YJFF - ECOLI - GREMLIN Contacts

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YJFF - Inner membrane ABC transporter permease protein YjfF

UniProt:	P37772	Sequences: MIKRNLPLMITIGVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIALQRGLTVLWENRQSSPVTRVNIAQQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12439
Length:	331 (275)
Sequences:	31079 (19853)
Seq/√Len:	1197.2

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
95_L	219_G	3.887	1.00
99_C	215_M	3.557	1.00
99_C	219_G	3.057	1.00
103_A	215_M	2.896	1.00
75_F	97_M	2.881	1.00
196_A	210_T	2.795	1.00
79_V	93_L	2.674	1.00
189_V	213_I	2.550	1.00
53_T	268_T	2.511	1.00
46_G	169_M	2.479	1.00
205_S	208_S	2.476	1.00
111_A	207_R	2.420	1.00
102_G	218_T	2.318	1.00
208_S	212_R	2.307	1.00
179_L	185_F	2.301	1.00
178_F	182_R	2.265	1.00
177_I	181_H	2.256	1.00
98_G	222_T	2.251	1.00
103_A	211_I	2.205	1.00
105_M	123_G	2.192	1.00
188_Q	209_T	2.148	1.00
246_D	279_Q	2.135	1.00
107_L	111_A	2.123	1.00
185_F	212_R	2.108	1.00
86_S	89_L	2.038	1.00
175_I	179_L	2.006	1.00
70_A	131_S	1.985	1.00
48_I	247_A	1.957	1.00
95_L	223_L	1.947	1.00
76_L	94_V	1.917	1.00
88_L	92_P	1.908	1.00
98_G	218_T	1.826	1.00
76_L	226_I	1.777	1.00
49_A	268_T	1.775	1.00
174_V	178_F	1.774	1.00
192_I	209_T	1.743	1.00
42_N	276_G	1.740	1.00
91_F	226_I	1.709	1.00
191_A	199_A	1.705	1.00
55_V	217_S	1.694	1.00
106_G	211_I	1.651	1.00
125_F	128_R	1.647	1.00
54_F	176_G	1.641	1.00
145_I	148_T	1.601	1.00
46_G	272_V	1.563	1.00
184_R	188_Q	1.559	1.00
42_N	273_A	1.552	1.00
57_L	190_Y	1.536	1.00
95_L	226_I	1.531	1.00
246_D	297_I	1.513	1.00
80_I	90_A	1.510	1.00
71_F	101_F	1.501	1.00
101_F	127_L	1.500	1.00
185_F	189_V	1.483	1.00
67_S	128_R	1.474	1.00
212_R	215_M	1.464	1.00
197_T	200_N	1.460	1.00
111_A	211_I	1.460	1.00
196_A	200_N	1.439	1.00
69_I	228_F	1.426	1.00
123_G	127_L	1.426	1.00
48_I	69_I	1.402	1.00
85_L	89_L	1.402	1.00
78_K	134_V	1.373	1.00
147_D	150_S	1.373	1.00
173_V	269_L	1.369	1.00
188_Q	204_I	1.358	1.00
264_T	267_G	1.355	1.00
58_S	213_I	1.347	1.00
47_I	224_A	1.346	1.00
89_L	92_P	1.345	1.00
79_V	85_L	1.335	1.00
78_K	82_D	1.316	1.00
54_F	213_I	1.306	1.00
188_Q	199_A	1.303	1.00
79_V	83_F	1.299	1.00
51_G	220_L	1.297	1.00
107_L	211_I	1.277	1.00
254_G	267_G	1.274	1.00
199_A	204_I	1.273	1.00
94_V	98_G	1.259	1.00
192_I	206_T	1.258	1.00
146_Y	149_L	1.256	1.00
254_G	271_G	1.244	1.00
78_K	135_S	1.240	1.00
110_D	207_R	1.239	1.00
47_I	227_V	1.237	1.00
211_I	215_M	1.224	1.00
65_V	221_A	1.223	1.00
90_A	94_V	1.223	1.00
204_I	209_T	1.219	1.00
46_G	269_L	1.215	1.00
34_V	280_T	1.203	1.00
92_P	96_V	1.201	1.00
