.00
90_I	94_E	0.534	1.00
178_I	181_I	0.534	1.00
263_L	313_A	0.533	1.00
292_L	297_V	0.532	1.00
61_V	187_W	0.531	1.00
156_E	160_L	0.530	1.00
57_A	61_V	0.530	1.00
134_M	254_E	0.529	1.00
95_V	100_A	0.528	1.00
52_Q	290_N	0.528	1.00
261_V	278_T	0.526	1.00
137_L	141_T	0.525	1.00
306_K	314_V	0.525	1.00
82_L	107_L	0.525	1.00
182_V	186_A	0.524	1.00
277_G	281_G	0.523	1.00
92_G	95_V	0.523	1.00
141_T	145_T	0.523	1.00
256_D	303_M	0.523	1.00
45_N	48_N	0.521	1.00
93_I	96_N	0.520	1.00
56_N	60_A	0.517	1.00
201_A	208_A	0.517	1.00
131_L	134_M	0.516	1.00
146_N	149_P	0.515	1.00
276_V	279_L	0.511	1.00
172_V	177_W	0.511	1.00
291_G	294_L	0.507	1.00
86_V	108_G	0.506	1.00
118_I	124_V	0.504	1.00
140_V	144_Y	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
4g1uA	2	0.8193	97.5	0.865	Contact Map
2qi9A	2	0.9097	97.3	0.87	Contact Map
2nq2A	2	0.8567	97	0.876	Contact Map
2kogA	1	0.1246	11.4	0.955	Contact Map
1u7gA	3	0.5826	11.3	0.955	Contact Map
4j72A	2	0.676	8.7	0.957	Contact Map
2m8rA	1	0.1308	6.4	0.959	Contact Map
2onkC	2	0.7352	5	0.961	Contact Map
4dveA	3	0.5483	4.1	0.963	Contact Map
1pw4A	1	0.5826	3.8	0.963	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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