DPPB - ECOLI - GREMLIN Contacts

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DPPB - Dipeptide transport system permease protein DppB

UniProt:	P0AEF8	Sequences: MLQFILRRLGLVIPTFIGITLLTFAFVHMIPGDPVMIMAGERGISPERHAQLLAELGLDKPMWQQYLHYIWGVMHGDLGISMKSRIPVWEEFVPRFQATLELGVCAMIFATAVGIPVGVLAAVKRGSIFDHTAVGLALTGYSMPIFWWGMMLIMLVSVHWNLTPVSGRVSDMVFLDDSNPLTGFMLIDTAIWGEDGNFIDAVAHMILPAIVLGTIPLAVIVRMTRSSMLEVLGEDYIRTARAKGLTRMRVIIVHALRNAMLPVVTVIGLQVGTLLAGAILTETIFSWPGLGRWLIDALQRRDYPVVQGGVLLVATMIILVNLLVDLLYGVVNPRIRHKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12625
Length:	339 (299)
Sequences:	21682 (13601)
Seq/√Len:	786.6

ECOLI - DPPB DDPB YEJB NIKB GSIC OPPB SAPB YEJE DPPC SAPC NIKC DDPC GSID OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMI2 Q9HMX0 Q9HMW3 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97VF8 Q97VK6 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
60_K	64_Q	3.352	1.00
60_K	68_H	3.255	1.00
28_H	65_Q	3.193	1.00
71_W	75_H	2.731	1.00
67_L	71_W	2.730	1.00
228_M	255_A	2.698	1.00
54_A	59_D	2.604	1.00
20_T	66_Y	2.591	1.00
46_P	50_A	2.458	1.00
105_C	209_A	2.405	1.00
241_R	247_R	2.393	1.00
292_R	296_D	2.380	1.00
249_R	253_V	2.355	1.00
117_V	133_A	2.327	1.00
98_A	287_W	2.301	1.00
33_D	53_L	2.293	1.00
21_L	66_Y	2.251	1.00
231_V	236_Y	2.240	1.00
237_I	255_A	2.190	1.00
130_D	225_R	2.090	1.00
231_V	234_E	2.088	1.00
63_W	67_L	2.077	1.00
248_M	252_I	2.054	1.00
91_E	293_W	2.046	1.00
246_T	249_R	2.025	1.00
49_H	53_L	1.993	1.00
268_G	324_V	1.983	1.00
3_Q	7_R	1.973	1.00
87_P	90_E	1.972	1.00
112_A	116_P	1.890	1.00
48_R	51_Q	1.876	1.00
163_T	203_A	1.866	1.00
232_L	255_A	1.861	1.00
245_L	249_R	1.849	1.00
109_F	213_G	1.847	1.00
124_K	127_S	1.823	1.00
19_I	314_A	1.801	1.00
51_Q	55_E	1.796	1.00
45_S	48_R	1.770	1.00
237_I	250_V	1.740	1.00
163_T	206_I	1.728	1.00
64_Q	68_H	1.727	1.00
128_I	132_T	1.724	1.00
120_L	124_K	1.719	1.00
86_I	90_E	1.715	1.00
157_S	165_V	1.693	1.00
88_V	308_G	1.667	1.00
89_W	93_V	1.667	1.00
124_K	129_F	1.662	1.00
50_A	53_L	1.660	1.00
72_G	77_D	1.648	1.00
235_D	238_R	1.623	1.00
264_V	331_V	1.601	1.00
50_A	54_A	1.599	1.00
122_A	228_M	1.596	1.00
119_V	228_M	1.593	1.00
129_F	133_A	1.588	1.00
113_V	116_P	1.548	1.00
120_L	129_F	1.536	1.00
68_H	71_W	1.534	1.00
239_T	243_K	1.530	1.00
123_V	251_I	1.522	1.00
16_F	315_T	1.502	1.00
