DDPC - ECOLI - GREMLIN Contacts

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DDPC - Probable D,D-dipeptide transport system permease protein DdpC

UniProt:	P77463	Sequences: MMLSEETSAVRPQKQTRFNGAKLVWMLKGSPLTVTSAVIIVLMLLMMIFSPWLATHDPNAIDLTARLLPPSAAHWFGTDEVGRDLFSRVLVGSQQSILAGLVVVAIAGMIGSLLGCLSGVLGGRADAIIMRIMDIMLSIPSLVLTMALAAALGPSLFNAMLAIAIVRIPFYVRLARGQALVVRQYTYVQAAKTFGASRWHLINWHILRNSLPPLIVQASLDIGSAILMAATLGFIGLGAQQPSAEWGAMVANGRNYVLDQWWYCAFPGAAILLTAVGFNLFGDGIRDLLDPKAGGKQS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13788
Length:	298 (255)
Sequences:	28622 (18059)
Seq/√Len:	1130.9

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
179_A	206_I	2.891	1.00
126_D	176_R	2.755	1.00
182_V	187_Y	2.508	1.00
196_A	200_H	2.506	1.00
192_K	198_R	2.492	1.00
200_H	204_W	2.448	1.00
102_V	160_M	2.445	1.00
114_L	129_I	2.415	1.00
106_I	164_A	2.379	1.00
182_V	185_Y	2.372	1.00
95_Q	234_F	2.345	1.00
197_S	200_H	2.310	1.00
199_W	203_N	2.282	1.00
62_D	65_A	2.268	1.00
186_T	189_Q	2.156	1.00
188_V	201_L	2.067	1.00
188_V	206_I	2.063	1.00
88_R	249_M	2.024	1.00
116_C	179_A	2.012	1.00
72_A	75_W	1.982	1.00
121_L	125_A	1.952	1.00
117_L	121_L	1.951	1.00
121_L	198_R	1.937	1.00
84_D	87_S	1.923	1.00
109_M	113_L	1.899	1.00
57_D	60_A	1.859	1.00
120_V	198_R	1.787	1.00
171_Y	221_D	1.773	1.00
79_D	83_R	1.772	1.00
119_G	179_A	1.767	1.00
239_A	252_N	1.759	1.00
187_Y	209_N	1.752	1.00
41_V	45_L	1.749	1.00
124_R	128_I	1.741	1.00
47_M	93_S	1.740	1.00
182_V	210_S	1.737	1.00
219_S	282_G	1.724	1.00
81_V	88_R	1.691	1.00
76_F	266_F	1.685	1.00
86_F	90_L	1.670	1.00
110_I	168_I	1.659	1.00
110_I	113_L	1.647	1.00
125_A	129_I	1.638	1.00
183_R	206_I	1.629	1.00
117_L	125_A	1.627	1.00
107_A	167_R	1.626	1.00
80_E	252_N	1.611	1.00
98_L	102_V	1.602	1.00
85_L	266_F	1.596	1.00
160_M	164_A	1.578	1.00
74_H	84_D	1.577	1.00
178_Q	181_V	1.575	1.00
91_V	94_Q	1.561	1.00
133_M	172_V	1.560	1.00
120_V	202_I	1.555	1.00
129_I	172_V	1.529	1.00
253_G	263_Y	1.527	1.00
108_G	218_A	1.514	1.00
83_R	87_S	1.487	1.00
33_T	284_G	1.479	1.00
181_V	185_Y	1.459	1.00
115_G	119_G	1.434	1.00
250_V	267_P	1.425	1.00
111_G	171_Y	1.422	1.00
115_G	175_A	1.390	1.00
131_R	134_D	1.388	1.00
36_S	277_G	1.385	1.00
49_F	52_W	1.378	1.00
190_A	194_F	1.378	1.00
104_V	218_A	1.375	1.00
124_R	127_A	1.360	1.00
114_L	172_V	1.345	1.00
143_V	147_A	1.341	1.00
89_V	270_A	1.330	1.00
95_Q	98_L	1.330	1.00
111_G	175_A	1.323	1.00
119_G	183_R	1.315	1.00
65_A	68_L	1.313	1.00
176_R	180_L	1.300	1.00
