DDPF - ECOLI - GREMLIN Contacts

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DDPF - Probable D,D-dipeptide transport ATP-binding protein DdpF

UniProt:	P77622	Sequences: MSDTLLTLRDVHINFPARKNWLGKTTEHVHAINGIDLQIRRGETLGIVGESGCGKSTLAQLLMGMLQPSHGQYIRSGSQRIMQMVFQDPLSSLNPRLPVWRIITEPLWIAKRSSEQQRRALAEELAVQVGIRPEYLDRLPHAFSGGQRQRIAIARALSSQPDVIVLDEPTSALDISVQAQILNLLVTLQENHGLTYVLISHNVSVIRHMSDRVAVMYLGQIVELGDAQQVLTAPAHPYTRLLLDSLPAIDKPLEEEWALRKTDLPGNRTLPQGCFFYERCPLATHGCEVRQSLAIREDGRELRCWRAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13786
Length:	308 (238)
Sequences:	63408 (38660)
Seq/√Len:	2506.0

ECOLI - DDPF OPPF DPPF CYSA PROV FBPC SAPD POTG OPPD MALK POTA DDPD YCJV DPPD UGPC YDCT METN MODC YEHX YADG GSIA ARAG YHES UUP RBSA MDLA MACB SAPF FEPC NIKE MDLB CYDC MLAF MSBA TAUB CYDD YTFR HISP YOJI YECC FECE PHNC ETTA SSUB GLNQ FHUC PHNK YHDZ ZNUC LSRA LPTB GLTL YPHE NIKD LIVG SUFC ARTP THIQ XYLG PSTB LIVF MODF ALSA LOLD FTSE BTUD MGLA FETA YDDA YBBA YEJF PHNL CCMA YNJD YBHF YBIT YHIH
BACSU - APPF OPUCA OPUBA OPPD YVRA OPUAA DPPD MSMX YURJ APPD YKFD METN TAGH YHCH YXLF OPPF YFIL YCBN YDBJ YKPA YHAQ YVFR YHEH YFMM YDIF ECFA1 YFIB YFIC YGAD YKNU YUSV YTRB YFMR BMRA SUNT RBSA YFMF YHEI YKNV CYDD YWJA FHUC ECFA2 TCYN YXDL YCLP YTLC SSUB CYDC YLMA ECSA SUFC BCEA NATA YXEO SKFE YTHP YVCR MNTB TCYC GLNQ ARTM YKOD YJKB FTSE PSTB1 YVRO ALBC EXPZ PSTB2 YKNY YCLH YHCG ZNUC YUFO YTRE YYBJ YYDI
HALSA - Q9HMX3 Q9HMW0 Q9HHQ5 BTUDA Q9HMX2 Q9HMT3 Q9HNZ9 Q9HR06 Q9HMG1 Q9HRJ6 Q9HMU8 Q9HSQ7 Q9HRH8 PSTB2 PHNC Q9HHM2 Q9HMG6 Q9HNY3 Q9HRV7 Q9HRZ9 Y2317 Y1631 PSTB1 Q9HR96 Q9HHR7 Q9HS04 Q9HQA8 Q9HT03 Q9HR21 Q9HMC1 Q9HMW1
SULSO - Q97YP7 Q97UF2 Q97VK8 Q97YP3 Q97VF5 Q97UY8 Q97YY4 Q97UH3 Q97YP8 Q97VC1 Q97VF4 Q97ZC0 Q7LX64 Q97VK9 Q97UJ9 Q97VH6 Q97YK2 Q97UD4 Q97X18 Q97YQ7 Q97U54 Y1893 Q97Z03 Q980W0 Q97UH4 Y2030 Q97W42 PSTB Q7LY07 Q97VY4 Q97V01 Q97V00 Q7LXM4 Q97VM2 Q7LX80 Q97Z56 Q97UG5 Q97YP4 Q97UC2 Q97Z96 Q980K5 Q97ZU0 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
43_E	212_R	4.135	1.00
81_I	162_D	3.383	1.00
30_H	33_N	3.165	1.00
212_R	224_L	3.040	1.00
45_L	214_A	2.954	1.00
40_R	43_E	2.927	1.00
46_G	210_S	2.681	1.00
72_Q	79_Q	2.673	1.00
226_D	229_Q	2.635	1.00
97_L	101_R	2.525	1.00
123_E	133_P	2.473	1.00
76_S	162_D	2.412	1.00
135_Y	138_R	2.408	1.00
214_A	221_I	2.354	1.00
128_Q	192_H	2.317	1.00
33_N	220_Q	2.220	1.00
207_R	228_Q	2.130	1.00
214_A	224_L	2.085	1.00
