YTFF - ECOLI - GREMLIN Contacts

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YTFF - Inner membrane protein YtfF

UniProt:	P39314	Sequences: MISGVLYALLAGLMWGLIFVGPLIVPEYPAMLQSMGRYLALGLIALPIAWLGRVRLRQLARRDWLTALMLTMMGNLIYYFCLASAIQRTGAPVSTMIIGTLPVVIPVFANLLYSQRDGKLAWGKLAPALICIGIGLACVNIAELNHGLPDFDWARYTSGIVLALVSVVCWAWYALRNARWLRENPDKHPMMWATAQALVTLPVSLIGYLVACYWLNTQTPDFSLPFGPRPLVFISLMVAIAVLCSWVGALCWNVASQLLPTVILGPLIVFETLAGLLYTFLLRQQMPPLMTLSGIALLVIGVVIAVRAKPEKPLTESVSES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12506
Length:	321 (275)
Sequences:	36389 (27149)
Seq/√Len:	1637.2

ECOLI - YTFF YICL YHBE YIJE RARD EAMA YDDG YEDA RHTA YIGM
BACSU - YETK YDFC YCXC YOAV YBFH YXXF YYAM YCBK YDED YVBV YRDR YWFM YDEK YOJE
HALSA - Q9HQ34 Q9HHP6 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
85_A	163_A	3.442	1.00
7_Y	254_V	3.015	1.00
93_V	160_I	2.823	1.00
254_V	258_L	2.813	1.00
279_T	285_Q	2.651	1.00
42_G	195_A	2.573	1.00
84_S	162_L	2.511	1.00
81_C	165_V	2.461	1.00
21_G	239_A	2.352	1.00
128_A	301_G	2.312	1.00
254_V	257_Q	2.281	1.00
16_G	274_A	2.266	1.00
60_A	63_D	2.254	1.00
206_I	209_L	2.247	1.00
95_T	275_G	2.158	1.00
231_L	235_S	2.155	1.00
104_V	167_V	2.092	1.00
35_M	205_L	2.085	1.00
108_F	175_L	2.057	1.00
40_A	241_A	2.049	1.00
81_C	162_L	2.039	1.00
23_L	285_Q	2.037	1.00
8_A	255_A	2.037	1.00
22_P	83_A	1.990	1.00
115_Q	178_A	1.869	1.00
77_I	169_C	1.853	1.00
63_D	183_E	1.841	1.00
16_G	278_Y	1.819	1.00
39_L	198_L	1.777	1.00
100_T	104_V	1.764	1.00
46_L	191_M	1.759	1.00
161_V	165_V	1.745	1.00
230_P	233_F	1.734	1.00
89_T	160_I	1.732	1.00
105_I	265_G	1.721	1.00
241_A	246_W	1.700	1.00
106_P	129_L	1.695	1.00
89_T	159_G	1.695	1.00
110_N	120_L	1.693	1.00
17_L	239_A	1.690	1.00
109_A	115_Q	1.688	1.00
88_R	158_S	1.680	1.00
81_C	169_C	1.660	1.00
13_L	274_A	1.654	1.00
42_G	198_L	1.653	1.00
185_P	188_H	1.597	1.00
122_W	125_L	1.593	1.00
260_P	263_I	1.578	1.00
303_V	307_R	1.564	1.00
104_V	171_A	1.550	1.00
28_Y	233_F	1.548	1.00
94_S	163_A	1.541	1.00
132_I	269_V	1.535	1.00
109_A	113_Y	1.523	1.00
47_P	50_W	1.519	1.00
288_P	291_T	1.514	1.00
116_R	120_L	1.486	1.00
199_V	206_I	1.483	1.00
14_M	243_L	1.477	1.00
128_A	305_A	1.464	1.00
11_A	255_A	1.463	1.00
84_S	88_R	1.459	1.00
35_M	198_L	1.433	1.00
7_Y	251_C	1.433	1.00
157_T	160_I	1.403	1.00
65_L	69_M	1.401	1.00
61_R	65_L	1.381	1.00
46_L	50_W	1.381	1.00
104_V	168_V	1.369	1.00
289_L	293_S	1.366	1.00
108_F	112_L	1.362	1.00
62_R	66_T	1.353	1.00
177_N	253_N	1.352	1.00
274_A	278_Y	1.343	1.00
231_L	234_I	1.340	1.00
89_T	93_V	1.339	1.00
278_Y	282_L	1.337	1.00
292_L	296_A	1.336	1.00
91_A	279_T	1.327	1.00
43_L	47_P	1.324	1.00
44_I	246_W	1.323	1.00
138_C	297_L	1.323	1.00