231_V	259_A	1.493	1.00
168_R	287_W	1.489	1.00
101_E	168_R	1.474	1.00
209_A	213_G	1.473	1.00
327_L	330_V	1.468	1.00
265_T	328_Y	1.468	1.00
294_L	309_G	1.454	1.00
113_V	217_L	1.441	1.00
236_Y	258_N	1.428	1.00
33_D	36_M	1.428	1.00
154_M	159_H	1.420	1.00
110_A	216_P	1.417	1.00
231_V	255_A	1.407	1.00
73_V	78_L	1.400	1.00
98_A	168_R	1.395	1.00
147_W	151_M	1.389	1.00
123_V	247_R	1.389	1.00
52_L	55_E	1.385	1.00
17_I	66_Y	1.385	1.00
231_V	237_I	1.379	1.00
86_I	94_P	1.378	1.00
78_L	308_G	1.377	1.00
220_I	270_Q	1.369	1.00
68_H	72_G	1.365	1.00
297_A	305_V	1.362	1.00
10_G	14_P	1.350	1.00
52_L	56_L	1.344	1.00
17_I	21_L	1.331	1.00
101_E	105_C	1.328	1.00
152_L	211_V	1.324	1.00
74_M	77_D	1.323	1.00
111_T	267_I	1.318	1.00
124_K	247_R	1.316	1.00
78_L	89_W	1.312	1.00
94_P	97_Q	1.307	1.00
12_V	318_I	1.304	1.00
243_K	254_H	1.288	1.00
64_Q	67_L	1.285	1.00
114_G	224_T	1.282	1.00
155_L	159_H	1.281	1.00
35_V	49_H	1.280	1.00
122_A	232_L	1.249	1.00
118_G	122_A	1.245	1.00
213_G	217_L	1.244	1.00
91_E	305_V	1.241	1.00
225_R	229_L	1.240	1.00
107_M	267_I	1.233	1.00
126_G	130_D	1.223	1.00
114_G	220_I	1.218	1.00
293_W	305_V	1.215	1.00
133_A	221_V	1.211	1.00
86_I	91_E	1.211	1.00
61_P	64_Q	1.205	1.00
140_G	218_A	1.205	1.00
6_L	10_G	1.203	1.00
25_A	28_H	1.203	1.00
155_L	160_W	1.201	1.00
80_I	87_P	1.192	1.00
118_G	224_T	1.189	1.00
223_M	266_V	1.188	1.00
57_G	60_K	1.184	1.00
60_K	63_W	1.182	1.00
143_M	148_W	1.182	1.00
20_T	69_Y	1.177	1.00
21_L	25_A	1.169	1.00
57_G	68_H	1.140	1.00
117_V	221_V	1.135	1.00
98_A	101_E	1.131	1.00
137_A	221_V	1.124	1.00
206_I	210_I	1.120	1.00
228_M	259_A	1.118	1.00
261_L	328_Y	1.114	1.00
224_T	263_V	1.112	1.00
121_A	133_A	1.111	1.00
128_I	131_H	1.110	1.00
81_S	86_I	1.093	1.00
170_S	204_H	1.091	1.00
326_L	330_V	1.090	1.00
272_G	317_I	1.089	1.00
309_G	313_V	1.089	1.00
51_Q	54_A	1.077	1.00
90_E	94_P	1.066	1.00
211_V	215_I	1.063	1.00
156_V	160_W	1.061	1.00
91_E	94_P	1.051	1.00
83_K	300_R	1.045	1.00
240_A	250_V	1.043	1.00
101_E	205_M	1.039	1.00
36_M	49_H	1.033	1.00
72_G	75_H	1.023	1.00
240_A	245_L	1.015	1.00
54_A	60_K	1.012	1.00
320_V	324_V	1.010	1.00
122_A	229_L	1.002	1.00
106_A	213_G	1.001	1.00
5_I	326_L	1.001	1.00
119_V	251_I	0.999	1.00
136_L	140_G	0.988	1.00
18_G	22_L	0.982	1.00
93_V	97_Q	0.980	1.00
295_I	299_Q	0.979	1.00
149_G	211_V	0.976	1.00