60_G	116_A	1.197	1.00
50_V	176_G	1.192	1.00
52_M	251_V	1.191	1.00
38_I	276_G	1.189	1.00
60_G	210_T	1.189	1.00
192_I	199_A	1.184	1.00
181_H	190_Y	1.184	1.00
38_I	277_L	1.183	1.00
148_T	151_S	1.176	1.00
75_F	79_V	1.162	1.00
85_L	93_L	1.154	1.00
68_V	101_F	1.145	1.00
49_A	250_S	1.143	1.00
96_V	99_C	1.137	1.00
177_I	182_R	1.129	1.00
215_M	219_G	1.128	1.00
52_M	247_A	1.125	1.00
42_N	272_V	1.117	1.00
60_G	214_Y	1.115	1.00
172_V	220_L	1.095	1.00
280_T	283_N	1.093	1.00
157_P	160_G	1.093	1.00
173_V	220_L	1.086	1.00
200_N	207_R	1.078	1.00
238_L	241_V	1.067	1.00
67_S	127_L	1.067	1.00
200_N	206_T	1.065	1.00
76_L	230_I	1.062	1.00
128_R	132_Y	1.058	1.00
108_L	119_I	1.058	1.00
212_R	216_L	1.056	1.00
51_G	65_V	1.054	1.00
94_V	226_I	1.054	1.00
171_A	175_I	1.052	1.00
209_T	212_R	1.048	1.00
174_V	177_I	1.046	1.00
77_A	81_G	1.043	1.00
99_C	222_T	1.043	1.00
176_G	216_L	1.039	1.00
74_V	131_S	1.039	1.00
243_V	246_D	1.037	1.00
49_A	251_V	1.036	1.00
100_A	103_A	1.029	1.00
53_T	251_V	1.028	1.00
218_T	222_T	1.021	1.00
57_L	263_G	1.018	1.00
292_W	295_I	1.014	1.00
36_C	40_T	1.013	1.00
92_P	95_L	1.011	1.00
110_D	120_T	1.009	1.00
48_I	224_A	1.004	1.00
167_L	171_A	1.001	1.00
43_A	166_G	1.000	1.00
124_M	128_R	1.000	1.00
279_Q	297_I	0.994	1.00
149_L	152_L	0.992	1.00
216_L	220_L	0.990	1.00
150_S	154_W	0.989	1.00
250_S	271_G	0.987	1.00
189_V	209_T	0.986	1.00
105_M	119_I	0.972	1.00
107_L	112_L	0.971	1.00
74_V	237_A	0.965	1.00
139_I	142_N	0.963	1.00
146_Y	150_S	0.962	1.00
250_S	272_V	0.958	1.00
177_I	266_L	0.956	1.00
56_I	251_V	0.953	1.00
225_G	229_S	0.951	1.00
79_V	90_A	0.949	1.00
294_K	297_I	0.942	1.00
185_F	209_T	0.939	1.00
164_A	167_L	0.938	1.00
73_G	229_S	0.935	1.00
71_F	75_F	0.934	1.00
266_L	270_F	0.934	1.00
143_H	146_Y	0.930	1.00
72_T	98_G	0.922	1.00
66_G	244_E	0.913	1.00
67_S	124_M	0.913	1.00
53_T	263_G	0.905	1.00
208_S	211_I	0.904	1.00
198_S	202_M	0.904	1.00
74_V	135_S	0.903	1.00
217_S	221_A	0.902	1.00
113_K	196_A	0.901	1.00
169_M	173_V	0.899	1.00
33_R	36_C	0.899	1.00
108_L	112_L	0.896	1.00
282_I	296_A	0.896	1.00
187_N	190_Y	0.893	1.00
140_P	143_H	0.891	1.00
57_L	181_H	0.888	1.00
58_S	189_V	0.885	1.00
41_D	45_L	0.885	1.00
109_I	119_I	0.884	1.00
96_V	100_A	0.883	1.00
44_F	224_A	0.882	1.00
275_Q	297_I	0.881	1.00
49_A	272_V	0.878	1.00
46_G	173_V	0.877	1.00
303_I	307_L	0.877	1.00
281_Y	285_D	0.876	1.00
69_I	243_V	0.875	1.00
170_L	174_V	0.875	1.00
52_M	65_V	0.874	1.00
78_K	83_F	0.871	1.00
72_T	94_V	0.871	1.00
160_G	167_L	0.870	1.00
35_I	281_Y	0.868	1.00
309_R	312_T	0.865	1.00
62_D	65_V	0.865	1.00
50_V	172_V	0.865	1.00
