DPPB - BACSU - GREMLIN Contacts

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DPPB - Dipeptide transport system permease protein DppB

UniProt:	P26903	Sequences: MARYMIKRFWAMAATILVITTLTFVLMKVIPGSPFNEERGTNEAVQKNLEAYYHLDDPLIFQYIFYLKSIITFDFGPSIKKPSDSVNDMLERGFPVSFELGMTAIVIAVISGLVLGVIAALRRNGFLDYAAMSLAVLGISIPNFILATLLIQQFAVNLKLFPAATWTSPIHMVLPTAALAVGPMAIIARLTRSSMVEVLTQDYIRTAKAKGLSPFKIIVKHALRNALMPVITVLGTLVASILTGSFVIEKIFAIPGMGKYFVESINQRDYPVIMGTTVFYSVILIIMLFLVDLAYGLLDPRIKLHKKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	308 (274)
Sequences:	25516 (16992)
Seq/√Len:	1026.5

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_D	61_F	3.028	1.00
57_D	65_F	2.915	1.00
28_K	62_Q	2.738	1.00
195_M	222_A	2.730	1.00
68_K	72_T	2.506	1.00
43_E	47_K	2.467	1.00
128_D	192_R	2.387	1.00
115_L	131_A	2.368	1.00
64_I	68_K	2.365	1.00
208_K	214_P	2.360	1.00
51_A	56_D	2.343	1.00
198_V	203_Y	2.338	1.00
96_V	254_I	2.313	1.00
103_T	176_T	2.260	1.00
216_K	220_K	2.248	1.00
259_K	263_E	2.237	1.00
20_T	63_Y	2.235	1.00
198_V	201_Q	2.164	1.00
212_L	216_K	2.149	1.00
213_S	216_K	2.122	1.00
215_F	219_V	2.066	1.00
107_I	180_A	2.038	1.00
204_I	222_A	2.030	1.00
235_G	291_V	1.970	1.00
89_M	260_Y	1.934	1.00
33_S	50_E	1.926	1.00
21_T	63_Y	1.920	1.00
85_S	88_D	1.840	1.00
202_D	205_R	1.826	1.00
110_I	114_V	1.814	1.00
122_R	125_G	1.810	1.00
118_I	122_R	1.803	1.00
117_V	195_M	1.792	1.00
60_I	64_I	1.788	1.00
45_V	48_N	1.786	1.00
204_I	217_I	1.771	1.00
46_Q	50_E	1.764	1.00
122_R	214_P	1.717	1.00
122_R	127_L	1.710	1.00
126_F	130_A	1.694	1.00
199_L	222_A	1.686	1.00
120_A	195_M	1.679	1.00
87_N	91_E	1.640	1.00
198_V	226_A	1.629	1.00
187_I	237_L	1.623	1.00
121_L	214_P	1.621	1.00
71_I	74_D	1.617	1.00
48_N	52_Y	1.606	1.00
86_V	275_G	1.592	1.00
127_L	131_A	1.588	1.00
47_K	50_E	1.580	1.00
61_F	65_F	1.573	1.00
78_S	84_D	1.541	1.00
69_S	74_D	1.520	1.00
111_S	114_V	1.514	1.00
203_Y	225_N	1.512	1.00
99_E	103_T	1.509	1.00
47_K	51_A	1.509	1.00
75_F	275_G	1.502	1.00
111_S	184_M	1.493	1.00
118_I	127_L	1.490	1.00
84_D	88_D	1.489	1.00
6_I	10_W	1.487	1.00
121_L	218_I	1.482	1.00
176_T	180_A	1.462	1.00
109_V	234_L	1.457	1.00
33_S	36_N	1.448	1.00
92_R	95_P	1.443	1.00
108_A	183_P	1.440	1.00
261_F	276_T	1.424	1.00
264_S	272_V	1.411	1.00
206_T	210_K	1.401	1.00
131_A	188_A	1.384	1.00
19_I	281_S	1.365	1.00
198_V	222_A	1.357	1.00
65_F	68_K	1.350	1.00
112_G	191_T	1.345	1.00
198_V	204_I	1.335	1.00
232_T	295_Y	1.330	1.00
105_I	234_L	1.326	1.00
116_G	120_A	1.313	1.00
231_I	298_L	1.299	1.00
10_W	14_A	1.286	1.00
112_G	187_I	1.273	1.00
96_V	99_E	1.267	1.00
150_L	178_A	1.265	1.00
75_F	87_N	1.261	1.00
294_A	297_L	1.259	1.00