152_L	207_L	0.974	1.00
328_Y	332_N	0.973	1.00
81_S	302_D	0.973	1.00
14_P	17_I	0.962	1.00
12_V	322_L	0.955	1.00
23_T	96_F	0.955	1.00
245_L	250_V	0.954	1.00
169_V	204_H	0.953	1.00
224_T	228_M	0.953	1.00
130_D	229_L	0.948	1.00
145_I	281_T	0.946	1.00
247_R	250_V	0.938	1.00
28_H	62_M	0.931	1.00
249_R	252_I	0.928	1.00
9_L	322_L	0.928	1.00
323_L	327_L	0.927	1.00
4_F	329_G	0.924	1.00
303_Y	307_Q	0.920	1.00
116_P	119_V	0.916	1.00
90_E	93_V	0.914	1.00
92_F	308_G	0.912	1.00
21_L	62_M	0.906	1.00
205_M	209_A	0.906	1.00
103_G	274_L	0.906	1.00
241_R	250_V	0.903	1.00
240_A	254_H	0.900	1.00
271_V	320_V	0.899	1.00
70_I	73_V	0.897	1.00
115_I	224_T	0.894	1.00
16_F	318_I	0.893	1.00
230_E	234_E	0.893	1.00
39_A	52_L	0.893	1.00
20_T	311_L	0.893	1.00
163_T	207_L	0.890	1.00
217_L	221_V	0.890	1.00
17_I	70_I	0.889	1.00
151_M	155_L	0.888	1.00
80_I	85_R	0.887	1.00
95_R	293_W	0.885	1.00
296_D	300_R	0.882	1.00
71_W	74_M	0.875	1.00
126_G	131_H	0.873	1.00
259_A	262_P	0.872	1.00
25_A	62_M	0.870	1.00
134_V	221_V	0.868	1.00
227_S	231_V	0.868	1.00
132_T	136_L	0.868	1.00
101_E	104_V	0.866	1.00
264_V	324_V	0.861	1.00
106_A	110_A	0.856	1.00
10_G	326_L	0.853	1.00
88_V	293_W	0.853	1.00
106_A	212_L	0.851	1.00
210_I	213_G	0.850	1.00
38_M	41_E	0.850	1.00
35_V	39_A	0.842	1.00
13_I	17_I	0.841	1.00
227_S	230_E	0.840	1.00
73_V	311_L	0.836	1.00
224_T	259_A	0.833	1.00
109_F	209_A	0.832	1.00
32_G	301_R	0.830	1.00
250_V	255_A	0.829	1.00
131_H	134_V	0.829	1.00
28_H	303_Y	0.829	1.00
104_V	108_I	0.828	1.00
111_T	116_P	0.827	1.00
293_W	297_A	0.827	1.00
319_L	323_L	0.817	1.00
329_G	335_I	0.815	1.00
119_V	256_L	0.814	1.00
149_G	284_I	0.814	1.00
47_E	51_Q	0.812	1.00
70_I	74_M	0.810	1.00
116_P	120_L	0.809	1.00
39_A	44_I	0.809	1.00
115_I	263_V	0.804	1.00
114_G	118_G	0.802	1.00
118_G	228_M	0.801	1.00
252_I	255_A	0.798	1.00
129_F	132_T	0.791	1.00
69_Y	73_V	0.789	1.00
105_C	287_W	0.789	1.00
227_S	259_A	0.787	1.00
14_P	18_G	0.786	1.00
328_Y	335_I	0.785	1.00
107_M	271_V	0.784	1.00
272_G	320_V	0.782	1.00
326_L	329_G	0.782	1.00
123_V	252_I	0.779	1.00
67_L	70_I	0.778	1.00
82_M	304_P	0.777	1.00
156_V	163_T	0.776	1.00
164_P	167_G	0.773	1.00
206_I	209_A	0.768	1.00
117_V	217_L	0.764	1.00
99_T	103_G	0.763	1.00
315_T	319_L	0.759	1.00
21_L	63_W	0.758	1.00
114_G	221_V	0.757	1.00
238_R	241_R	0.755	1.00
110_A	213_G	0.753	1.00