34_V	38_V	1.300	1.00
118_S	129_I	1.293	1.00
157_F	161_L	1.290	1.00
216_V	286_R	1.285	1.00
182_V	188_V	1.275	1.00
76_F	86_F	1.273	1.00
285_I	288_L	1.268	1.00
116_C	202_I	1.266	1.00
148_L	162_A	1.262	1.00
43_M	272_L	1.254	1.00
182_V	206_I	1.249	1.00
174_L	217_Q	1.245	1.00
45_L	49_F	1.243	1.00
261_W	265_A	1.239	1.00
191_A	205_H	1.235	1.00
256_Y	259_D	1.226	1.00
164_A	168_I	1.223	1.00
215_I	289_L	1.216	1.00
286_R	290_D	1.199	1.00
71_S	76_F	1.194	1.00
31_P	34_V	1.186	1.00
99_A	229_A	1.182	1.00
191_A	201_L	1.167	1.00
83_R	88_R	1.165	1.00
40_I	273_L	1.158	1.00
191_A	196_A	1.155	1.00
122_G	183_R	1.151	1.00
179_A	210_S	1.146	1.00
136_M	169_P	1.136	1.00
284_G	288_L	1.129	1.00
189_Q	192_K	1.120	1.00
116_C	207_L	1.116	1.00
83_R	91_V	1.110	1.00
127_A	131_R	1.105	1.00
175_A	214_L	1.096	1.00
76_F	89_V	1.091	1.00
267_P	271_I	1.088	1.00
112_S	175_A	1.085	1.00
175_A	179_A	1.078	1.00
168_I	172_V	1.075	1.00
200_H	203_N	1.072	1.00
162_A	166_V	1.069	1.00
194_F	205_H	1.062	1.00
178_Q	182_V	1.062	1.00
139_I	144_L	1.055	1.00
223_G	275_A	1.050	1.00
145_T	162_A	1.050	1.00
113_L	116_C	1.050	1.00
94_Q	98_L	1.046	1.00
155_S	158_N	1.046	1.00
78_T	84_D	1.040	1.00
157_F	160_M	1.027	1.00
36_S	284_G	1.026	1.00
50_S	91_V	1.024	1.00
54_A	87_S	1.016	1.00
85_L	249_M	1.013	1.00
132_I	136_M	1.011	1.00
103_V	164_A	1.006	1.00
253_G	264_C	1.004	1.00
40_I	277_G	1.002	1.00
126_D	130_M	0.998	1.00
192_K	201_L	0.997	1.00
130_M	172_V	0.996	1.00
43_M	274_T	0.991	1.00
85_L	263_Y	0.987	1.00
88_R	263_Y	0.980	1.00
249_M	263_Y	0.979	1.00
98_L	156_L	0.979	1.00
38_V	42_L	0.978	1.00
35_T	38_V	0.974	1.00
39_I	277_G	0.973	1.00
126_D	180_L	0.969	1.00
175_A	210_S	0.968	1.00
103_V	107_A	0.967	1.00
262_W	266_F	0.966	1.00
36_S	276_V	0.965	1.00
191_A	194_F	0.962	1.00
38_V	41_V	0.961	1.00
122_G	184_Q	0.961	1.00
266_F	269_A	0.957	1.00
128_I	132_I	0.947	1.00
89_V	266_F	0.939	1.00
103_V	163_I	0.936	1.00
196_A	201_L	0.935	1.00
217_Q	221_D	0.933	1.00
87_S	91_V	0.931	1.00
98_L	101_L	0.930	1.00
92_G	249_M	0.930	1.00
42_L	46_M	0.926	1.00
37_A	41_V	0.924	1.00
123_G	126_D	0.923	1.00
198_R	201_L	0.922	1.00
125_A	128_I	0.916	1.00
74_H	78_T	0.914	1.00
141_S	228_M	0.914	1.00
71_S	74_H	0.913	1.00
115_G	179_A	0.909	1.00
71_S	75_W	0.908	1.00
56_H	73_A	0.907	1.00
68_L	71_S	0.901	1.00
212_P	286_R	0.898	1.00
127_A	130_M	0.898	1.00
36_S	280_L	0.898	1.00
152_L	158_N	0.895	1.00
278_F	282_G	0.883	1.00
277_G	281_F	0.881	1.00
112_S	214_L	0.873	1.00
108_G	112_S	0.872	1.00
64_T	68_L	0.868	1.00
