Q97VK6 - SULSO - GREMLIN Contacts

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Q97VK6 - Dipeptide ABC transporter permease protein (DppB-3)

UniProt:	Q97VK6	Sequences: MSINIVFFIIRRIINAFITLILLIILVFIMIHIIAPNPLALARLYTGPHATYTELEQVAKQYGLDQPLYIQIINYIINVLHGNFGIDPTYKVPVITLIGKYLPRTLELVIPATILSVVIGLFTGAIAASNRNKPLDYLVRGVYLVTWASPPFLIAVILQLVIAYYLRLLPPTGTVNPVLTPPKSITPFPLLNAMLAGDWPYFSSLVHHMVLPVIAIALVSFGIVTRIARASMLDYMESDFAKLSLMKGLSRRRVVYGVVLRNASIPLVTLIALLFGYSVAGAVVIEDIFQYHGMGYFITQAIESLDYTSILGTTIIVGIAIIIANLIADILYGVLDPRVRIVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	343 (287)
Sequences:	23469 (14807)
Seq/√Len:	874.0

ECOLI - DDPB DPPB YEJB NIKB GSIC OPPB SAPB YEJE DPPC SAPC GSID DDPC NIKC OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMI2 Q9HMX0 Q9HMW3 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97VK6 Q97VF8 Q97YQ0 Q97UH1 Q97UG4 Q97YP1 Q97VK7 Q97UG3 Q97UH2 Q97YP9 Q97YP2 Q97VF6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_Q	70_I	3.204	1.00
66_Q	74_N	3.130	1.00
32_H	71_Q	2.962	1.00
232_M	259_V	2.780	1.00
77_I	81_H	2.742	1.00
73_I	77_I	2.695	1.00
52_Y	56_E	2.629	1.00
60_K	65_D	2.549	1.00
24_I	72_I	2.509	1.00
123_T	139_V	2.457	1.00
104_R	291_Y	2.435	1.00
245_L	251_R	2.388	1.00
111_P	213_V	2.371	1.00
253_R	257_G	2.360	1.00
296_Y	300_Q	2.308	1.00
235_Y	240_F	2.273	1.00
241_A	259_V	2.215	1.00
37_N	59_A	2.174	1.00
235_Y	238_S	2.158	1.00
136_D	229_R	2.146	1.00
25_I	72_I	2.111	1.00
252_R	256_Y	2.084	1.00
250_S	253_R	2.076	1.00
249_L	253_R	2.033	1.00
97_L	297_F	2.012	1.00
272_A	328_A	2.006	1.00
93_P	96_T	1.963	1.00
69_Y	73_I	1.963	1.00
5_I	9_I	1.941	1.00
115_L	217_A	1.937	1.00
55_L	59_A	1.896	1.00
118_V	122_F	1.884	1.00
54_E	57_Q	1.874	1.00
236_M	259_V	1.844	1.00
51_T	54_E	1.832	1.00
130_N	133_K	1.812	1.00
90_Y	97_L	1.776	1.00
241_A	254_V	1.772	1.00
126_I	130_N	1.770	1.00
57_Q	61_Q	1.763	1.00
7_F	11_R	1.762	1.00
134_P	138_L	1.755	1.00
56_E	59_A	1.753	1.00
20_L	319_I	1.738	1.00
130_N	135_L	1.731	1.00
239_D	242_K	1.727	1.00
128_A	232_M	1.627	1.00
95_I	99_G	1.622	1.00
125_A	232_M	1.619	1.00
70_I	74_N	1.617	1.00
23_L	318_G	1.615	1.00
78_N	83_N	1.601	1.00
56_E	60_K	1.591	1.00
94_V	312_G	1.588	1.00
92_V	96_T	1.588	1.00
130_N	251_R	1.585	1.00
235_Y	263_A	1.580	1.00
126_I	135_L	1.579	1.00
