YESP - BACSU - GREMLIN Contacts

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YESP - Probable ABC transporter permease protein YesP

UniProt:	O31519	Sequences: MTGNGADAMKKSRSIRKDNLAGYAFISPFIIGFLCFTVIPMGASLFLSFTSYDLFTAPKWIGLDNFKEMFTGDEKYWQSLKVTFTYVLAGVPLRLGFALFIAVILNNAAKGTAIYRTLFYLPSIIGGSVAVAIMWRNIFGNDGVINALLFFVGIDQKILWYQNPTSALWTLILLSVWQFGSSMLIFLAGLKNIPSSYLEAASVDGANRVQRFFKITLPILTPIIFFNLVMQTISAFMTFTPAYIISKGEGGPLDGTLLYSLYLFQRAFNYFQMGYASAMAWVMLVIVGLITLILFKTSSYWVHYESKEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	309 (254)
Sequences:	69912 (45878)
Seq/√Len:	2878.7

ECOLI - POTH YCJO UGPA YDCU POTB PSTC MALG MALF CYSW PSTA POTI YCJP UGPE CYST YNJC THIP POTC YDCV MODB TAUC YEHY SSUC PHNE PROW YEHW METI
BACSU - YESP AMYD GANP ARAP YTEP LPLB MDXF YURN YESQ YURM LPLC MDXG GANQ ARAQ YQGH YTCP YQGI AMYC SSUC YVGM YTLD OPUAB OPUCB OPUBB TCYB METP TCYL OPUBD YXEN OPUCD
HALSA - Q9HP01 Q9HHQ7 Q9HMT4 Q9HML6 Q9HP02 Q9HR05 Q9HHQ6 Q9HPK3 Q9HS11 Q9HNI9 Q9HS12
SULSO - Q97YY2 Q97UZ0 Q97UF3 Q97UF4 Q97YY3 Q97ZC2 Q97UY9 Q97VC0 Q97ZC1 Q97ZT7 Q97ZT6 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
210_Q	214_K	3.896	1.00
81_K	85_T	3.242	1.00
202_S	211_R	3.133	1.00
187_L	191_K	2.980	1.00
78_Q	81_K	2.650	1.00
79_S	262_Y	2.553	1.00
257_L	265_Q	2.535	1.00
189_G	223_I	2.508	1.00
207_N	210_Q	2.493	1.00
93_L	176_V	2.467	1.00
48_S	66_F	2.440	1.00
67_K	71_T	2.435	1.00
107_N	198_L	2.429	1.00
201_A	211_R	2.408	1.00
77_W	81_K	2.380	1.00
198_L	216_T	2.375	1.00
89_A	172_I	2.363	1.00
208_R	211_R	2.309	1.00
64_D	67_K	2.306	1.00
91_V	228_L	2.279	1.00
209_V	213_F	2.164	1.00
64_D	68_E	2.155	1.00
186_F	224_I	2.143	1.00
272_Q	275_Y	2.138	1.00
109_A	112_T	2.128	1.00
206_A	210_Q	2.075	1.00
210_Q	213_F	2.009	1.00
85_T	168_L	1.961	1.00
46_F	50_T	1.948	1.00
182_S	227_N	1.939	1.00
99_L	212_F	1.925	1.00
197_Y	219_I	1.925	1.00
151_F	155_D	1.903	1.00
201_A	206_A	1.893	1.00
106_N	191_K	1.880	1.00
190_L	220_L	1.866	1.00
116_R	187_L	1.848	1.00
99_L	220_L	1.830	1.00
42_G	46_F	1.808	1.00
292_L	296_K	1.752	1.00
254_D	257_L	1.747	1.00
78_Q	82_V	1.732	1.00
90_G	235_A	1.708	1.00
95_L	228_L	1.702	1.00
85_T	89_A	1.676	1.00
202_S	208_R	1.668	1.00
198_L	211_R	1.666	1.00
68_E	275_Y	1.638	1.00
99_L	186_F	1.625	1.00
98_A	182_S	1.606	1.00
87_V	232_T	1.599	1.00
262_Y	266_R	1.585	1.00
198_L	202_S	1.578	1.00
101_I	183_M	1.574	1.00
195_S	198_L	1.528	1.00
27_S	31_I	1.512	1.00
168_L	256_T	1.508	1.00
68_E	71_T	1.507	1.00
105_L	183_M	1.497	1.00
111_G	114_I	1.439	1.00
75_K	78_Q	1.431	1.00
45_L	281_W	1.426	1.00
43_A	47_L	1.419	1.00
182_S	231_Q	1.390	1.00