297_A	306_V	0.751	1.00
35_V	53_L	0.749	1.00
88_V	305_V	0.746	1.00
294_L	297_A	0.745	1.00
145_I	149_G	0.742	1.00
113_V	213_G	0.739	1.00
307_Q	310_V	0.738	1.00
92_F	309_G	0.736	1.00
66_Y	70_I	0.732	1.00
104_V	271_V	0.729	1.00
100_L	104_V	0.728	1.00
46_P	49_H	0.726	1.00
148_W	214_T	0.723	1.00
283_T	292_R	0.722	1.00
156_V	207_L	0.714	1.00
35_V	52_L	0.712	1.00
23_T	310_V	0.711	1.00
224_T	227_S	0.708	1.00
159_H	162_L	0.707	1.00
240_A	243_K	0.704	1.00
329_G	336_R	0.702	1.00
168_R	205_M	0.702	1.00
156_V	162_L	0.701	1.00
141_Y	218_A	0.700	1.00
278_A	281_T	0.700	1.00
247_R	251_I	0.697	1.00
38_M	52_L	0.697	1.00
78_L	92_F	0.695	1.00
293_W	309_G	0.694	1.00
137_A	218_A	0.693	1.00
25_A	29_M	0.692	1.00
308_G	312_L	0.690	1.00
283_T	295_I	0.685	1.00
47_E	50_A	0.684	1.00
16_F	319_L	0.684	1.00
97_Q	101_E	0.684	1.00
313_V	317_I	0.682	1.00
121_A	130_D	0.681	1.00
216_P	219_V	0.678	1.00
93_V	96_F	0.677	1.00
298_L	301_R	0.677	1.00
19_I	316_M	0.672	1.00
106_A	278_A	0.671	1.00
317_I	321_N	0.670	1.00
145_I	214_T	0.666	1.00
97_Q	100_L	0.660	1.00
96_F	100_L	0.660	1.00
113_V	117_V	0.656	1.00
135_G	138_L	0.655	1.00
71_W	76_G	0.650	1.00
130_D	134_V	0.643	1.00
245_L	254_H	0.641	1.00
7_R	10_G	0.640	1.00
131_H	135_G	0.634	1.00
82_M	296_D	0.634	1.00
91_E	95_R	0.633	1.00
153_I	165_V	0.632	1.00
133_A	137_A	0.631	1.00
140_G	214_T	0.630	1.00
132_T	135_G	0.629	1.00
166_S	286_S	0.626	1.00
211_V	281_T	0.626	1.00
111_T	220_I	0.624	1.00
36_M	40_G	0.622	1.00
223_M	227_S	0.622	1.00
105_C	108_I	0.622	1.00
44_I	49_H	0.620	1.00
219_V	270_Q	0.619	1.00
296_D	299_Q	0.618	1.00
102_L	209_A	0.618	1.00
238_R	242_A	0.615	1.00
294_L	313_V	0.612	1.00
112_A	115_I	0.610	1.00
288_P	292_R	0.608	1.00
307_Q	311_L	0.608	1.00
204_H	207_L	0.607	1.00
105_C	206_I	0.606	1.00
261_L	335_I	0.605	1.00
22_L	93_V	0.605	1.00
220_I	224_T	0.603	1.00
15_T	318_I	0.602	1.00
145_I	148_W	0.602	1.00
268_G	320_V	0.602	1.00
207_L	211_V	0.601	1.00
213_G	216_P	0.600	1.00
99_T	278_A	0.600	1.00
219_V	266_V	0.600	1.00
154_M	158_V	0.599	1.00
135_G	139_T	0.599	1.00
157_S	207_L	0.598	1.00
48_R	52_L	0.598	1.00
15_T	319_L	0.598	1.00
224_T	256_L	0.596	1.00
20_T	70_I	0.595	1.00
170_S	203_A	0.593	1.00
50_A	59_D	0.592	1.00
35_V	56_L	0.591	1.00
8_R	11_L	0.591	1.00
99_T	282_E	0.590	1.00
266_V	270_Q	0.589	1.00
167_G	204_H	0.589	1.00
264_V	327_L	0.589	1.00