76_L	80_I	0.865	1.00
207_R	210_T	0.861	1.00
69_I	240_G	0.861	1.00
68_V	221_A	0.861	1.00
89_L	93_L	0.859	1.00
73_G	235_G	0.858	1.00
165_M	227_V	0.855	1.00
55_V	62_D	0.854	1.00
150_S	153_A	0.852	1.00
180_A	189_V	0.852	1.00
79_V	82_D	0.846	1.00
54_F	216_L	0.846	1.00
129_G	132_Y	0.845	1.00
47_I	169_M	0.843	1.00
104_F	108_L	0.842	1.00
166_G	170_L	0.837	1.00
264_T	268_T	0.834	1.00
192_I	213_I	0.834	1.00
195_N	198_S	0.833	1.00
206_T	210_T	0.833	1.00
221_A	225_G	0.828	1.00
133_L	292_W	0.828	1.00
75_F	78_K	0.822	1.00
137_E	140_P	0.822	1.00
151_S	154_W	0.820	1.00
163_S	167_L	0.819	1.00
72_T	225_G	0.818	1.00
68_V	98_G	0.815	1.00
50_V	268_T	0.808	1.00
95_L	222_T	0.804	1.00
73_G	239_A	0.798	1.00
48_I	65_V	0.795	1.00
77_A	235_G	0.794	1.00
219_G	222_T	0.791	1.00
192_I	210_T	0.791	1.00
37_N	41_D	0.791	1.00
54_F	180_A	0.788	1.00
280_T	284_F	0.784	1.00
207_R	211_I	0.783	1.00
106_G	110_D	0.780	1.00
146_Y	151_S	0.780	1.00
154_W	157_P	0.780	1.00
262_V	266_L	0.778	1.00
63_L	248_I	0.777	1.00
164_A	168_L	0.769	1.00
219_G	223_L	0.761	1.00
106_G	111_A	0.759	1.00
196_A	206_T	0.757	1.00
179_L	182_R	0.756	1.00
147_D	151_S	0.751	1.00
103_A	107_L	0.750	1.00
175_I	178_F	0.744	1.00
51_G	221_A	0.744	1.00
48_I	51_G	0.743	1.00
128_R	241_V	0.743	1.00
156_I	160_G	0.739	1.00
268_T	272_V	0.736	1.00
299_I	303_I	0.736	1.00
47_I	172_V	0.732	1.00
100_A	104_F	0.731	1.00
95_L	99_C	0.731	1.00
308_Q	311_L	0.719	1.00
126_F	130_V	0.719	1.00
116_A	214_Y	0.717	1.00
45_L	246_D	0.714	1.00
71_F	98_G	0.714	1.00
69_I	224_A	0.713	1.00
249_A	301_L	0.712	1.00
76_L	90_A	0.704	1.00
291_W	294_K	0.699	1.00
188_Q	205_S	0.698	1.00
148_T	152_L	0.697	1.00
55_V	214_Y	0.697	1.00
43_A	169_M	0.695	1.00
145_I	149_L	0.692	1.00
42_N	46_G	0.689	1.00
40_T	166_G	0.675	1.00
279_Q	293_T	0.673	1.00
80_I	230_I	0.671	1.00
110_D	211_I	0.669	1.00
273_A	277_L	0.669	1.00
228_F	232_T	0.668	1.00
91_F	95_L	0.667	1.00
38_I	280_T	0.664	1.00
272_V	276_G	0.664	1.00
68_V	105_M	0.660	1.00
68_V	218_T	0.659	1.00
141_I	144_P	0.651	1.00
85_L	90_A	0.651	1.00
72_T	97_M	0.646	1.00
45_L	250_S	0.646	1.00
102_G	215_M	0.645	1.00
228_F	243_V	0.643	1.00
39_L	43_A	0.640	1.00
71_F	127_L	0.638	1.00
68_V	72_T	0.637	1.00
98_G	102_G	0.634	1.00
178_F	181_H	0.634	1.00
128_R	244_E	0.634	1.00
176_G	180_A	0.633	1.00
206_T	209_T	0.632	1.00
51_G	55_V	0.632	1.00
308_Q	312_T	0.631	1.00
58_S	192_I	0.628	1.00
56_I	248_I	0.628	1.00
72_T	221_A	0.627	1.00
34_V	284_F	0.627	1.00
60_G	196_A	0.626	1.00
40_T	231_Y	0.625	1.00
172_V	223_L	0.624	1.00
216_L	219_G	0.624	1.00
53_T	57_L	0.623	1.00
297_I	301_L	0.623	1.00
185_F	216_L	0.622	1.00