145_I	149_L	1.258	1.00
135_A	188_A	1.257	1.00
115_L	188_A	1.257	1.00
152_Q	157_N	1.252	1.00
17_L	21_T	1.247	1.00
58_P	61_F	1.247	1.00
124_N	128_D	1.243	1.00
84_D	92_R	1.243	1.00
239_A	284_L	1.241	1.00
192_R	196_V	1.235	1.00
49_L	53_Y	1.235	1.00
49_L	52_Y	1.225	1.00
194_S	197_E	1.220	1.00
190_L	233_V	1.219	1.00
79_I	263_E	1.217	1.00
197_E	201_Q	1.216	1.00
180_A	184_M	1.214	1.00
295_Y	299_D	1.209	1.00
84_D	89_M	1.206	1.00
120_A	199_L	1.203	1.00
65_F	69_S	1.203	1.00
57_D	60_I	1.201	1.00
119_A	131_A	1.199	1.00
24_F	28_K	1.194	1.00
70_I	75_F	1.184	1.00
73_F	85_S	1.183	1.00
16_I	282_V	1.174	1.00
173_V	177_A	1.173	1.00
35_F	46_Q	1.173	1.00
138_G	185_A	1.169	1.00
126_F	129_Y	1.152	1.00
116_G	191_T	1.145	1.00
17_L	63_Y	1.142	1.00
270_Y	274_M	1.138	1.00
61_F	64_I	1.129	1.00
178_A	182_G	1.122	1.00
207_A	217_I	1.113	1.00
133_S	136_V	1.112	1.00
195_M	226_A	1.108	1.00
207_A	221_H	1.108	1.00
210_K	221_H	1.107	1.00
67_L	70_I	1.099	1.00
117_V	218_I	1.098	1.00
191_T	230_V	1.091	1.00
89_M	272_V	1.089	1.00
77_P	85_S	1.088	1.00
260_Y	272_V	1.075	1.00
207_A	212_L	1.060	1.00
293_L	297_L	1.058	1.00
54_H	57_D	1.054	1.00
276_T	280_Y	1.052	1.00
36_N	46_Q	1.052	1.00
141_I	146_L	1.047	1.00
12_M	285_I	1.029	1.00
153_Q	157_N	1.027	1.00
262_V	266_N	1.021	1.00
191_T	195_M	1.020	1.00
99_E	172_M	1.019	1.00
9_F	13_A	1.017	1.00
134_L	138_G	1.004	1.00
25_V	28_K	1.004	1.00
48_N	51_A	1.003	1.00
114_V	117_V	0.993	1.00
31_P	34_P	0.992	1.00
117_V	223_L	0.988	1.00
12_M	15_T	0.987	1.00
20_T	66_Y	0.984	1.00
216_K	219_V	0.973	1.00
194_S	198_V	0.972	1.00
18_V	22_L	0.971	1.00
69_S	72_T	0.967	1.00
287_M	291_V	0.964	1.00
147_A	178_A	0.961	1.00
238_V	287_M	0.956	1.00
113_L	191_T	0.953	1.00
88_D	92_R	0.951	1.00
228_M	295_Y	0.947	1.00
208_K	217_I	0.942	1.00
212_L	217_I	0.939	1.00
104_A	180_A	0.938	1.00
132_M	188_A	0.935	1.00
54_H	65_F	0.932	1.00
93_G	260_Y	0.932	1.00
10_W	13_A	0.930	1.00
104_A	179_L	0.929	1.00
128_D	196_V	0.928	1.00
75_F	90_L	0.927	1.00
205_R	208_K	0.926	1.00
99_E	102_M	0.922	1.00
184_M	188_A	0.921	1.00
129_Y	133_S	0.919	1.00
100_L	249_E	0.914	1.00
89_M	92_R	0.914	1.00
231_I	291_V	0.913	1.00
91_E	95_P	0.913	1.00
130_A	134_L	0.906	1.00
86_V	272_V	0.904	1.00
191_T	226_A	0.900	1.00
91_E	94_F	0.898	1.00
261_F	264_S	0.891	1.00
14_A	17_L	0.888	1.00
104_A	108_A	0.883	1.00
34_P	37_E	0.879	1.00
214_P	217_I	0.878	1.00
64_I	67_L	0.875	1.00
21_T	25_V	0.869	1.00
226_A	229_P	0.869	1.00
172_M	176_T	0.866	1.00
95_P	99_E	0.865	1.00
173_V	176_T	0.863	1.00
286_I	290_L	0.855	1.00
143_N	248_I	0.854	1.00
207_A	210_K	0.853	1.00
86_V	260_Y	0.853	1.00
150_L	174_L	0.844	1.00
51_A	57_D	0.839	1.00
