DDPD - ECOLI - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

DDPD - Probable D,D-dipeptide transport ATP-binding protein DdpD

UniProt:	P77268	Sequences: MTQPVLDIQQLHLSFPGFNGDVHALNNVSLQINRGEIVGLVGESGSGKSVTAMLIMRLLPTGSYCVHRGQISLLGEDVLNAREKQLRQWRGARVAMIFQEPMTALNPTRRIGLQMMDVIRHHQPISRREARAKAIDLLEEMQIPDAVEVMSRYPFELSGGMRQRVMIALAFSCEPQLIIADEPTTALDVTVQLQVLRLLKHKARASGTAVLFISHDMAVVSQLCDSVYVMYAGSVIESGVTADVIHHPRHPYTIGLLQCAPEHGVPRQLLPAIPGTVPNLTHLPDGCAFRDRCYAAGAQCENVPALTACGDNNQRCACWYPQQEVISV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13787
Length:	328 (264)
Sequences:	54072 (33844)
Seq/√Len:	2082.9

ECOLI - DDPD OPPD PROV DPPD POTG FBPC CYSA METN MALK POTA DPPF SAPD YCJV OPPF UGPC YDCT YEHX DDPF MODC YADG GSIA MACB ARAG RBSA YHES SAPF UUP FEPC HISP MLAF MDLA NIKE YTFR MDLB CYDC TAUB CYDD FHUC MSBA FECE PHNK ALSA YECC YOJI PHNC LSRA YPHE SSUB GLNQ LIVG YHDZ XYLG LPTB LOLD GLTL SUFC LIVF ETTA MGLA BTUD ZNUC THIQ MODF ARTP PSTB FTSE NIKD YEJF FETA YBBA PHNL YDDA CCMA YNJD YBHF YBIT YHIH
BACSU - DPPD APPD OPUCA YVRA OPUAA OPUBA OPPD MSMX METN APPF YURJ OPPF YKFD YKPA TAGH YVFR YDBJ YHCH YFMM YFIL YXLF YHAQ YUSV YCBN YHEH RBSA ECFA1 YDIF YTRB YFMF FHUC TCYN SUNT YFIC SUFC YFIB YGAD BMRA YKNU YHEI YCLP YWJA YKNV BCEA YFMR YLMA YTLC YKOD YXDL ECFA2 CYDC YXEO CYDD YVCR ECSA GLNQ TCYC NATA ARTM SKFE YJKB MNTB PSTB1 SSUB FTSE YKNY YVRO YTHP ALBC PSTB2 YUFO EXPZ YCLH YHCG ZNUC YYBJ YTRE YYDI
HALSA - Q9HMX3 Q9HMW0 BTUDA Q9HMX2 Q9HHQ5 Q9HNZ9 Q9HR06 Q9HMT3 Q9HMG1 Q9HRJ6 Q9HSQ7 Q9HMU8 Q9HRH8 Q9HMG6 PHNC PSTB2 Q9HNY3 Q9HHM2 Q9HRZ9 Q9HRV7 Y1631 Y2317 PSTB1 Q9HR96 Q9HHR7 Q9HT03 Q9HR21 Q9HQA8 Q9HS04 Q9HMC1 Q9HMW1
SULSO - Q97UH3 Q97UF2 Q97YP3 Q97YP7 Q97VK8 Q97YY4 Q97UY8 Q97VF5 Q97YP8 Q97ZC0 Q97VF4 Q97VC1 Q7LX64 Q97VK9 Q97UJ9 Q97VH6 Q97YK2 Q97X18 Q97UD4 Y1893 Y2030 Q97YQ7 Q97U54 Q97Z03 Q980W0 Q97UH4 Q7LY07 PSTB Q97W42 Q97V00 Q97V01 Q7LXM4 Q97VM2 Q97VY4 Q7LX80 Q97UG5 Q97Z56 Q97YP4 Q97Z96 Q97UC2 Q97ZU0 Q980K5 Q980E6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_E	226_S	4.074	1.00
93_R	176_Q	3.412	1.00
10_Q	27_N	3.239	1.00
7_D	31_Q	3.129	1.00
9_Q	70_Q	3.057	1.00
23_H	26_N	2.826	1.00
13_L	54_L	2.805	1.00
38_V	228_Y	2.792	1.00
70_Q	77_D	2.525	1.00
39_G	224_C	2.465	1.00
240_V	243_D	2.457	1.00
33_N	36_E	2.378	1.00
140_E	206_S	2.374	1.00