119_I	122_F	1.548	1.00
135_L	139_V	1.540	1.00
74_N	77_I	1.531	1.00
213_V	217_A	1.528	1.00
129_S	251_R	1.511	1.00
107_E	111_P	1.510	1.00
268_V	335_L	1.508	1.00
243_L	247_K	1.503	1.00
119_I	221_F	1.499	1.00
80_L	83_N	1.496	1.00
129_S	255_V	1.487	1.00
224_V	274_L	1.465	1.00
84_F	312_G	1.465	1.00
240_F	262_N	1.440	1.00
21_I	72_I	1.436	1.00
116_S	220_S	1.426	1.00
269_T	332_Y	1.416	1.00
117_V	271_I	1.410	1.00
331_L	334_V	1.409	1.00
298_I	313_T	1.403	1.00
301_A	309_S	1.400	1.00
14_I	18_I	1.381	1.00
235_Y	241_A	1.374	1.00
28_F	32_H	1.369	1.00
37_N	40_A	1.358	1.00
153_L	157_I	1.337	1.00
87_D	92_V	1.331	1.00
58_V	62_Y	1.328	1.00
120_G	228_A	1.321	1.00
66_Q	69_Y	1.316	1.00
104_R	107_E	1.316	1.00
235_Y	259_V	1.313	1.00
92_V	100_K	1.310	1.00
67_P	70_I	1.299	1.00
84_F	95_I	1.298	1.00
74_N	78_N	1.294	1.00
100_K	103_P	1.290	1.00
58_V	61_Q	1.289	1.00
28_F	31_I	1.279	1.00
120_G	224_V	1.275	1.00
229_R	233_L	1.272	1.00
158_L	215_A	1.266	1.00
79_V	84_F	1.259	1.00
92_V	97_L	1.244	1.00
132_N	136_D	1.243	1.00
139_V	225_T	1.241	1.00
124_G	128_A	1.232	1.00
247_K	258_V	1.224	1.00
113_T	271_I	1.220	1.00
6_V	9_I	1.220	1.00
24_I	75_Y	1.220	1.00
63_G	66_Q	1.214	1.00
217_A	221_F	1.209	1.00
70_I	73_I	1.194	1.00
332_Y	336_D	1.185	1.00
128_A	236_M	1.181	1.00
146_T	222_G	1.176	1.00
227_I	270_L	1.172	1.00
21_I	25_I	1.169	1.00
134_P	137_Y	1.161	1.00
127_A	139_V	1.158	1.00
232_M	263_A	1.151	1.00
297_F	309_S	1.148	1.00
210_V	214_I	1.145	1.00
16_A	322_I	1.145	1.00
123_T	225_T	1.143	1.00
124_G	228_A	1.138	1.00
143_Y	225_T	1.136	1.00
276_G	321_I	1.132	1.00
86_I	93_P	1.121	1.00
149_S	154_I	1.114	1.00
25_I	29_I	1.109	1.00
14_I	330_I	1.108	1.00
125_A	255_V	1.105	1.00
89_T	304_S	1.102	1.00
10_I	14_I	1.095	1.00
39_L	55_L	1.095	1.00
265_I	332_Y	1.093	1.00
97_L	309_S	1.093	1.00
215_A	219_V	1.087	1.00
228_A	267_L	1.064	1.00
313_T	317_V	1.055	1.00
29_I	32_H	1.055	1.00
228_A	232_M	1.049	1.00
78_N	81_H	1.047	1.00
13_I	17_F	1.041	1.00
40_A	55_L	1.037	1.00
107_E	209_M	1.035	1.00
299_T	303_E	1.033	1.00
330_I	334_V	1.032	1.00
142_V	146_T	1.024	1.00
96_T	100_K	1.016	1.00
324_A	328_A	1.012	1.00
63_G	74_N	1.006	1.00
57_Q	60_K	0.999	1.00
234_D	238_S	0.999	1.00
231_S	234_D	0.998	1.00
244_S	254_V	0.996	1.00
136_D	233_L	0.995	1.00
244_S	249_L	0.987	1.00
