DDPB - ECOLI - GREMLIN Contacts

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DDPB - Probable D,D-dipeptide transport system permease protein DdpB

UniProt:	P77308	Sequences: MTFWSILRQRCWGLVLVVAGVCVITFIISHLIPGDPARLLAGDRASDAIVENIRQQLGLDQPLYVQFYRYVSDLFHGDLGTSIRTGRPVLEELRIFFPATLELAFGALLLALLIGIPLGILSAVWRNRWLDHLVRIMAITGISTPAFWLGLGVIVLFYGHLQILPGGGRLDDWLDPPTHVTGFYLLDALLEGNGEVFFNALQHLILPALTLAFVHLGIVARQIRSAMLEQLSEDYIRTARASGLPGWYIVLCYALPNALIPSITVLGLALGDLLYGAVLTETVFAWPGMGAWVVTSIQALDFPAVMGFAVVVSFAYVLVNLVVDLLYLWIDPRIGRGGGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13789
Length:	340 (294)
Sequences:	22627 (14507)
Seq/√Len:	846.0

ECOLI - DDPB DPPB YEJB NIKB GSIC OPPB SAPB YEJE DPPC SAPC DDPC NIKC GSID OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMX0 Q9HMI2 Q9HMW3 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97YQ0 Q97VK6 Q97VF8 Q97UH1 Q97UG4 Q97YP1 Q97VK7 Q97UG3 Q97UH2 Q97YP2 Q97YP9 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
61_Q	65_V	3.319	1.00
61_Q	69_R	3.273	1.00
30_H	66_Q	3.153	1.00
227_M	254_A	2.764	1.00
68_Y	72_S	2.758	1.00
72_S	76_H	2.715	1.00
47_D	51_E	2.652	1.00
55_Q	60_D	2.549	1.00
22_C	67_F	2.546	1.00
118_L	134_V	2.444	1.00
240_R	246_G	2.434	1.00
106_G	208_A	2.429	1.00
99_A	286_W	2.429	1.00
248_Y	252_C	2.392	1.00
291_A	295_T	2.375	1.00
230_Q	235_Y	2.241	1.00
236_I	254_A	2.213	1.00
35_D	54_R	2.195	1.00
131_D	224_R	2.148	1.00
23_V	67_F	2.136	1.00
230_Q	233_E	2.132	1.00
247_W	251_L	2.112	1.00
64_Y	68_Y	2.076	1.00
245_P	248_Y	2.037	1.00
267_G	323_V	2.022	1.00
92_E	292_W	2.009	1.00
88_P	91_E	2.008	1.00
110_L	212_A	1.936	1.00
5_S	9_Q	1.919	1.00
49_I	52_N	1.918	1.00
244_L	248_Y	1.916	1.00
50_V	54_R	1.909	1.00
113_L	117_P	1.888	1.00
231_L	254_A	1.839	1.00
85_T	92_E	1.826	1.00
164_L	202_Q	1.817	1.00
46_S	49_I	1.813	1.00
125_W	128_R	1.789	1.00
21_V	313_S	1.776	1.00
236_I	249_I	1.764	1.00
129_W	133_L	1.759	1.00
158_Y	166_G	1.751	1.00
52_N	56_Q	1.742	1.00
65_V	69_R	1.712	1.00
51_E	55_Q	1.708	1.00
234_D	237_R	1.706	1.00
87_R	91_E	1.686	1.00
164_L	205_I	1.667	1.00
90_L	94_R	1.663	1.00
89_V	307_G	1.655	1.00
51_E	54_R	1.640	1.00
120_I	227_M	1.639	1.00
69_R	72_S	1.632	1.00
123_A	227_M	1.619	1.00
130_L	134_V	1.606	1.00
121_L	130_L	1.579	1.00
73_D	78_D	1.572	1.00
263_I	330_I	1.567	1.00
114_I	117_P	1.537	1.00