29_P	32_L	1.319	1.00
24_I	236_L	1.318	1.00
61_R	64_W	1.315	1.00
27_E	233_F	1.286	1.00
296_A	300_I	1.277	1.00
128_A	304_I	1.274	1.00
41_L	194_T	1.265	1.00
232_V	235_S	1.262	1.00
62_R	65_L	1.259	1.00
33_Q	240_I	1.255	1.00
135_G	294_G	1.251	1.00
126_A	130_I	1.245	1.00
179_R	182_R	1.238	1.00
20_V	278_Y	1.231	1.00
130_I	134_I	1.230	1.00
123_G	127_P	1.223	1.00
270_F	274_A	1.223	1.00
96_M	295_I	1.222	1.00
235_S	239_A	1.220	1.00
138_C	290_M	1.219	1.00
84_S	87_Q	1.212	1.00
69_M	176_R	1.211	1.00
171_A	175_L	1.208	1.00
124_K	304_I	1.207	1.00
76_L	200_T	1.205	1.00
68_L	196_Q	1.203	1.00
209_L	212_C	1.196	1.00
66_T	176_R	1.192	1.00
232_V	236_L	1.188	1.00
92_P	276_L	1.188	1.00
207_G	210_V	1.184	1.00
113_Y	175_L	1.179	1.00
287_P	292_L	1.172	1.00
132_I	301_G	1.171	1.00
157_T	161_V	1.163	1.00
42_G	191_M	1.161	1.00
6_L	10_L	1.142	1.00
90_G	93_V	1.137	1.00
207_G	211_A	1.136	1.00
108_F	172_W	1.136	1.00
179_R	183_E	1.131	1.00
97_I	167_V	1.127	1.00
48_I	52_G	1.127	1.00
21_G	236_L	1.121	1.00
35_M	39_L	1.121	1.00
72_M	200_T	1.121	1.00
37_R	245_S	1.120	1.00
17_L	278_Y	1.119	1.00
88_R	162_L	1.117	1.00
15_W	248_G	1.116	1.00
178_A	260_P	1.115	1.00
139_V	294_G	1.107	1.00
11_A	251_C	1.102	1.00
124_K	307_R	1.098	1.00
88_R	156_Y	1.084	1.00
11_A	15_W	1.079	1.00
123_G	126_A	1.072	1.00
27_E	230_P	1.070	1.00
206_I	210_V	1.065	1.00
105_I	261_T	1.049	1.00
108_F	171_A	1.047	1.00
76_L	201_L	1.046	1.00
82_L	86_I	1.043	1.00
91_A	283_R	1.042	1.00
111_L	114_S	1.037	1.00
158_S	162_L	1.036	1.00
86_I	94_S	1.023	1.00
15_W	252_W	1.020	1.00
22_P	86_I	1.017	1.00
34_S	83_A	1.016	1.00
256_S	264_L	1.011	1.00
89_T	163_A	1.008	1.00
108_F	168_V	1.002	1.00
88_R	159_G	0.994	1.00
44_I	242_V	0.992	1.00
66_T	180_W	0.992	1.00
115_Q	125_L	0.991	1.00
10_L	251_C	0.990	1.00
65_L	68_L	0.990	1.00
97_I	163_A	0.989	1.00
5_V	267_L	0.985	1.00
120_L	126_A	0.983	1.00
108_F	111_L	0.979	1.00
238_V	241_A	0.978	1.00
234_I	238_V	0.976	1.00
105_I	174_A	0.970	1.00
158_S	161_V	0.956	1.00
63_D	184_N	0.953	1.00
178_A	261_T	0.953	1.00
73_M	172_W	0.951	1.00
260_P	264_L	0.948	1.00
235_S	238_V	0.946	1.00
20_V	282_L	0.945	1.00
273_L	295_I	0.945	1.00
256_S	260_P	0.944	1.00
105_I	171_A	0.940	1.00
31_M	80_F	0.940	1.00
91_A	285_Q	0.935	1.00
135_G	298_L	0.933	1.00
14_M	251_C	0.928	1.00
30_A	34_S	0.926	1.00
141_I	288_P	0.920	1.00
124_K	308_A	0.912	1.00
23_L	26_P	0.912	1.00
97_I	160_I	0.911	1.00
71_T	196_Q	0.910	1.00
167_V	171_A	0.910	1.00
259_L	264_L	0.909	1.00
96_M	137_A	0.905	1.00
243_L	247_V	0.904	1.00
63_D	66_T	0.902	1.00
239_A	243_L	0.898	1.00
100_T	136_L	0.895	1.00
289_L	292_L	0.887	1.00
200_T	206_I	0.887	1.00
229_R	234_I	0.887	1.00
131_C	301_G	0.878	1.00