74_L	176_Q	2.373	1.00
226_S	238_S	2.365	1.00
26_N	234_S	2.355	1.00
14_S	23_H	2.312	1.00
228_Y	235_V	2.305	1.00
149_V	152_R	2.296	1.00
7_D	72_S	2.295	1.00
201_H	205_A	2.215	1.00
8_I	11_L	2.150	1.00
126_S	129_E	2.142	1.00
12_H	68_R	2.112	1.00
12_H	27_N	2.072	1.00
133_K	136_D	2.067	1.00
34_R	176_Q	2.055	1.00
52_A	213_I	2.027	1.00
221_S	242_A	2.027	1.00
140_E	205_A	2.011	1.00
77_D	80_N	1.991	1.00
15_F	50_V	1.945	1.00
82_R	85_Q	1.935	1.00
133_K	174_E	1.912	1.00
137_L	172_S	1.887	1.00
239_G	244_V	1.875	1.00
9_Q	72_S	1.857	1.00
214_S	220_V	1.833	1.00
135_I	150_M	1.812	1.00
57_R	86_L	1.786	1.00
12_H	23_H	1.735	1.00
39_G	220_V	1.699	1.00
109_R	113_L	1.695	1.00
145_D	148_E	1.677	1.00
15_F	24_A	1.655	1.00
52_A	179_I	1.644	1.00
116_M	130_A	1.626	1.00
13_L	59_L	1.599	1.00
152_R	156_E	1.589	1.00
76_E	85_Q	1.565	1.00
228_Y	238_S	1.556	1.00
112_G	151_S	1.550	1.00
174_E	206_S	1.548	1.00
116_M	134_A	1.543	1.00
239_G	243_D	1.541	1.00
136_D	140_E	1.511	1.00
13_L	67_H	1.504	1.00
74_L	93_R	1.502	1.00
14_S	67_H	1.490	1.00
10_Q	29_S	1.489	1.00
8_I	30_L	1.485	1.00
112_G	150_M	1.477	1.00
16_P	21_D	1.475	1.00
200_K	222_Q	1.463	1.00
131_R	135_I	1.463	1.00
149_V	157_L	1.460	1.00
14_S	21_D	1.443	1.00
243_D	247_H	1.440	1.00
120_R	130_A	1.438	1.00
12_H	26_N	1.414	1.00
144_P	148_E	1.412	1.00
180_A	210_V	1.411	1.00
200_K	203_A	1.393	1.00
81_A	85_Q	1.385	1.00
11_L	66_V	1.379	1.00
115_M	138_L	1.366	1.00
37_I	203_A	1.344	1.00
140_E	201_H	1.314	1.00
196_L	219_V	1.310	1.00
97_I	180_A	1.272	1.00
36_E	225_D	1.269	1.00
9_Q	31_Q	1.268	1.00
110_R	113_L	1.268	1.00
102_M	162_R	1.266	1.00
112_G	116_M	1.246	1.00
32_I	38_V	1.241	1.00
144_P	149_V	1.238	1.00
8_I	55_I	1.232	1.00
135_I	145_D	1.221	1.00
148_E	152_R	1.221	1.00
112_G	131_R	1.213	1.00
37_I	210_V	1.202	1.00
30_L	51_T	1.193	1.00
9_Q	29_S	1.189	1.00
157_L	165_V	1.187	1.00
131_R	150_M	1.179	1.00
110_R	151_S	1.175	1.00
40_L	211_L	1.166	1.00
30_L	228_Y	1.162	1.00
199_L	210_V	1.158	1.00
114_Q	169_L	1.152	1.00
28_V	51_T	1.149	1.00
38_V	238_S	1.148	1.00
57_R	65_C	1.147	1.00
113_L	116_M	1.146	1.00
56_M	96_M	1.137	1.00
72_S	77_D	1.136	1.00
254_I	258_Q	1.133	1.00
132_A	136_D	1.124	1.00
76_E	81_A	1.124	1.00
251_P	254_I	1.121	1.00
54_L	66_V	1.108	1.00
38_V	226_S	1.107	1.00
242_A	246_H	1.104	1.00
33_N	226_S	1.099	1.00