68_V	127_L	0.618	1.00
176_G	220_L	0.618	1.00
38_I	42_N	0.618	1.00
37_N	280_T	0.617	1.00
173_V	177_I	0.616	1.00
45_L	272_V	0.614	1.00
53_T	265_V	0.614	1.00
179_L	212_R	0.612	1.00
306_A	310_G	0.612	1.00
109_I	116_A	0.610	1.00
137_E	142_N	0.610	1.00
50_V	177_I	0.607	1.00
68_V	102_G	0.603	1.00
179_L	183_T	0.601	1.00
222_T	226_I	0.601	1.00
157_P	161_R	0.600	1.00
54_F	179_L	0.598	1.00
151_S	155_K	0.596	1.00
32_T	35_I	0.594	1.00
253_I	304_F	0.590	1.00
109_I	214_Y	0.590	1.00
253_I	271_G	0.589	1.00
44_F	228_F	0.588	1.00
58_S	210_T	0.587	1.00
99_C	102_G	0.585	1.00
288_L	292_W	0.583	1.00
75_F	93_L	0.583	1.00
250_S	268_T	0.582	1.00
218_T	221_A	0.579	1.00
95_L	98_G	0.578	1.00
79_V	97_M	0.577	1.00
131_S	135_S	0.576	1.00
87_P	230_I	0.575	1.00
162_L	165_M	0.574	1.00
246_D	294_K	0.569	1.00
251_V	268_T	0.568	1.00
113_K	207_R	0.568	1.00
267_G	271_G	0.567	1.00
162_L	167_L	0.567	1.00
76_L	225_G	0.566	1.00
50_V	173_V	0.564	1.00
64_S	105_M	0.561	1.00
45_L	243_V	0.559	1.00
171_A	174_V	0.557	1.00
145_I	150_S	0.557	1.00
295_I	299_I	0.554	1.00
177_I	264_T	0.553	1.00
124_M	244_E	0.552	1.00
210_T	213_I	0.552	1.00
125_F	129_G	0.547	1.00
39_L	42_N	0.547	1.00
78_K	81_G	0.546	1.00
144_P	147_D	0.546	1.00
215_M	218_T	0.546	1.00
70_A	240_G	0.544	1.00
34_V	37_N	0.544	1.00
121_L	124_M	0.542	1.00
79_V	84_G	0.539	1.00
99_C	218_T	0.539	1.00
121_L	125_F	0.538	1.00
75_F	94_V	0.537	1.00
254_G	268_T	0.535	1.00
181_H	184_R	0.532	1.00
199_A	206_T	0.532	1.00
50_V	174_V	0.532	1.00
33_R	37_N	0.530	1.00
241_V	244_E	0.529	1.00
55_V	60_G	0.528	1.00
85_L	88_L	0.525	1.00
41_D	280_T	0.521	1.00
250_S	275_Q	0.521	1.00
62_D	217_S	0.521	1.00
247_A	251_V	0.520	1.00
250_S	254_G	0.519	1.00
76_L	79_V	0.519	1.00
44_F	231_Y	0.518	1.00
35_I	38_I	0.517	1.00
46_G	170_L	0.514	1.00
71_F	97_M	0.511	1.00
137_E	141_I	0.511	1.00
138_S	142_N	0.509	1.00
266_L	269_L	0.509	1.00
46_G	50_V	0.508	1.00
197_T	201_L	0.508	1.00
45_L	49_A	0.507	1.00
152_L	156_I	0.505	1.00
139_I	143_H	0.505	1.00
65_V	217_S	0.503	1.00
35_I	39_L	0.502	1.00
87_P	91_F	0.501	1.00
75_F	98_G	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
2nq2A	2	0.8278	97.3	0.877	Contact Map
4g1uA	2	0.8006	96.9	0.884	Contact Map
2qi9A	2	0.855	96.7	0.886	Contact Map
2gfpA	2	0.5921	50.9	0.94	Contact Map
2cfqA	1	0.6224	29.2	0.948	Contact Map
1u7gA	3	0.5468	27.5	0.949	Contact Map
3wdoA	1	0.9184	26.3	0.949	Contact Map
4ikvA	1	0.9003	17.1	0.953	Contact Map
2kluA	1	0.1571	15.6	0.954	Contact Map
4j05A	3	0.8912	14.4	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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