133_M	169_P	0.861	1.00
88_R	91_V	0.860	1.00
163_I	228_M	0.860	1.00
37_A	281_F	0.856	1.00
210_S	213_P	0.854	1.00
90_L	94_Q	0.852	1.00
39_I	273_L	0.852	1.00
222_I	278_F	0.848	1.00
123_G	127_A	0.842	1.00
203_N	206_I	0.842	1.00
249_M	267_P	0.836	1.00
109_M	112_S	0.834	1.00
78_T	82_G	0.834	1.00
161_L	164_A	0.833	1.00
56_H	87_S	0.831	1.00
46_M	90_L	0.830	1.00
156_L	160_M	0.830	1.00
108_G	113_L	0.826	1.00
198_R	202_I	0.821	1.00
215_I	282_G	0.816	1.00
154_P	158_N	0.814	1.00
103_V	225_A	0.812	1.00
87_S	90_L	0.807	1.00
153_G	158_N	0.803	1.00
179_A	183_R	0.800	1.00
148_L	158_N	0.795	1.00
33_T	280_L	0.795	1.00
113_L	117_L	0.793	1.00
177_G	180_L	0.790	1.00
141_S	145_T	0.790	1.00
93_S	274_T	0.788	1.00
251_A	254_R	0.782	1.00
265_A	269_A	0.782	1.00
185_Y	189_Q	0.779	1.00
196_A	205_H	0.777	1.00
114_L	168_I	0.776	1.00
102_V	234_F	0.775	1.00
56_H	74_H	0.772	1.00
52_W	261_W	0.772	1.00
33_T	37_A	0.770	1.00
182_V	209_N	0.770	1.00
119_G	180_L	0.767	1.00
101_L	105_A	0.764	1.00
108_G	171_Y	0.764	1.00
158_N	161_L	0.762	1.00
106_I	160_M	0.760	1.00
137_L	169_P	0.753	1.00
201_L	206_I	0.751	1.00
118_S	126_D	0.745	1.00
102_V	105_A	0.743	1.00
189_Q	193_T	0.743	1.00
230_A	239_A	0.741	1.00
266_F	270_A	0.736	1.00
96_S	100_G	0.736	1.00
79_D	260_Q	0.734	1.00
221_D	224_S	0.732	1.00
49_F	53_L	0.730	1.00
175_A	178_Q	0.729	1.00
287_D	293_A	0.729	1.00
286_R	293_A	0.720	1.00
46_M	93_S	0.718	1.00
178_Q	213_P	0.716	1.00
110_I	164_A	0.714	1.00
271_I	275_A	0.709	1.00
55_T	87_S	0.707	1.00
199_W	202_I	0.704	1.00
75_W	86_F	0.702	1.00
252_N	255_N	0.702	1.00
223_G	278_F	0.697	1.00
227_L	230_A	0.697	1.00
90_L	93_S	0.692	1.00
167_R	170_F	0.690	1.00
273_L	277_G	0.686	1.00
43_M	273_L	0.684	1.00
32_L	36_S	0.681	1.00
40_I	278_F	0.677	1.00
65_A	74_H	0.677	1.00
31_P	35_T	0.676	1.00
62_D	66_R	0.675	1.00
44_L	269_A	0.674	1.00
166_V	169_P	0.672	1.00
70_P	262_W	0.668	1.00
51_P	94_Q	0.667	1.00
275_A	279_N	0.666	1.00
178_Q	210_S	0.665	1.00
111_G	115_G	0.664	1.00
36_S	39_I	0.662	1.00
35_T	39_I	0.660	1.00
71_S	269_A	0.658	1.00
48_I	52_W	0.656	1.00
281_F	285_I	0.655	1.00
141_S	144_L	0.651	1.00
107_A	164_A	0.649	1.00
265_A	268_G	0.649	1.00
180_L	183_R	0.645	1.00
254_R	257_V	0.641	1.00
159_A	229_A	0.640	1.00
170_F	221_D	0.640	1.00
56_H	259_D	0.638	1.00
89_V	267_P	0.635	1.00
55_T	86_F	0.634	1.00
75_W	84_D	0.634	1.00
128_I	131_R	0.632	1.00
154_P	157_F	0.631	1.00
120_V	183_R	0.630	1.00
122_G	126_D	0.630	1.00
110_I	114_L	0.630	1.00
130_M	133_M	0.624	1.00