244_S	258_V	0.986	1.00
307_Y	311_L	0.965	1.00
122_F	125_A	0.963	1.00
170_P	173_G	0.963	1.00
112_A	217_A	0.962	1.00
17_F	323_I	0.961	1.00
99_G	103_P	0.953	1.00
245_L	254_V	0.949	1.00
251_R	254_V	0.945	1.00
128_A	233_L	0.936	1.00
155_A	215_A	0.933	1.00
46_T	50_A	0.931	1.00
140_R	225_T	0.923	1.00
97_L	100_K	0.922	1.00
107_E	110_I	0.921	1.00
231_S	235_Y	0.918	1.00
76_I	79_V	0.917	1.00
249_L	254_V	0.917	1.00
125_A	260_L	0.917	1.00
112_A	216_I	0.905	1.00
263_A	266_P	0.903	1.00
300_Q	304_S	0.902	1.00
9_I	15_N	0.895	1.00
151_P	285_I	0.892	1.00
112_A	116_S	0.887	1.00
96_T	99_G	0.885	1.00
20_L	322_I	0.885	1.00
86_I	91_K	0.880	1.00
221_F	225_T	0.875	1.00
16_A	326_L	0.872	1.00
275_F	324_A	0.868	1.00
101_Y	297_F	0.864	1.00
6_V	10_I	0.863	1.00
28_F	102_L	0.860	1.00
214_I	217_A	0.854	1.00
209_M	213_V	0.850	1.00
268_V	328_A	0.848	1.00
121_L	228_A	0.847	1.00
32_H	68_L	0.846	1.00
253_R	256_Y	0.846	1.00
158_L	211_L	0.844	1.00
115_L	213_V	0.843	1.00
60_K	66_Q	0.843	1.00
327_I	331_L	0.843	1.00
24_I	315_I	0.842	1.00
27_V	31_I	0.839	1.00
94_V	309_S	0.839	1.00
46_T	58_V	0.838	1.00
138_L	142_V	0.836	1.00
157_I	161_V	0.828	1.00
21_I	76_I	0.825	1.00
12_R	15_N	0.824	1.00
9_I	330_I	0.823	1.00
111_P	291_Y	0.822	1.00
52_Y	55_L	0.819	1.00
53_T	57_Q	0.817	1.00
132_N	137_Y	0.816	1.00
117_V	122_F	0.813	1.00
323_I	327_I	0.813	1.00
122_F	126_I	0.812	1.00
8_F	333_G	0.811	1.00
13_I	326_L	0.810	1.00
228_A	263_A	0.810	1.00
22_L	26_L	0.809	1.00
45_Y	50_A	0.809	1.00
98_I	312_G	0.806	1.00
297_F	301_A	0.804	1.00
26_L	30_M	0.803	1.00
242_K	245_L	0.799	1.00
87_D	306_D	0.797	1.00
79_V	315_I	0.797	1.00
120_G	124_G	0.796	1.00
137_Y	140_R	0.792	1.00
94_V	297_F	0.790	1.00
124_G	232_M	0.787	1.00
29_I	68_L	0.786	1.00
18_I	22_L	0.786	1.00
300_Q	303_E	0.782	1.00
110_I	114_I	0.782	1.00
256_Y	259_V	0.777	1.00
151_P	155_A	0.775	1.00
113_T	275_F	0.774	1.00
121_L	267_L	0.770	1.00
332_Y	339_V	0.770	1.00
135_L	138_L	0.769	1.00
84_F	98_I	0.769	1.00
105_T	109_V	0.766	1.00
333_G	339_V	0.765	1.00
103_P	107_E	0.763	1.00
254_V	259_V	0.763	1.00
141_G	144_L	0.758	1.00
25_I	68_L	0.757	1.00
82_G	93_P	0.757	1.00
89_T	300_Q	0.754	1.00
27_V	32_H	0.749	1.00
36_P	305_L	0.747	1.00
210_V	213_V	0.744	1.00
251_R	255_V	0.744	1.00
129_S	256_Y	0.743	1.00
301_A	310_I	0.742	1.00
207_H	210_V	0.740	1.00