230_Q	258_A	1.524	1.00
18_V	314_F	1.521	1.00
208_A	212_A	1.518	1.00
121_L	125_W	1.515	1.00
124_V	250_V	1.512	1.00
238_T	242_S	1.505	1.00
114_I	216_L	1.485	1.00
35_D	38_R	1.480	1.00
79_L	307_G	1.461	1.00
124_V	246_G	1.456	1.00
326_L	329_W	1.440	1.00
111_A	215_H	1.440	1.00
264_T	327_Y	1.437	1.00
219_V	269_A	1.435	1.00
293_V	308_F	1.434	1.00
235_Y	257_N	1.429	1.00
230_Q	254_A	1.417	1.00
14_L	317_V	1.413	1.00
296_S	304_A	1.412	1.00
102_E	106_G	1.406	1.00
200_A	203_H	1.398	1.00
74_L	79_L	1.373	1.00
148_W	152_G	1.368	1.00
112_L	266_L	1.365	1.00
230_Q	236_I	1.363	1.00
79_L	90_L	1.360	1.00
69_R	73_D	1.359	1.00
53_I	56_Q	1.355	1.00
87_R	95_I	1.351	1.00
125_W	130_L	1.347	1.00
155_V	160_H	1.343	1.00
19_A	23_V	1.332	1.00
19_A	67_F	1.317	1.00
75_F	78_D	1.301	1.00
99_A	102_E	1.296	1.00
65_V	68_Y	1.292	1.00
95_I	98_P	1.291	1.00
62_P	65_V	1.290	1.00
53_I	57_L	1.289	1.00
153_V	210_T	1.281	1.00
12_W	16_L	1.279	1.00
102_E	200_A	1.272	1.00
115_G	223_I	1.270	1.00
134_V	220_A	1.260	1.00
27_I	30_H	1.256	1.00
222_Q	265_V	1.243	1.00
115_G	219_V	1.241	1.00
119_G	123_A	1.232	1.00
108_L	266_L	1.229	1.00
141_G	217_G	1.218	1.00
242_S	253_Y	1.217	1.00
37_A	50_V	1.213	1.00
87_R	92_E	1.208	1.00
8_R	12_W	1.206	1.00
82_S	87_R	1.205	1.00
212_A	216_L	1.205	1.00
127_N	131_D	1.198	1.00
224_R	228_L	1.188	1.00
61_Q	64_Y	1.186	1.00
123_A	231_L	1.183	1.00
81_T	88_P	1.177	1.00
292_W	304_A	1.172	1.00
156_L	160_H	1.169	1.00
22_C	70_Y	1.163	1.00
227_M	258_A	1.160	1.00
199_N	203_H	1.159	1.00
271_G	316_Y	1.158	1.00
118_L	220_A	1.156	1.00
129_W	132_H	1.149	1.00
199_N	202_Q	1.147	1.00
122_S	134_V	1.145	1.00
23_V	27_I	1.141	1.00
144_T	149_L	1.138	1.00
58_G	61_Q	1.135	1.00
327_Y	331_D	1.132	1.00
4_W	7_L	1.126	1.00
138_A	220_A	1.125	1.00
92_E	304_A	1.115	1.00
119_G	223_I	1.112	1.00
25_T	97_F	1.112	1.00
205_I	209_L	1.108	1.00
260_I	327_Y	1.093	1.00
308_F	312_V	1.080	1.00
223_I	262_S	1.072	1.00
239_A	249_I	1.069	1.00
239_A	244_L	1.062	1.00
294_V	298_Q	1.051	1.00
38_R	50_V	1.050	1.00
325_L	329_W	1.050	1.00
120_I	250_V	1.047	1.00
91_E	95_I	1.040	1.00
58_G	69_R	1.037	1.00
210_T	214_V	1.033	1.00
319_V	323_V	1.023	1.00
20_G	24_I	1.022	1.00
201_L	205_I	1.020	1.00
52_N	55_Q	1.010	1.00
223_I	227_M	0.997	1.00
137_M	141_G	0.996	1.00
73_D	76_H	0.992	1.00
102_E	204_L	0.991	1.00