114_S	117_Q	2.071	1.00
59_A	165_V	2.041	1.00
225_G	229_Q	1.946	1.00
41_R	162_D	1.905	1.00
59_A	199_I	1.889	1.00
123_E	136_L	1.819	1.00
100_W	104_T	1.817	1.00
17_A	20_N	1.795	1.00
20_N	24_K	1.776	1.00
18_R	72_Q	1.773	1.00
186_V	208_H	1.747	1.00
225_G	230_V	1.739	1.00
123_E	127_V	1.712	1.00
121_L	124_E	1.683	1.00
188_L	194_L	1.677	1.00
227_A	238_Y	1.667	1.00
138_R	142_A	1.667	1.00
125_L	158_S	1.655	1.00
121_L	160_Q	1.652	1.00
21_W	34_G	1.645	1.00
37_L	214_A	1.639	1.00
124_E	128_Q	1.625	1.00
46_G	206_I	1.606	1.00
200_S	206_I	1.598	1.00
98_P	101_R	1.581	1.00
100_W	137_D	1.534	1.00
229_Q	233_A	1.529	1.00
160_Q	194_L	1.528	1.00
100_W	136_L	1.522	1.00
39_I	45_L	1.516	1.00
239_T	243_L	1.510	1.00
18_R	74_I	1.493	1.00
234_P	239_T	1.479	1.00
76_S	81_I	1.463	1.00
37_L	58_L	1.453	1.00
22_L	26_T	1.410	1.00
45_L	212_R	1.397	1.00
64_G	67_Q	1.392	1.00
116_Q	120_A	1.374	1.00
223_E	233_A	1.368	1.00
43_E	211_D	1.365	1.00
44_T	210_S	1.364	1.00
104_T	118_R	1.353	1.00
119_R	123_E	1.351	1.00
63_M	84_M	1.333	1.00
44_T	189_Q	1.315	1.00
217_Y	222_V	1.300	1.00
135_Y	143_F	1.294	1.00
166_L	196_Y	1.284	1.00
160_Q	192_H	1.284	1.00
83_Q	161_P	1.278	1.00
114_S	118_R	1.271	1.00
122_A	125_L	1.268	1.00
44_T	196_Y	1.268	1.00
237_P	240_R	1.265	1.00
23_G	30_H	1.249	1.00
104_T	122_A	1.247	1.00
35_I	58_L	1.246	1.00
40_R	212_R	1.244	1.00
96_R	141_H	1.244	1.00
240_R	244_D	1.223	1.00
126_A	136_L	1.214	1.00
108_W	118_R	1.207	1.00
61_L	68_P	1.204	1.00
74_I	79_Q	1.204	1.00
90_L	148_R	1.199	1.00
45_L	224_L	1.187	1.00
103_I	126_A	1.185	1.00
66_L	69_S	1.183	1.00
127_V	133_P	1.159	1.00
182_L	205_V	1.155	1.00
189_Q	196_Y	1.149	1.00
21_W	30_H	1.148	1.00
85_V	166_L	1.145	1.00
173_L	181_I	1.143	1.00
83_Q	156_A	1.137	1.00
101_R	104_T	1.135	1.00
223_E	234_P	1.127	1.00
124_E	127_V	1.118	1.00
20_N	26_T	1.106	1.00
228_Q	232_T	1.105	1.00
98_P	137_D	1.100	1.00
41_R	76_S	1.094	1.00
102_I	155_R	1.093	1.00
229_Q	232_T	1.092	1.00
143_F	151_I	1.092	1.00
58_L	216_M	1.089	1.00
237_P	241_L	1.083	1.00
44_T	198_L	1.077	1.00
21_W	24_K	1.071	1.00
21_W	70_H	1.069	1.00
117_Q	120_A	1.066	1.00
132_R	135_Y	1.065	1.00
47_I	214_A	1.064	1.00
115_E	118_R	1.063	1.00
127_V	132_R	1.062	1.00
60_Q	65_M	1.052	1.00
32_I	61_L	1.049	1.00
120_A	124_E	1.045	1.00
39_I	197_V	1.034	1.00
103_I	158_S	1.028	1.00
213_V	227_A	1.026	1.00
113_S	118_R	1.024	1.00
178_Q	202_N	1.023	1.00
119_R	136_L	1.021	1.00
60_Q	66_L	1.021	1.00