108_T	155_F	1.093	1.00
138_L	150_M	1.090	1.00
34_R	74_L	1.079	1.00
37_I	224_C	1.074	1.00
81_A	86_L	1.070	1.00
128_R	132_A	1.060	1.00
112_G	134_A	1.057	1.00
133_K	137_L	1.043	1.00
145_D	149_V	1.027	1.00
203_A	225_D	1.016	1.00
34_R	207_G	1.012	1.00
115_M	172_S	1.011	1.00
187_L	195_V	1.011	1.00
129_E	132_A	1.008	1.00
227_V	241_T	1.002	1.00
142_Q	201_H	0.993	1.00
130_A	134_A	0.991	1.00
178_I	208_T	0.988	1.00
136_D	139_E	0.985	1.00
55_I	211_L	0.984	1.00
125_I	129_E	0.978	1.00
203_A	210_V	0.969	1.00
51_T	230_M	0.966	1.00
109_R	117_D	0.960	1.00
212_F	223_L	0.955	1.00
243_D	246_H	0.954	1.00
14_S	26_N	0.953	1.00
25_L	54_L	0.953	1.00
32_I	177_L	0.951	1.00
10_Q	68_R	0.950	1.00
178_I	210_V	0.946	1.00
139_E	144_P	0.943	1.00
174_E	208_T	0.942	1.00
119_I	172_S	0.937	1.00
116_M	131_R	0.933	1.00
116_M	120_R	0.913	1.00
53_M	58_L	0.910	1.00
135_I	139_E	0.909	1.00
137_L	140_E	0.908	1.00
33_N	209_A	0.907	1.00
5_V	74_L	0.906	1.00
125_I	130_A	0.900	1.00
40_L	51_T	0.900	1.00
8_I	71_I	0.897	1.00
13_L	50_V	0.892	1.00
139_E	145_D	0.884	1.00
95_A	170_A	0.882	1.00
111_I	157_L	0.878	1.00
262_E	265_V	0.871	1.00
105_L	162_R	0.871	1.00
192_Q	219_V	0.868	1.00
143_I	149_V	0.863	1.00
24_A	50_V	0.861	1.00
280_L	283_L	0.859	1.00
40_L	228_Y	0.859	1.00
192_Q	216_D	0.856	1.00
46_S	230_M	0.850	1.00
16_P	20_G	0.848	1.00
200_K	223_L	0.845	1.00
53_M	59_L	0.844	1.00
11_L	54_L	0.842	1.00
94_V	177_L	0.842	1.00
153_Y	156_E	0.840	1.00
110_R	153_Y	0.838	1.00
5_V	73_L	0.838	1.00
97_I	167_I	0.836	1.00
180_A	199_L	0.835	1.00
111_I	165_V	0.831	1.00
95_A	175_P	0.831	1.00
123_Q	133_K	0.829	1.00
56_M	179_I	0.828	1.00
250_H	253_T	0.827	1.00
54_L	71_I	0.826	1.00
202_K	208_T	0.826	1.00
251_P	255_G	0.824	1.00
137_L	168_A	0.818	1.00
219_V	223_L	0.815	1.00
73_L	93_R	0.814	1.00
255_G	259_C	0.813	1.00
37_I	200_K	0.813	1.00
76_E	93_R	0.813	1.00
244_V	253_T	0.813	1.00
13_L	25_L	0.809	1.00
54_L	59_L	0.807	1.00
41_V	220_V	0.804	1.00
245_I	248_P	0.801	1.00
83_E	86_L	0.799	1.00
6_L	55_I	0.798	1.00
127_R	130_A	0.790	1.00
197_R	222_Q	0.790	1.00
198_L	201_H	0.788	1.00
109_R	114_Q	0.784	1.00
118_V	173_C	0.781	1.00
134_A	150_M	0.779	1.00
77_D	81_A	0.778	1.00
142_Q	194_Q	0.777	1.00
92_A	123_Q	0.775	1.00
84_K	87_R	0.774	1.00
126_S	130_A	0.771	1.00
157_L	161_M	0.770	1.00
241_T	245_I	0.768	1.00
224_C	227_V	0.759	1.00