63_L	67_K	1.389	1.00
39_I	43_A	1.375	1.00
266_R	270_Y	1.356	1.00
106_N	187_L	1.354	1.00
94_R	231_Q	1.346	1.00
246_S	256_T	1.340	1.00
226_F	230_M	1.317	1.00
217_L	224_I	1.307	1.00
190_L	216_T	1.307	1.00
257_L	262_Y	1.302	1.00
239_F	243_Y	1.293	1.00
102_A	186_F	1.292	1.00
86_Y	258_L	1.282	1.00
96_G	100_F	1.280	1.00
195_S	199_E	1.275	1.00
186_F	227_N	1.271	1.00
241_P	245_I	1.240	1.00
196_S	199_E	1.236	1.00
139_F	170_T	1.230	1.00
20_L	24_A	1.229	1.00
103_V	190_L	1.222	1.00
265_Q	269_N	1.221	1.00
172_I	176_V	1.220	1.00
99_L	224_I	1.217	1.00
114_I	117_T	1.217	1.00
62_G	65_N	1.214	1.00
239_F	264_F	1.201	1.00
201_A	215_I	1.200	1.00
107_N	195_S	1.199	1.00
83_T	259_Y	1.194	1.00
31_I	35_C	1.192	1.00
174_L	245_I	1.181	1.00
92_P	96_G	1.178	1.00
95_L	224_I	1.176	1.00
266_R	272_Q	1.168	1.00
193_I	219_I	1.154	1.00
82_V	85_T	1.144	1.00
89_A	92_P	1.142	1.00
221_T	225_F	1.140	1.00
21_A	25_F	1.135	1.00
54_L	60_W	1.130	1.00
22_G	26_I	1.113	1.00
43_A	46_F	1.112	1.00
167_A	256_T	1.111	1.00
24_A	28_P	1.110	1.00
207_N	211_R	1.110	1.00
296_K	299_S	1.089	1.00
114_I	118_L	1.079	1.00
51_S	54_L	1.077	1.00
258_L	261_L	1.073	1.00
24_A	27_S	1.069	1.00
186_F	223_I	1.057	1.00
168_L	172_I	1.056	1.00
44_S	281_W	1.054	1.00
171_L	242_A	1.043	1.00
242_A	258_L	1.041	1.00
179_F	183_M	1.041	1.00
140_G	151_F	1.040	1.00
21_A	24_A	1.031	1.00
89_A	93_L	1.029	1.00
90_G	94_R	1.024	1.00
106_N	190_L	1.019	1.00
198_L	208_R	1.018	1.00
19_N	22_G	1.016	1.00
253_L	256_T	0.995	1.00
219_I	222_P	0.993	1.00
103_V	208_R	0.992	1.00
185_I	227_N	0.991	1.00
100_F	104_I	0.989	1.00
93_L	172_I	0.984	1.00
84_F	88_L	0.974	1.00
103_V	212_F	0.972	1.00
238_T	241_P	0.968	1.00
262_Y	265_Q	0.968	1.00
296_K	300_Y	0.965	1.00
57_A	60_W	0.965	1.00
68_E	73_D	0.963	1.00
206_A	211_R	0.963	1.00
293_I	297_T	0.961	1.00
70_F	77_W	0.961	1.00
92_P	228_L	0.954	1.00
169_W	172_I	0.951	1.00
85_T	169_W	0.951	1.00
267_A	276_A	0.943	1.00
257_L	261_L	0.938	1.00
66_F	281_W	0.937	1.00
211_R	214_K	0.935	1.00
85_T	88_L	0.925	1.00
243_Y	261_L	0.923	1.00
169_W	173_L	0.921	1.00
90_G	175_S	0.915	1.00
90_G	172_I	0.914	1.00
53_D	56_T	0.906	1.00
23_Y	27_S	0.906	1.00
80_L	259_Y	0.894	1.00
174_L	241_P	0.892	1.00
262_Y	279_M	0.888	1.00
75_K	254_D	0.886	1.00
238_T	242_A	0.880	1.00
82_V	168_L	0.876	1.00
88_L	92_P	0.876	1.00
50_T	54_L	0.870	1.00
19_N	23_Y	0.870	1.00
34_L	38_V	0.869	1.00
102_A	106_N	0.867	1.00
47_L	277_S	0.865	1.00
266_R	275_Y	0.858	1.00
69_M	282_V	0.856	1.00
94_R	98_A	0.853	1.00
221_T	224_I	0.844	1.00
93_L	96_G	0.836	1.00
26_I	30_I	0.836	1.00
120_Y	184_L	0.836	1.00