123_T	221_F	0.735	1.00
32_H	307_Y	0.731	1.00
18_I	21_I	0.730	1.00
77_I	80_L	0.730	1.00
244_S	247_K	0.729	1.00
231_S	263_A	0.727	1.00
162_I	211_L	0.724	1.00
147_W	222_G	0.722	1.00
72_I	76_I	0.721	1.00
276_G	324_A	0.720	1.00
120_G	225_T	0.720	1.00
36_P	39_L	0.718	1.00
228_A	231_S	0.717	1.00
73_I	76_I	0.717	1.00
27_V	314_T	0.717	1.00
112_A	282_A	0.711	1.00
173_G	208_H	0.709	1.00
249_L	258_V	0.708	1.00
99_G	102_L	0.706	1.00
220_S	223_I	0.705	1.00
116_S	217_A	0.701	1.00
98_I	316_I	0.700	1.00
298_I	301_A	0.700	1.00
208_H	211_L	0.699	1.00
143_Y	222_G	0.695	1.00
50_A	55_L	0.693	1.00
53_T	56_E	0.692	1.00
154_I	218_L	0.690	1.00
155_A	288_I	0.689	1.00
21_I	323_I	0.688	1.00
297_F	313_T	0.683	1.00
319_I	323_I	0.683	1.00
137_Y	141_G	0.683	1.00
312_G	316_I	0.679	1.00
108_L	286_E	0.678	1.00
98_I	313_T	0.678	1.00
317_V	321_I	0.677	1.00
139_V	143_Y	0.674	1.00
106_L	110_I	0.673	1.00
15_N	19_T	0.673	1.00
311_L	315_I	0.673	1.00
82_G	86_I	0.671	1.00
127_A	136_D	0.671	1.00
39_L	59_A	0.667	1.00
39_L	58_V	0.666	1.00
330_I	333_G	0.666	1.00
299_T	302_I	0.666	1.00
8_F	327_I	0.662	1.00
287_D	296_Y	0.660	1.00
23_L	27_V	0.660	1.00
118_V	121_L	0.658	1.00
311_L	314_T	0.654	1.00
102_L	320_A	0.646	1.00
54_E	58_V	0.644	1.00
108_L	213_V	0.643	1.00
119_I	217_A	0.639	1.00
119_I	123_T	0.638	1.00
138_L	141_G	0.637	1.00
160_L	164_Y	0.636	1.00
117_V	224_V	0.635	1.00
29_I	33_I	0.635	1.00
224_V	270_L	0.635	1.00
16_A	19_T	0.632	1.00
102_L	106_L	0.632	1.00
110_I	275_F	0.631	1.00
270_L	274_L	0.628	1.00
111_P	114_I	0.627	1.00
136_D	140_R	0.627	1.00
35_A	38_P	0.621	1.00
282_A	285_I	0.620	1.00
47_G	50_A	0.619	1.00
15_N	18_I	0.617	1.00
242_K	246_M	0.615	1.00
103_P	106_L	0.614	1.00
333_G	340_R	0.612	1.00
219_V	222_G	0.610	1.00
66_Q	71_Q	0.609	1.00
50_A	54_E	0.608	1.00
75_Y	79_V	0.608	1.00
20_L	323_I	0.605	1.00
241_A	245_L	0.605	1.00
151_P	218_L	0.603	1.00
25_I	69_Y	0.602	1.00
163_A	211_L	0.602	1.00
252_R	255_V	0.601	1.00
211_L	214_I	0.601	1.00
216_I	285_I	0.597	1.00
117_V	121_L	0.594	1.00
151_P	154_I	0.593	1.00
45_Y	48_P	0.592	1.00
76_I	80_L	0.592	1.00
77_I	82_G	0.591	1.00
105_T	286_E	0.588	1.00
97_L	101_Y	0.588	1.00
44_L	47_G	0.587	1.00
250_S	254_V	0.586	1.00
272_A	324_A	0.585	1.00
292_H	296_Y	0.585	1.00
223_I	270_L	0.583	1.00