104_V	221_D	0.623	1.00
227_L	231_T	0.622	1.00
196_A	199_W	0.622	1.00
66_R	70_P	0.621	1.00
34_V	37_A	0.618	1.00
252_N	258_L	0.618	1.00
264_C	268_G	0.617	1.00
118_S	130_M	0.614	1.00
67_L	70_P	0.610	1.00
50_S	53_L	0.608	1.00
39_I	43_M	0.605	1.00
133_M	168_I	0.605	1.00
228_M	231_T	0.605	1.00
131_R	135_I	0.604	1.00
100_G	225_A	0.603	1.00
171_Y	175_A	0.602	1.00
64_T	67_L	0.601	1.00
63_L	66_R	0.599	1.00
219_S	223_G	0.598	1.00
80_E	256_Y	0.596	1.00
144_L	166_V	0.596	1.00
122_G	180_L	0.594	1.00
69_P	262_W	0.590	1.00
97_I	101_L	0.583	1.00
67_L	260_Q	0.582	1.00
229_A	233_G	0.581	1.00
129_I	133_M	0.580	1.00
226_I	230_A	0.579	1.00
47_M	268_G	0.576	1.00
147_A	151_A	0.575	1.00
119_G	126_D	0.575	1.00
105_A	109_M	0.575	1.00
203_N	208_R	0.572	1.00
94_Q	97_I	0.571	1.00
121_L	202_I	0.567	1.00
136_M	168_I	0.567	1.00
102_V	157_F	0.566	1.00
141_S	165_I	0.564	1.00
54_A	91_V	0.564	1.00
287_D	294_G	0.561	1.00
165_I	168_I	0.561	1.00
104_V	108_G	0.561	1.00
104_V	222_I	0.561	1.00
108_G	214_L	0.559	1.00
171_Y	217_Q	0.559	1.00
225_A	228_M	0.558	1.00
93_S	97_I	0.557	1.00
280_L	284_G	0.556	1.00
51_P	91_V	0.552	1.00
219_S	278_F	0.552	1.00
120_V	203_N	0.550	1.00
249_M	252_N	0.550	1.00
46_M	50_S	0.547	1.00
68_L	78_T	0.547	1.00
188_V	192_K	0.543	1.00
250_V	271_I	0.541	1.00
230_A	251_A	0.532	1.00
256_Y	263_Y	0.532	1.00
88_R	92_G	0.532	1.00
249_M	253_G	0.532	1.00
169_P	172_V	0.530	1.00
118_S	176_R	0.529	1.00
134_D	137_L	0.529	1.00
66_R	69_P	0.528	1.00
197_S	201_L	0.528	1.00
114_L	117_L	0.528	1.00
32_L	280_L	0.527	1.00
158_N	162_A	0.526	1.00
40_I	281_F	0.525	1.00
111_G	172_V	0.524	1.00
161_L	165_I	0.519	1.00
61_I	81_V	0.516	1.00
283_D	286_R	0.516	1.00
164_A	167_R	0.516	1.00
149_A	153_G	0.514	1.00
130_M	134_D	0.510	1.00
67_L	263_Y	0.510	1.00
100_G	222_I	0.509	1.00
216_V	219_S	0.507	1.00
217_Q	220_L	0.505	1.00
167_R	221_D	0.504	1.00
62_D	74_H	0.504	1.00
99_A	159_A	0.504	1.00
262_W	265_A	0.502	1.00
174_L	178_Q	0.502	1.00
251_A	255_N	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
4tquM	1	0.849	99.9	0.605	Contact Map
3d31C	2	0.7752	99.9	0.633	Contact Map
3tuiA	2	0.6779	99.9	0.641	Contact Map
2onkC	2	0.7953	99.9	0.644	Contact Map
3rlfF	1	0.9128	99.8	0.662	Contact Map
4tquN	1	0.8658	99.8	0.667	Contact Map
3rlfG	1	0.8658	99.8	0.672	Contact Map
4ymuD	2	0.7013	99.8	0.675	Contact Map
3j9pD	4	0.7752	88	0.92	Contact Map
3rvyA	3	0.6913	27.8	0.949	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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