279_I	283_T	0.585	1.00
92_F	312_L	0.585	1.00
283_T	296_D	0.585	1.00
103_G	278_A	0.583	1.00
245_L	248_M	0.580	1.00
248_M	251_I	0.579	1.00
105_C	109_F	0.579	1.00
76_G	80_I	0.576	1.00
121_A	134_V	0.574	1.00
73_V	76_G	0.572	1.00
215_I	218_A	0.571	1.00
203_A	206_I	0.569	1.00
127_S	131_H	0.567	1.00
108_I	112_A	0.565	1.00
127_S	132_T	0.565	1.00
227_S	262_P	0.565	1.00
218_A	221_V	0.563	1.00
324_V	328_Y	0.562	1.00
103_G	107_M	0.562	1.00
252_I	257_R	0.562	1.00
5_I	11_L	0.561	1.00
111_T	115_I	0.561	1.00
279_I	295_I	0.560	1.00
234_E	238_R	0.558	1.00
95_R	292_R	0.558	1.00
260_M	264_V	0.557	1.00
102_L	282_E	0.556	1.00
11_L	14_P	0.556	1.00
220_I	266_V	0.555	1.00
53_L	58_L	0.555	1.00
260_M	263_V	0.551	1.00
41_E	44_I	0.550	1.00
246_T	250_V	0.547	1.00
27_V	306_V	0.547	1.00
24_F	28_H	0.546	1.00
127_S	130_D	0.545	1.00
124_K	130_D	0.542	1.00
4_F	322_L	0.542	1.00
231_V	258_N	0.542	1.00
30_I	90_E	0.541	1.00
306_V	310_V	0.540	1.00
55_E	85_R	0.538	1.00
124_K	251_I	0.538	1.00
251_I	255_A	0.538	1.00
123_V	232_L	0.537	1.00
76_G	87_P	0.535	1.00
228_M	232_L	0.535	1.00
28_H	307_Q	0.534	1.00
109_F	210_I	0.533	1.00
145_I	215_I	0.533	1.00
147_W	211_V	0.532	1.00
322_L	326_L	0.531	1.00
210_I	214_T	0.529	1.00
53_L	59_D	0.529	1.00
219_V	223_M	0.529	1.00
152_L	210_I	0.527	1.00
105_C	213_G	0.527	1.00
304_P	307_Q	0.524	1.00
134_V	137_A	0.524	1.00
64_Q	71_W	0.522	1.00
316_M	320_V	0.521	1.00
237_I	241_R	0.521	1.00
44_I	48_R	0.521	1.00
96_F	316_M	0.521	1.00
107_M	111_T	0.521	1.00
216_P	270_Q	0.521	1.00
226_S	229_L	0.521	1.00
77_D	89_W	0.514	1.00
236_Y	240_A	0.514	1.00
143_M	147_W	0.513	1.00
228_M	256_L	0.512	1.00
214_T	217_L	0.510	1.00
32_G	76_G	0.510	1.00
122_A	130_D	0.509	1.00
147_W	150_M	0.508	1.00
9_L	13_I	0.508	1.00
137_A	140_G	0.506	1.00
26_F	94_P	0.504	1.00
105_C	205_M	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	0.6165	99.9	0.678	Contact Map
4tquM	1	0.7935	99.9	0.691	Contact Map
3rlfF	1	0.7876	99.9	0.698	Contact Map
4ymuD	2	0.6195	99.8	0.71	Contact Map
3d31C	2	0.7286	99.8	0.715	Contact Map
2onkC	2	0.6991	99.8	0.715	Contact Map
4tquN	1	0.7522	99.7	0.742	Contact Map
3rlfG	1	0.8171	99.7	0.752	Contact Map
2p02A	2	0.2566	7.6	0.965	Contact Map
1p7lA	4	0.2714	7.5	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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