107_A	212_A	0.988	1.00
117_P	120_I	0.988	1.00
302_F	306_M	0.985	1.00
239_A	253_Y	0.972	1.00
248_Y	251_L	0.965	1.00
92_E	95_I	0.964	1.00
48_A	52_N	0.961	1.00
4_W	8_R	0.958	1.00
123_A	228_L	0.953	1.00
16_L	19_A	0.948	1.00
94_R	98_P	0.948	1.00
12_W	325_L	0.946	1.00
150_G	210_T	0.942	1.00
157_F	163_I	0.941	1.00
55_Q	61_Q	0.931	1.00
7_L	325_L	0.928	1.00
229_E	233_E	0.921	1.00
246_G	249_I	0.919	1.00
30_H	63_L	0.913	1.00
131_D	228_L	0.906	1.00
14_L	321_L	0.904	1.00
91_E	94_R	0.899	1.00
81_T	86_G	0.898	1.00
41_A	53_I	0.896	1.00
244_L	249_I	0.895	1.00
19_A	71_V	0.893	1.00
116_I	223_I	0.892	1.00
82_S	301_D	0.890	1.00
240_R	249_I	0.890	1.00
96_F	292_W	0.889	1.00
258_A	261_P	0.888	1.00
102_E	105_F	0.885	1.00
146_A	280_T	0.885	1.00
107_A	111_A	0.883	1.00
226_A	229_E	0.883	1.00
14_L	318_L	0.883	1.00
71_V	74_L	0.882	1.00
153_V	206_L	0.877	1.00
164_L	206_L	0.872	1.00
15_V	19_A	0.872	1.00
295_T	298_Q	0.872	1.00
133_L	137_M	0.871	1.00
135_R	220_A	0.865	1.00
18_V	317_V	0.865	1.00
209_L	212_A	0.861	1.00
270_L	319_V	0.859	1.00
107_A	211_L	0.856	1.00
72_S	75_F	0.853	1.00
204_L	208_A	0.849	1.00
112_L	117_P	0.847	1.00
160_H	163_I	0.845	1.00
216_L	220_A	0.845	1.00
295_T	299_A	0.842	1.00
322_V	326_L	0.841	1.00
110_L	208_A	0.839	1.00
11_C	321_L	0.839	1.00
127_N	132_H	0.838	1.00
263_I	323_V	0.838	1.00
93_L	307_G	0.838	1.00
27_I	63_L	0.836	1.00
226_A	230_Q	0.832	1.00
120_I	255_L	0.832	1.00
223_I	258_A	0.832	1.00
23_V	63_L	0.826	1.00
132_H	135_R	0.822	1.00
292_W	296_S	0.818	1.00
115_G	119_G	0.815	1.00
6_I	328_L	0.813	1.00
89_V	304_A	0.813	1.00
89_V	292_W	0.813	1.00
105_F	109_L	0.812	1.00
157_F	206_L	0.811	1.00
152_G	156_L	0.811	1.00
74_L	310_V	0.809	1.00
48_A	51_E	0.805	1.00
328_L	334_I	0.798	1.00
249_I	254_A	0.797	1.00
237_R	240_R	0.797	1.00
84_R	295_T	0.795	1.00
130_L	133_L	0.791	1.00
271_G	319_V	0.791	1.00
318_L	322_V	0.790	1.00
22_C	310_V	0.788	1.00
34_G	300_L	0.787	1.00
146_A	150_G	0.787	1.00
251_L	254_A	0.786	1.00
100_T	104_A	0.784	1.00
16_L	20_G	0.783	1.00
124_V	251_L	0.782	1.00
327_Y	334_I	0.780	1.00
106_G	286_W	0.775	1.00
47_D	50_V	0.774	1.00
116_I	262_S	0.768	1.00
108_L	270_L	0.766	1.00
119_G	227_M	0.765	1.00
126_R	130_L	0.763	1.00
98_P	102_E	0.762	1.00
68_Y	71_V	0.762	1.00
30_H	302_F	0.760	1.00
296_S	305_V	0.756	1.00
118_L	216_L	0.753	1.00
117_P	121_L	0.753	1.00