159_G	163_A	0.877	1.00
66_T	70_L	0.876	1.00
9_L	274_A	0.876	1.00
35_M	208_Y	0.875	1.00
137_A	141_I	0.866	1.00
38_Y	197_A	0.856	1.00
31_M	207_G	0.855	1.00
45_A	246_W	0.854	1.00
259_L	263_I	0.851	1.00
238_V	242_V	0.851	1.00
12_G	16_G	0.851	1.00
12_G	274_A	0.841	1.00
36_G	40_A	0.841	1.00
230_P	234_I	0.839	1.00
107_V	111_L	0.837	1.00
178_A	182_R	0.832	1.00
110_N	114_S	0.830	1.00
34_S	201_L	0.824	1.00
47_P	51_L	0.824	1.00
67_A	184_N	0.824	1.00
276_L	287_P	0.822	1.00
64_W	196_Q	0.822	1.00
76_L	80_F	0.821	1.00
154_A	157_T	0.818	1.00
60_A	64_W	0.811	1.00
205_L	208_Y	0.809	1.00
20_V	279_T	0.808	1.00
280_F	287_P	0.807	1.00
12_G	270_F	0.804	1.00
75_N	173_Y	0.797	1.00
105_I	175_L	0.795	1.00
19_F	82_L	0.793	1.00
237_M	241_A	0.793	1.00
134_I	138_C	0.789	1.00
247_V	251_C	0.784	1.00
73_M	169_C	0.783	1.00
196_Q	199_V	0.782	1.00
293_S	297_L	0.776	1.00
66_T	179_R	0.774	1.00
49_A	191_M	0.768	1.00
134_I	297_L	0.767	1.00
138_C	293_S	0.766	1.00
80_F	84_S	0.765	1.00
103_V	132_I	0.765	1.00
110_N	116_R	0.763	1.00
64_W	67_A	0.763	1.00
290_M	293_S	0.762	1.00
156_Y	160_I	0.761	1.00
208_Y	211_A	0.755	1.00
255_A	264_L	0.754	1.00
228_P	231_L	0.750	1.00
276_L	295_I	0.749	1.00
20_V	91_A	0.749	1.00
32_L	208_Y	0.746	1.00
136_L	140_N	0.746	1.00
46_L	195_A	0.746	1.00
127_P	131_C	0.743	1.00
280_F	286_M	0.740	1.00
78_Y	169_C	0.740	1.00
77_I	81_C	0.739	1.00
191_M	195_A	0.736	1.00
44_I	241_A	0.735	1.00
106_P	120_L	0.733	1.00
236_L	239_A	0.733	1.00
197_A	201_L	0.731	1.00
195_A	199_V	0.728	1.00
184_N	189_P	0.726	1.00
206_I	212_C	0.723	1.00
44_I	47_P	0.721	1.00
163_A	167_V	0.720	1.00
141_I	144_L	0.719	1.00
122_W	126_A	0.716	1.00
196_Q	200_T	0.707	1.00
192_W	196_Q	0.706	1.00
102_P	269_V	0.702	1.00
113_Y	178_A	0.702	1.00
42_G	46_L	0.701	1.00
170_W	174_A	0.699	1.00
64_W	68_L	0.697	1.00
55_R	185_P	0.690	1.00
104_V	164_L	0.686	1.00
106_P	125_L	0.686	1.00
66_T	69_M	0.685	1.00
32_L	36_G	0.684	1.00
28_Y	33_Q	0.682	1.00
295_I	299_V	0.682	1.00
229_R	233_F	0.680	1.00
8_A	267_L	0.678	1.00
50_W	53_R	0.675	1.00
39_L	205_L	0.672	1.00
116_R	124_K	0.671	1.00
172_W	176_R	0.669	1.00
85_A	159_G	0.668	1.00
300_I	304_I	0.668	1.00
100_T	103_V	0.668	1.00
18_I	244_C	0.668	1.00
279_T	283_R	0.667	1.00
190_M	253_N	0.667	1.00
208_Y	212_C	0.666	1.00
28_Y	32_L	0.665	1.00
73_M	176_R	0.665	1.00
107_V	129_L	0.662	1.00
89_T	94_S	0.662	1.00
192_W	195_A	0.661	1.00
270_F	273_L	0.658	1.00
69_M	72_M	0.653	1.00
8_A	259_L	0.652	1.00
287_P	291_T	0.651	1.00
67_A	71_T	0.650	1.00
85_A	94_S	0.650	1.00
266_P	305_A	0.650	1.00
97_I	164_L	0.648	1.00
50_W	54_V	0.645	1.00
71_T	76_L	0.645	1.00
60_A	65_L	0.641	1.00
230_P	235_S	0.639	1.00
170_W	252_W	0.639	1.00
68_L	71_T	0.637	1.00