132_A	136_R	0.835	1.00
189_G	220_L	0.834	1.00
86_Y	168_L	0.833	1.00
287_V	291_T	0.830	1.00
65_N	274_G	0.830	1.00
104_I	109_A	0.829	1.00
86_Y	175_S	0.828	1.00
220_L	223_I	0.828	1.00
76_Y	279_M	0.827	1.00
113_A	116_R	0.826	1.00
98_A	183_M	0.825	1.00
206_A	214_K	0.822	1.00
112_T	191_K	0.821	1.00
47_L	50_T	0.821	1.00
110_K	113_A	0.819	1.00
175_S	235_A	0.817	1.00
231_Q	235_A	0.817	1.00
80_L	84_F	0.815	1.00
186_F	220_L	0.814	1.00
105_L	116_R	0.813	1.00
154_I	169_W	0.812	1.00
74_E	78_Q	0.810	1.00
293_I	296_K	0.810	1.00
211_R	216_T	0.807	1.00
289_L	293_I	0.799	1.00
266_R	279_M	0.798	1.00
182_S	186_F	0.796	1.00
213_F	217_L	0.791	1.00
294_L	297_T	0.789	1.00
81_K	84_F	0.787	1.00
52_Y	56_T	0.786	1.00
212_F	217_L	0.785	1.00
136_R	140_G	0.785	1.00
208_R	212_F	0.781	1.00
135_W	174_L	0.771	1.00
73_D	77_W	0.761	1.00
102_A	183_M	0.758	1.00
65_N	68_E	0.757	1.00
25_F	28_P	0.744	1.00
94_R	182_S	0.743	1.00
89_A	176_V	0.738	1.00
132_A	240_T	0.735	1.00
197_Y	215_I	0.735	1.00
221_T	297_T	0.728	1.00
120_Y	123_S	0.726	1.00
200_A	204_D	0.724	1.00
135_W	245_I	0.724	1.00
94_R	235_A	0.721	1.00
275_Y	279_M	0.719	1.00
238_T	258_L	0.718	1.00
102_A	190_L	0.716	1.00
49_F	61_I	0.710	1.00
259_Y	283_M	0.706	1.00
137_N	140_G	0.705	1.00
98_A	186_F	0.705	1.00
28_P	31_I	0.703	1.00
44_S	280_A	0.703	1.00
79_S	82_V	0.700	1.00
39_I	42_G	0.698	1.00
95_L	186_F	0.695	1.00
91_V	232_T	0.695	1.00
51_S	60_W	0.694	1.00
224_I	227_N	0.693	1.00
50_T	58_P	0.691	1.00
105_L	115_Y	0.689	1.00
68_E	272_Q	0.689	1.00
108_A	112_T	0.687	1.00
283_M	287_V	0.685	1.00
277_S	281_W	0.679	1.00
44_S	277_S	0.675	1.00
200_A	203_V	0.675	1.00
264_F	268_F	0.674	1.00
212_F	216_T	0.674	1.00
261_L	265_Q	0.673	1.00
67_K	70_F	0.672	1.00
195_S	202_S	0.672	1.00
105_L	187_L	0.671	1.00
263_L	279_M	0.671	1.00
193_I	220_L	0.670	1.00
25_F	29_F	0.666	1.00
288_G	292_L	0.664	1.00
54_L	59_K	0.663	1.00
91_V	95_L	0.662	1.00
132_A	244_I	0.662	1.00
77_W	80_L	0.661	1.00
87_V	91_V	0.661	1.00
170_T	174_L	0.661	1.00
131_V	177_W	0.657	1.00
33_F	37_T	0.656	1.00
30_I	34_L	0.653	1.00
223_I	227_N	0.652	1.00
79_S	259_Y	0.652	1.00
246_S	257_L	0.651	1.00
242_A	261_L	0.650	1.00
34_L	37_T	0.650	1.00
186_F	190_L	0.649	1.00
74_E	77_W	0.646	1.00
86_Y	171_L	0.641	1.00
109_A	115_Y	0.640	1.00
101_I	179_F	0.636	1.00
129_V	244_I	0.635	1.00
75_K	262_Y	0.635	1.00
51_S	59_K	0.635	1.00
101_I	119_F	0.634	1.00
135_W	139_F	0.631	1.00
297_T	300_Y	0.631	1.00
135_W	138_I	0.629	1.00
260_S	283_M	0.625	1.00
224_I	228_L	0.622	1.00
61_I	64_D	0.622	1.00
47_L	51_S	0.622	1.00
216_T	219_I	0.621	1.00
277_S	280_A	0.617	1.00
23_Y	26_I	0.616	1.00