77_P	83_S	0.838	1.00
19_I	23_T	0.837	1.00
116_G	195_M	0.834	1.00
113_L	230_V	0.834	1.00
177_A	180_A	0.831	1.00
109_V	187_I	0.830	1.00
120_A	196_V	0.828	1.00
129_Y	132_M	0.821	1.00
88_D	91_E	0.818	1.00
44_A	48_N	0.814	1.00
80_K	267_Q	0.812	1.00
114_V	118_I	0.811	1.00
103_T	254_I	0.811	1.00
262_V	265_I	0.807	1.00
205_R	209_A	0.805	1.00
124_N	129_Y	0.805	1.00
90_L	279_F	0.803	1.00
263_E	266_N	0.801	1.00
127_L	130_A	0.797	1.00
78_S	269_D	0.796	1.00
16_I	285_I	0.796	1.00
9_F	289_F	0.794	1.00
27_M	31_P	0.791	1.00
296_G	302_I	0.791	1.00
264_S	273_I	0.790	1.00
233_V	237_L	0.784	1.00
43_E	46_Q	0.782	1.00
44_A	47_K	0.779	1.00
154_F	174_L	0.776	1.00
143_N	147_A	0.772	1.00
109_V	114_V	0.771	1.00
260_Y	276_T	0.769	1.00
28_K	59_L	0.764	1.00
32_G	35_F	0.764	1.00
275_G	278_V	0.761	1.00
21_T	59_L	0.761	1.00
179_L	248_I	0.760	1.00
139_I	185_A	0.757	1.00
94_F	283_I	0.756	1.00
135_A	185_A	0.755	1.00
97_S	101_G	0.755	1.00
12_M	289_F	0.752	1.00
102_M	106_V	0.751	1.00
115_L	184_M	0.746	1.00
282_V	286_I	0.745	1.00
239_A	287_M	0.743	1.00
112_G	116_G	0.742	1.00
25_V	59_L	0.739	1.00
68_K	71_I	0.738	1.00
38_E	49_L	0.738	1.00
212_L	221_H	0.738	1.00
128_D	132_M	0.737	1.00
194_S	226_A	0.737	1.00
90_L	275_G	0.731	1.00
295_Y	302_I	0.731	1.00
274_M	278_V	0.730	1.00
217_I	222_A	0.730	1.00
107_I	176_T	0.730	1.00
214_P	218_I	0.728	1.00
219_V	222_A	0.726	1.00
290_L	294_A	0.725	1.00
17_L	67_L	0.721	1.00
157_N	174_L	0.720	1.00
70_I	278_V	0.716	1.00
263_E	267_Q	0.715	1.00
275_G	279_F	0.714	1.00
20_T	24_F	0.713	1.00
271_P	275_G	0.708	1.00
183_P	186_I	0.707	1.00
280_Y	284_L	0.706	1.00
73_F	77_P	0.705	1.00
7_K	10_W	0.705	1.00
260_Y	264_S	0.701	1.00
193_S	196_V	0.700	1.00
149_L	153_Q	0.696	1.00
109_V	113_L	0.696	1.00
110_I	113_L	0.694	1.00
122_R	218_I	0.693	1.00
119_A	128_D	0.690	1.00
235_G	287_M	0.685	1.00
274_M	277_T	0.681	1.00
155_A	174_L	0.679	1.00
121_L	219_V	0.678	1.00
63_Y	67_L	0.678	1.00
28_K	270_Y	0.675	1.00
103_T	106_V	0.671	1.00
105_I	238_V	0.670	1.00
12_M	18_V	0.670	1.00
104_A	245_S	0.668	1.00
191_T	194_S	0.668	1.00
23_T	277_T	0.668	1.00
45_V	49_L	0.668	1.00
201_Q	205_R	0.667	1.00
215_F	218_I	0.665	1.00
108_A	180_A	0.664	1.00
24_F	27_M	0.662	1.00
111_S	115_L	0.659	1.00
22_L	25_V	0.659	1.00
66_Y	70_I	0.655	1.00
111_S	180_A	0.650	1.00
119_A	132_M	0.650	1.00
20_T	278_V	0.650	1.00
9_F	12_M	0.648	1.00
174_L	177_A	0.646	1.00
70_I	73_F	0.645	1.00
90_L	276_T	0.642	1.00
13_A	17_L	0.638	1.00
273_I	277_T	0.635	1.00
100_L	176_T	0.635	1.00
23_T	27_M	0.633	1.00
74_D	85_S	0.632	1.00
112_G	188_A	0.630	1.00
130_A	133_S	0.627	1.00
11_A	15_T	0.625	1.00
245_S	248_I	0.622	1.00
98_F	102_M	0.620	1.00