205_I	208_A	0.747	1.00
23_V	64_Y	0.740	1.00
70_Y	74_L	0.738	1.00
49_I	53_I	0.734	1.00
293_V	296_S	0.732	1.00
126_R	232_S	0.726	1.00
67_F	71_V	0.725	1.00
150_G	283_V	0.723	1.00
314_F	318_L	0.723	1.00
115_G	220_A	0.722	1.00
215_H	218_I	0.721	1.00
226_A	258_A	0.720	1.00
157_F	164_L	0.720	1.00
37_A	41_A	0.715	1.00
18_V	318_L	0.714	1.00
21_V	315_A	0.712	1.00
142_I	217_G	0.711	1.00
136_I	139_I	0.710	1.00
292_W	308_F	0.707	1.00
239_A	242_S	0.707	1.00
246_G	250_V	0.705	1.00
105_F	270_L	0.704	1.00
24_I	94_R	0.704	1.00
307_G	311_V	0.698	1.00
138_A	217_G	0.696	1.00
325_L	328_L	0.694	1.00
111_A	212_A	0.692	1.00
306_M	309_A	0.692	1.00
25_T	309_A	0.688	1.00
312_V	316_Y	0.684	1.00
149_L	213_F	0.682	1.00
122_S	131_D	0.682	1.00
101_L	105_F	0.681	1.00
79_L	93_L	0.679	1.00
94_R	97_F	0.678	1.00
77_G	88_P	0.676	1.00
112_L	219_V	0.676	1.00
45_A	50_V	0.673	1.00
7_L	13_G	0.673	1.00
114_I	212_A	0.673	1.00
328_L	335_G	0.672	1.00
37_A	53_I	0.670	1.00
93_L	308_F	0.668	1.00
277_A	280_T	0.668	1.00
244_L	253_Y	0.666	1.00
132_H	136_I	0.659	1.00
223_I	226_A	0.658	1.00
82_S	85_T	0.654	1.00
37_A	54_R	0.653	1.00
134_V	138_A	0.652	1.00
107_A	277_A	0.651	1.00
71_V	75_F	0.651	1.00
10_R	13_G	0.651	1.00
282_T	291_A	0.650	1.00
84_R	299_A	0.648	1.00
97_F	101_L	0.641	1.00
27_I	31_L	0.638	1.00
13_G	16_L	0.638	1.00
282_T	294_V	0.638	1.00
133_L	136_I	0.636	1.00
114_I	118_L	0.633	1.00
103_L	281_E	0.631	1.00
72_S	77_G	0.631	1.00
201_L	204_L	0.627	1.00
98_P	101_L	0.626	1.00
77_G	81_T	0.624	1.00
316_Y	320_N	0.619	1.00
218_I	265_V	0.619	1.00
106_G	201_L	0.618	1.00
294_V	297_I	0.617	1.00
155_V	159_G	0.612	1.00
237_R	241_A	0.611	1.00
41_A	45_A	0.610	1.00
17_V	318_L	0.610	1.00
165_P	203_H	0.609	1.00
247_W	250_V	0.609	1.00
206_L	209_L	0.607	1.00
113_L	116_I	0.607	1.00
218_I	269_A	0.607	1.00
9_Q	12_W	0.605	1.00
136_I	140_T	0.605	1.00
306_M	310_V	0.604	1.00
126_R	228_L	0.604	1.00
106_G	109_L	0.601	1.00
265_V	269_A	0.601	1.00
211_L	280_T	0.596	1.00
32_I	91_E	0.595	1.00
93_L	311_V	0.595	1.00
92_E	96_F	0.594	1.00
42_G	45_A	0.592	1.00
104_A	277_A	0.592	1.00
106_G	205_I	0.591	1.00
210_T	280_T	0.591	1.00
131_D	135_R	0.590	1.00
259_L	262_S	0.589	1.00
223_I	255_L	0.588	1.00
17_V	314_F	0.586	1.00
112_L	116_I	0.585	1.00
146_A	213_F	0.582	1.00
219_V	223_I	0.581	1.00
40_L	53_I	0.580	1.00