119_F	180_G	0.614	1.00
104_I	108_A	0.613	1.00
167_A	170_T	0.613	1.00
291_T	295_F	0.612	1.00
20_L	23_Y	0.611	1.00
110_K	114_I	0.609	1.00
111_G	115_Y	0.600	1.00
86_Y	172_I	0.594	1.00
171_L	175_S	0.593	1.00
240_T	244_I	0.593	1.00
60_W	63_L	0.590	1.00
48_S	278_A	0.585	1.00
83_T	260_S	0.583	1.00
97_F	176_V	0.583	1.00
82_V	256_T	0.583	1.00
228_L	231_Q	0.582	1.00
171_L	246_S	0.581	1.00
225_F	228_L	0.580	1.00
273_M	277_S	0.577	1.00
48_S	52_Y	0.576	1.00
175_S	238_T	0.575	1.00
211_R	215_I	0.574	1.00
185_I	223_I	0.573	1.00
50_T	60_W	0.573	1.00
113_A	117_T	0.572	1.00
94_R	176_V	0.572	1.00
213_F	216_T	0.571	1.00
172_I	175_S	0.569	1.00
116_R	184_L	0.568	1.00
97_F	179_F	0.566	1.00
286_I	289_L	0.564	1.00
151_F	154_I	0.564	1.00
52_Y	58_P	0.564	1.00
153_G	156_Q	0.563	1.00
103_V	216_T	0.561	1.00
87_V	235_A	0.560	1.00
240_T	243_Y	0.559	1.00
63_L	66_F	0.559	1.00
117_T	121_L	0.558	1.00
86_Y	90_G	0.557	1.00
234_S	237_M	0.555	1.00
83_T	236_F	0.554	1.00
292_L	295_F	0.553	1.00
233_I	237_M	0.552	1.00
75_K	257_L	0.552	1.00
29_F	33_F	0.551	1.00
132_A	135_W	0.550	1.00
69_M	279_M	0.550	1.00
60_W	64_D	0.547	1.00
174_L	178_Q	0.546	1.00
32_G	36_F	0.542	1.00
38_V	42_G	0.540	1.00
102_A	187_L	0.540	1.00
49_F	62_G	0.538	1.00
274_G	277_S	0.538	1.00
95_L	99_L	0.537	1.00
123_S	181_S	0.536	1.00
90_G	176_V	0.535	1.00
98_A	179_F	0.533	1.00
235_A	238_T	0.532	1.00
122_P	180_G	0.530	1.00
294_L	298_S	0.529	1.00
87_V	236_F	0.529	1.00
118_L	122_P	0.528	1.00
82_V	258_L	0.528	1.00
123_S	180_G	0.528	1.00
109_A	113_A	0.525	1.00
116_R	191_K	0.523	1.00
273_M	276_A	0.522	1.00
193_I	198_L	0.522	1.00
66_F	278_A	0.521	1.00
59_K	62_G	0.521	1.00
101_I	104_I	0.521	1.00
254_D	265_Q	0.516	1.00
69_M	275_Y	0.514	1.00
134_M	137_N	0.512	1.00
261_L	264_F	0.512	1.00
35_C	39_I	0.511	1.00
36_F	40_P	0.511	1.00
45_L	49_F	0.510	1.00
246_S	253_L	0.509	1.00
265_Q	270_Y	0.508	1.00
140_G	155_D	0.506	1.00
156_Q	253_L	0.504	1.00
50_T	59_K	0.503	1.00
58_P	61_I	0.503	1.00
285_V	289_L	0.501	1.00
81_K	168_L	0.501	1.00
231_Q	234_S	0.500	1.00
137_N	151_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
2onkC	2	0.8058	100	0.331	Contact Map
4tquM	1	0.8997	100	0.348	Contact Map
3d31C	2	0.7961	100	0.362	Contact Map
4tquN	1	0.8447	100	0.398	Contact Map
3rlfG	1	0.8706	100	0.4	Contact Map
3rlfF	1	0.9159	100	0.408	Contact Map
4ymuD	2	0.6893	99.9	0.546	Contact Map
3tuiA	2	0.6699	99.9	0.569	Contact Map
2kogA	1	0.1521	19.7	0.946	Contact Map
2m20A	2	0.1133	17.2	0.947	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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