131_R	151_S	0.759	1.00
118_V	169_L	0.758	1.00
255_G	258_Q	0.757	1.00
235_V	238_S	0.756	1.00
25_L	28_V	0.752	1.00
177_L	211_L	0.751	1.00
10_Q	13_L	0.749	1.00
32_I	209_A	0.748	1.00
278_P	284_P	0.745	1.00
27_N	234_S	0.743	1.00
258_Q	271_P	0.740	1.00
141_M	168_A	0.738	1.00
132_A	135_I	0.738	1.00
259_C	262_E	0.732	1.00
122_H	173_C	0.732	1.00
179_I	211_L	0.731	1.00
37_I	223_L	0.730	1.00
196_L	222_Q	0.727	1.00
145_D	150_M	0.726	1.00
123_Q	126_S	0.726	1.00
277_V	280_L	0.724	1.00
28_V	235_V	0.721	1.00
280_L	284_P	0.720	1.00
120_R	127_R	0.719	1.00
137_L	171_F	0.717	1.00
193_L	197_R	0.716	1.00
182_E	215_H	0.716	1.00
212_F	224_C	0.712	1.00
279_N	283_L	0.710	1.00
217_M	245_I	0.708	1.00
154_P	165_V	0.707	1.00
224_C	241_T	0.703	1.00
149_V	161_M	0.703	1.00
279_N	282_H	0.701	1.00
279_N	284_P	0.700	1.00
231_Y	234_S	0.700	1.00
15_F	59_L	0.698	1.00
106_N	109_R	0.695	1.00
59_L	65_C	0.695	1.00
37_I	225_D	0.691	1.00
197_R	200_K	0.688	1.00
184_T	219_V	0.687	1.00
253_T	257_L	0.685	1.00
275_G	278_P	0.684	1.00
97_I	170_A	0.684	1.00
25_L	51_T	0.681	1.00
229_V	248_P	0.679	1.00
131_R	134_A	0.679	1.00
177_L	209_A	0.677	1.00
272_A	276_T	0.677	1.00
115_M	134_A	0.677	1.00
105_L	165_V	0.674	1.00
231_Y	255_G	0.674	1.00
41_V	229_V	0.673	1.00
105_L	114_Q	0.669	1.00
112_G	135_I	0.666	1.00
271_P	275_G	0.664	1.00
38_V	211_L	0.659	1.00
197_R	201_H	0.657	1.00
66_V	79_L	0.651	1.00
58_L	98_F	0.646	1.00
110_R	114_Q	0.645	1.00
236_I	250_H	0.645	1.00
123_Q	130_A	0.645	1.00
273_I	277_V	0.644	1.00
27_N	68_R	0.644	1.00
70_Q	79_L	0.643	1.00
53_M	96_M	0.640	1.00
49_S	53_M	0.640	1.00
32_I	211_L	0.640	1.00
129_E	133_K	0.639	1.00
274_P	277_V	0.637	1.00
247_H	250_H	0.635	1.00
270_L	273_I	0.633	1.00
54_L	67_H	0.632	1.00
73_L	78_V	0.630	1.00
202_K	206_S	0.629	1.00
14_S	68_R	0.626	1.00
276_T	279_N	0.623	1.00
174_E	205_A	0.623	1.00
8_I	51_T	0.621	1.00
114_Q	154_P	0.620	1.00
5_V	177_L	0.620	1.00
56_M	94_V	0.618	1.00
78_V	94_V	0.616	1.00
72_S	75_G	0.616	1.00
281_T	284_P	0.614	1.00
70_Q	80_N	0.614	1.00
275_G	279_N	0.612	1.00
43_E	231_Y	0.611	1.00
34_R	209_A	0.611	1.00
55_I	71_I	0.609	1.00
73_L	177_L	0.608	1.00
143_I	161_M	0.607	1.00
229_V	244_V	0.606	1.00
220_V	227_V	0.605	1.00
132_A	139_E	0.605	1.00
277_V	281_T	0.603	1.00
82_R	86_L	0.602	1.00
167_I	195_V	0.602	1.00
142_Q	149_V	0.599	1.00