154_I	166_G	0.578	1.00
103_L	208_A	0.578	1.00
28_I	95_I	0.577	1.00
219_V	265_V	0.574	1.00
157_F	160_H	0.571	1.00
217_G	220_A	0.570	1.00
226_A	261_P	0.569	1.00
287_P	291_A	0.567	1.00
233_E	237_R	0.566	1.00
214_V	217_G	0.566	1.00
222_Q	226_A	0.565	1.00
206_L	210_T	0.563	1.00
100_T	277_A	0.561	1.00
282_T	295_T	0.560	1.00
109_L	113_L	0.559	1.00
96_F	291_A	0.558	1.00
158_Y	206_L	0.558	1.00
24_I	97_F	0.558	1.00
37_A	57_L	0.558	1.00
212_A	215_H	0.557	1.00
141_G	213_F	0.556	1.00
278_V	282_T	0.554	1.00
100_T	281_E	0.553	1.00
17_V	317_V	0.551	1.00
267_G	319_V	0.550	1.00
244_L	247_W	0.550	1.00
74_L	77_G	0.550	1.00
293_V	312_V	0.547	1.00
260_I	334_I	0.547	1.00
128_R	131_D	0.547	1.00
146_A	149_L	0.544	1.00
14_L	18_V	0.543	1.00
305_V	309_A	0.543	1.00
278_V	294_V	0.541	1.00
15_V	322_V	0.541	1.00
97_F	315_A	0.539	1.00
45_A	49_I	0.539	1.00
245_P	249_I	0.538	1.00
29_S	305_V	0.533	1.00
122_S	135_R	0.531	1.00
230_Q	257_N	0.529	1.00
6_I	321_L	0.528	1.00
218_I	222_Q	0.526	1.00
135_R	138_A	0.524	1.00
56_Q	86_G	0.524	1.00
106_G	110_L	0.523	1.00
6_I	322_V	0.521	1.00
215_H	269_A	0.519	1.00
263_I	326_L	0.519	1.00
200_A	286_W	0.519	1.00
65_V	72_S	0.518	1.00
26_F	30_H	0.518	1.00
63_L	66_Q	0.518	1.00
118_L	121_L	0.518	1.00
251_L	256_P	0.518	1.00
14_L	17_V	0.516	1.00
124_V	231_L	0.516	1.00
269_A	272_D	0.515	1.00
160_H	206_L	0.514	1.00
54_R	60_D	0.514	1.00
165_P	202_Q	0.513	1.00
227_M	231_L	0.512	1.00
146_A	214_V	0.511	1.00
236_I	240_R	0.511	1.00
153_V	209_L	0.510	1.00
323_V	327_Y	0.510	1.00
321_L	325_L	0.510	1.00
215_H	272_D	0.509	1.00
218_I	272_D	0.508	1.00
144_T	148_W	0.507	1.00
259_L	263_I	0.506	1.00
202_Q	205_I	0.505	1.00
78_D	90_L	0.503	1.00
125_W	246_G	0.503	1.00
225_S	228_L	0.502	1.00
213_F	216_L	0.501	1.00
51_E	60_D	0.501	1.00
104_A	108_L	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	0.6147	99.9	0.681	Contact Map
4tquM	1	0.7971	99.9	0.698	Contact Map
3rlfF	1	0.7912	99.9	0.707	Contact Map
4ymuD	2	0.6176	99.8	0.715	Contact Map
3d31C	2	0.7265	99.8	0.717	Contact Map
2onkC	2	0.7353	99.8	0.723	Contact Map
4tquN	1	0.7559	99.8	0.735	Contact Map
3rlfG	1	0.7765	99.8	0.74	Contact Map
2yevC	1	0.0941	12.4	0.963	Contact Map
4lz6A	1	0.25	9.5	0.964	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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