96_M	140_N	0.636	1.00
19_F	95_T	0.633	1.00
233_F	236_L	0.628	1.00
50_W	55_R	0.626	1.00
190_M	193_A	0.624	1.00
24_I	283_R	0.623	1.00
288_P	292_L	0.622	1.00
135_G	301_G	0.621	1.00
75_N	249_A	0.619	1.00
78_Y	173_Y	0.617	1.00
39_L	43_L	0.615	1.00
188_H	192_W	0.615	1.00
106_P	110_N	0.613	1.00
40_A	44_I	0.612	1.00
5_V	263_I	0.605	1.00
14_M	244_C	0.604	1.00
301_G	305_A	0.600	1.00
173_Y	253_N	0.595	1.00
48_I	187_K	0.590	1.00
68_L	72_M	0.590	1.00
277_L	280_F	0.589	1.00
174_A	252_W	0.589	1.00
131_C	304_I	0.589	1.00
162_L	165_V	0.586	1.00
58_Q	61_R	0.585	1.00
250_L	254_V	0.585	1.00
14_M	248_G	0.582	1.00
36_G	237_M	0.580	1.00
40_A	237_M	0.579	1.00
51_L	54_V	0.578	1.00
41_L	241_A	0.577	1.00
52_G	55_R	0.576	1.00
205_L	209_L	0.575	1.00
82_L	94_S	0.573	1.00
116_R	123_G	0.570	1.00
184_N	188_H	0.570	1.00
99_G	136_L	0.570	1.00
125_L	260_P	0.566	1.00
99_G	102_P	0.566	1.00
75_N	193_A	0.564	1.00
54_V	57_R	0.560	1.00
133_G	269_V	0.559	1.00
277_L	281_L	0.556	1.00
99_G	167_V	0.554	1.00
168_V	172_W	0.553	1.00
10_L	14_M	0.550	1.00
291_T	295_I	0.547	1.00
112_L	172_W	0.544	1.00
190_M	194_T	0.539	1.00
9_L	12_G	0.539	1.00
286_M	290_M	0.538	1.00
18_I	240_I	0.538	1.00
16_G	271_E	0.537	1.00
29_P	211_A	0.537	1.00
81_C	166_S	0.536	1.00
140_N	160_I	0.535	1.00
255_A	259_L	0.535	1.00
239_A	242_V	0.534	1.00
100_T	167_V	0.534	1.00
195_A	198_L	0.534	1.00
68_L	200_T	0.532	1.00
276_L	280_F	0.531	1.00
302_V	305_A	0.531	1.00
56_L	59_L	0.530	1.00
82_L	166_S	0.528	1.00
8_A	252_W	0.527	1.00
198_L	205_L	0.525	1.00
17_L	20_V	0.525	1.00
64_W	192_W	0.523	1.00
174_A	265_G	0.523	1.00
189_P	192_W	0.521	1.00
29_P	212_C	0.520	1.00
25_V	86_I	0.520	1.00
34_S	80_F	0.519	1.00
278_Y	281_L	0.517	1.00
31_M	201_L	0.516	1.00
201_L	206_I	0.516	1.00
20_V	275_G	0.515	1.00
95_T	99_G	0.513	1.00
133_G	137_A	0.512	1.00
173_Y	177_N	0.510	1.00
85_A	89_T	0.509	1.00
292_L	295_I	0.509	1.00
43_L	46_L	0.509	1.00
286_M	291_T	0.508	1.00
41_L	246_W	0.506	1.00
78_Y	82_L	0.506	1.00
19_F	23_L	0.505	1.00
154_A	158_S	0.505	1.00
280_F	292_L	0.505	1.00
173_Y	193_A	0.504	1.00
134_I	137_A	0.503	1.00
16_G	275_G	0.503	1.00
268_I	271_E	0.502	1.00
67_A	189_P	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	0.2399	98.9	0.771	Contact Map
3b5dA	2	0.3146	98.5	0.802	Contact Map
1pw4A	1	0.9128	76	0.914	Contact Map
2cfqA	1	0.5763	58.7	0.924	Contact Map
3wdoA	1	0.8941	53.2	0.926	Contact Map
4j05A	3	0.9065	45.9	0.929	Contact Map
4he8J	1	0.4891	22.1	0.94	Contact Map
4pypA	1	0.567	18.3	0.942	Contact Map
4tphA	2	0.8474	17	0.943	Contact Map
4xnjA	1	0.8847	16	0.944	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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