293_L	296_G	0.616	1.00
74_D	87_N	0.616	1.00
194_S	229_P	0.616	1.00
35_F	50_E	0.614	1.00
143_N	146_L	0.614	1.00
261_F	265_I	0.613	1.00
101_G	245_S	0.613	1.00
7_K	13_A	0.612	1.00
131_A	135_A	0.611	1.00
284_L	288_L	0.607	1.00
186_I	237_L	0.605	1.00
124_N	199_L	0.604	1.00
185_A	188_A	0.603	1.00
103_T	173_V	0.603	1.00
79_I	271_P	0.602	1.00
14_A	18_V	0.601	1.00
296_G	303_K	0.599	1.00
182_G	185_A	0.596	1.00
34_P	38_E	0.596	1.00
35_F	38_E	0.595	1.00
152_Q	156_V	0.594	1.00
7_K	11_A	0.591	1.00
183_P	240_S	0.591	1.00
125_G	128_D	0.591	1.00
89_M	93_G	0.591	1.00
95_P	98_F	0.590	1.00
249_E	253_A	0.588	1.00
147_A	251_I	0.587	1.00
106_V	110_I	0.587	1.00
212_L	215_F	0.585	1.00
204_I	208_K	0.585	1.00
195_M	199_L	0.583	1.00
13_A	18_V	0.583	1.00
121_L	199_L	0.583	1.00
143_N	181_V	0.578	1.00
187_I	233_V	0.577	1.00
250_K	259_K	0.576	1.00
186_I	233_V	0.576	1.00
247_V	250_K	0.575	1.00
289_F	293_L	0.574	1.00
250_K	262_V	0.574	1.00
10_W	293_L	0.572	1.00
70_I	74_D	0.572	1.00
190_L	194_S	0.570	1.00
132_M	135_A	0.568	1.00
237_L	240_S	0.567	1.00
247_V	251_I	0.567	1.00
246_F	250_K	0.566	1.00
102_M	238_V	0.564	1.00
198_V	225_N	0.563	1.00
105_I	237_L	0.559	1.00
219_V	224_R	0.559	1.00
187_I	191_T	0.559	1.00
32_G	268_R	0.556	1.00
183_P	237_L	0.555	1.00
154_F	157_N	0.551	1.00
31_P	35_F	0.551	1.00
146_L	181_V	0.549	1.00
29_V	33_S	0.547	1.00
174_L	178_A	0.543	1.00
237_L	245_S	0.536	1.00
22_L	26_L	0.533	1.00
248_I	251_I	0.533	1.00
196_V	199_L	0.531	1.00
135_A	184_M	0.530	1.00
261_F	280_Y	0.530	1.00
181_V	184_M	0.528	1.00
94_F	98_F	0.528	1.00
186_I	190_L	0.528	1.00
25_V	29_V	0.525	1.00
246_F	262_V	0.525	1.00
119_A	192_R	0.525	1.00
35_F	49_L	0.523	1.00
23_T	28_K	0.518	1.00
125_G	130_A	0.516	1.00
29_V	94_F	0.516	1.00
227_L	231_I	0.516	1.00
80_K	84_D	0.516	1.00
99_E	254_I	0.515	1.00
67_L	71_I	0.515	1.00
31_P	36_N	0.514	1.00
178_A	248_I	0.511	1.00
115_L	118_I	0.510	1.00
12_M	29_V	0.509	1.00
120_A	128_D	0.507	1.00
46_Q	49_L	0.506	1.00
8_R	11_A	0.502	1.00
213_S	217_I	0.501	1.00
59_L	62_Q	0.500	1.00
29_V	32_G	0.500	1.00
105_I	109_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
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
3tuiA	2	0.6786	99.9	0.639	Contact Map
4tquM	1	0.8442	99.9	0.648	Contact Map
3rlfF	1	0.8312	99.8	0.668	Contact Map
4ymuD	2	0.6818	99.8	0.681	Contact Map
2onkC	2	0.8052	99.8	0.685	Contact Map
3d31C	2	0.789	99.8	0.688	Contact Map
4tquN	1	0.8377	99.7	0.703	Contact Map
3rlfG	1	0.8539	99.7	0.703	Contact Map
4ltoA	3	0.3344	11.4	0.958	Contact Map
4cbcA	3	0.2987	7.4	0.961	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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