17_F	330_I	0.582	1.00
111_P	210_V	0.582	1.00
283_V	287_D	0.576	1.00
232_M	236_M	0.576	1.00
287_D	299_T	0.575	1.00
308_T	312_G	0.574	1.00
127_A	140_R	0.574	1.00
211_L	215_A	0.572	1.00
227_I	231_S	0.569	1.00
264_S	267_L	0.568	1.00
83_N	95_I	0.568	1.00
249_L	252_R	0.566	1.00
265_I	339_V	0.566	1.00
224_V	228_A	0.562	1.00
217_A	220_S	0.561	1.00
223_I	274_L	0.560	1.00
146_T	218_L	0.559	1.00
215_A	285_I	0.559	1.00
8_F	326_L	0.557	1.00
222_G	225_T	0.556	1.00
17_F	21_I	0.555	1.00
230_A	233_L	0.555	1.00
310_I	314_T	0.554	1.00
284_V	288_I	0.553	1.00
129_S	236_M	0.553	1.00
109_V	282_A	0.549	1.00
111_P	115_L	0.549	1.00
296_Y	299_T	0.547	1.00
231_S	266_P	0.547	1.00
67_P	71_Q	0.546	1.00
321_I	325_N	0.545	1.00
39_L	62_Y	0.544	1.00
114_I	118_V	0.544	1.00
105_T	282_A	0.540	1.00
287_D	300_Q	0.539	1.00
238_S	242_K	0.539	1.00
31_I	310_I	0.538	1.00
143_Y	146_T	0.536	1.00
298_I	317_V	0.535	1.00
130_N	255_V	0.534	1.00
24_I	76_I	0.534	1.00
59_A	65_D	0.532	1.00
87_D	90_Y	0.530	1.00
312_G	315_I	0.527	1.00
268_V	331_L	0.524	1.00
170_P	208_H	0.524	1.00
14_I	17_F	0.523	1.00
283_V	299_T	0.520	1.00
107_E	213_V	0.519	1.00
11_R	14_I	0.519	1.00
151_P	219_V	0.518	1.00
107_E	291_Y	0.517	1.00
128_A	136_D	0.517	1.00
133_K	136_D	0.517	1.00
228_A	260_L	0.516	1.00
220_S	274_L	0.515	1.00
256_Y	261_R	0.515	1.00
109_V	113_T	0.515	1.00
115_L	214_I	0.514	1.00
101_Y	296_Y	0.514	1.00
61_Q	91_K	0.512	1.00
90_Y	309_S	0.510	1.00
16_A	20_L	0.508	1.00
113_T	117_V	0.507	1.00
328_A	332_Y	0.506	1.00
216_I	282_A	0.506	1.00
218_L	221_F	0.505	1.00
170_P	207_H	0.504	1.00
284_V	287_D	0.504	1.00
9_I	12_R	0.503	1.00
153_L	156_V	0.501	1.00
141_G	145_V	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
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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
4tquM	1	0.7988	99.9	0.678	Contact Map
3tuiA	2	0.6093	99.9	0.68	Contact Map
3d31C	2	0.7201	99.9	0.701	Contact Map
3rlfF	1	0.8076	99.8	0.706	Contact Map
4ymuD	2	0.6122	99.8	0.713	Contact Map
2onkC	2	0.7289	99.8	0.714	Contact Map
4tquN	1	0.7551	99.8	0.722	Contact Map
3rlfG	1	0.8047	99.7	0.75	Contact Map
2yevC	1	0.0875	12.2	0.962	Contact Map
1v54I	1	0.2012	7.7	0.965	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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