231_Y	236_I	0.599	1.00
152_R	157_L	0.597	1.00
277_V	284_P	0.597	1.00
6_L	177_L	0.594	1.00
10_Q	69_G	0.594	1.00
275_G	280_L	0.593	1.00
127_R	131_R	0.592	1.00
273_I	276_T	0.589	1.00
43_E	46_S	0.587	1.00
112_G	115_M	0.585	1.00
278_P	281_T	0.583	1.00
282_H	285_D	0.582	1.00
171_F	208_T	0.573	1.00
115_M	118_V	0.572	1.00
78_V	81_A	0.569	1.00
203_A	206_S	0.569	1.00
31_Q	238_S	0.568	1.00
83_E	87_R	0.568	1.00
36_E	238_S	0.567	1.00
243_D	249_R	0.567	1.00
116_M	150_M	0.566	1.00
6_L	73_L	0.566	1.00
134_A	137_L	0.565	1.00
241_T	252_Y	0.562	1.00
268_Q	271_P	0.561	1.00
260_A	264_G	0.558	1.00
13_L	66_V	0.557	1.00
163_Q	186_A	0.556	1.00
43_E	252_Y	0.553	1.00
35_G	209_A	0.553	1.00
119_I	125_I	0.552	1.00
280_L	285_D	0.552	1.00
184_T	195_V	0.550	1.00
159_G	164_R	0.548	1.00
252_Y	255_G	0.548	1.00
119_I	124_P	0.547	1.00
99_Q	159_G	0.547	1.00
244_V	248_P	0.547	1.00
231_Y	250_H	0.546	1.00
5_V	209_A	0.546	1.00
71_I	79_L	0.544	1.00
272_A	277_V	0.544	1.00
220_V	224_C	0.544	1.00
44_S	182_E	0.543	1.00
138_L	149_V	0.541	1.00
252_Y	256_L	0.541	1.00
237_E	248_P	0.540	1.00
276_T	280_L	0.539	1.00
105_L	166_M	0.539	1.00
133_K	140_E	0.538	1.00
59_L	66_V	0.535	1.00
221_S	241_T	0.534	1.00
232_A	280_L	0.534	1.00
239_G	248_P	0.533	1.00
100_E	162_R	0.526	1.00
158_S	161_M	0.526	1.00
119_I	123_Q	0.525	1.00
16_P	65_C	0.523	1.00
125_I	133_K	0.522	1.00
196_L	223_L	0.521	1.00
137_L	141_M	0.519	1.00
281_T	285_D	0.518	1.00
14_S	24_A	0.515	1.00
239_G	245_I	0.512	1.00
123_Q	127_R	0.512	1.00
275_G	284_P	0.511	1.00
269_L	272_A	0.511	1.00
241_T	244_V	0.509	1.00
23_H	27_N	0.509	1.00
220_V	241_T	0.508	1.00
123_Q	174_E	0.508	1.00
254_I	257_L	0.507	1.00
278_P	283_L	0.505	1.00
124_P	130_A	0.504	1.00
228_Y	236_I	0.504	1.00
111_I	115_M	0.502	1.00
273_I	280_L	0.501	1.00
119_I	173_C	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
4fwiB	1	0.9268	100	0.207	Contact Map
3tuiC	2	0.9299	100	0.208	Contact Map
1oxxK	1	0.9482	100	0.234	Contact Map
1g291	4	0.9024	100	0.235	Contact Map
1v43A	2	0.8963	100	0.236	Contact Map
2it1A	1	0.8537	100	0.236	Contact Map
2yyzA	1	0.9238	100	0.236	Contact Map
4mkiB	2	0.8598	100	0.238	Contact Map
1b0uA	2	0.753	100	0.238	Contact Map
3rlfA	2	0.9268	100	0.239	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.

Page generated in 0.0123 seconds.