47_I	197_V	1.014	1.00
47_I	58_L	1.010	1.00
99_V	143_F	1.000	1.00
100_W	112_R	1.000	1.00
107_L	111_K	0.999	1.00
164_I	194_L	0.997	1.00
134_E	138_R	0.997	1.00
104_T	108_W	0.996	1.00
107_L	158_S	0.995	1.00
61_L	66_L	0.983	1.00
25_T	28_H	0.978	1.00
107_L	110_A	0.976	1.00
186_V	189_Q	0.976	1.00
179_A	183_N	0.975	1.00
21_W	26_T	0.973	1.00
168_E	201_H	0.971	1.00
164_I	196_Y	0.961	1.00
117_Q	121_L	0.955	1.00
223_E	235_A	0.955	1.00
62_L	197_V	0.949	1.00
115_E	119_R	0.948	1.00
182_L	208_H	0.946	1.00
185_L	196_Y	0.942	1.00
41_R	193_G	0.938	1.00
53_C	216_M	0.936	1.00
113_S	117_Q	0.936	1.00
114_S	123_E	0.935	1.00
100_W	119_R	0.935	1.00
32_I	35_I	0.916	1.00
248_A	251_K	0.916	1.00
85_V	153_I	0.900	1.00
129_V	154_A	0.896	1.00
93_L	148_R	0.889	1.00
40_R	195_T	0.889	1.00
50_E	217_Y	0.888	1.00
97_L	102_I	0.884	1.00
97_L	105_E	0.883	1.00
85_V	156_A	0.877	1.00
24_K	57_T	0.872	1.00
227_A	231_L	0.872	1.00
100_W	122_A	0.870	1.00
178_Q	205_V	0.869	1.00
166_L	185_L	0.865	1.00
61_L	69_S	0.864	1.00
106_P	109_I	0.864	1.00
44_T	186_V	0.863	1.00
63_M	165_V	0.861	1.00
48_V	206_I	0.860	1.00
165_V	197_V	0.859	1.00
184_L	187_T	0.854	1.00
139_L	142_A	0.851	1.00
39_I	195_T	0.850	1.00
118_R	123_E	0.849	1.00
99_V	151_I	0.847	1.00
125_L	154_A	0.847	1.00
198_L	210_S	0.846	1.00
223_E	230_V	0.835	1.00
183_N	186_V	0.834	1.00
163_V	195_T	0.834	1.00
186_V	209_M	0.831	1.00
246_L	249_I	0.817	1.00
250_D	253_L	0.814	1.00
125_L	128_Q	0.812	1.00
140_P	151_I	0.812	1.00
236_H	239_T	0.811	1.00
24_K	27_E	0.807	1.00
39_I	163_V	0.806	1.00
45_L	197_V	0.804	1.00
215_V	234_P	0.802	1.00
94_N	97_L	0.798	1.00
104_T	119_R	0.792	1.00
34_G	220_Q	0.791	1.00
222_V	237_P	0.790	1.00
121_L	125_L	0.789	1.00
217_Y	220_Q	0.786	1.00
198_L	209_M	0.785	1.00
217_Y	241_L	0.778	1.00
230_V	239_T	0.777	1.00
61_L	73_Y	0.774	1.00
31_A	57_T	0.771	1.00
24_K	69_S	0.770	1.00
20_N	72_Q	0.770	1.00
210_S	213_V	0.770	1.00
244_D	258_A	0.765	1.00
145_G	150_R	0.761	1.00
256_E	259_L	0.759	1.00
221_I	224_L	0.759	1.00
98_P	102_I	0.757	1.00
116_Q	119_R	0.757	1.00
110_A	159_S	0.754	1.00
130_G	187_T	0.750	1.00
222_V	236_H	0.750	1.00
246_L	250_D	0.750	1.00
98_P	139_L	0.749	1.00
102_I	140_P	0.748	1.00
183_N	187_T	0.744	1.00
128_Q	187_T	0.742	1.00
82_M	163_V	0.742	1.00
35_I	221_I	0.740	1.00
48_V	215_V	0.735	1.00
205_V	209_M	0.732	1.00
189_Q	211_D	0.732	1.00
118_R	122_A	0.729	1.00
231_L	234_P	0.728	1.00
78_S	81_I	0.726	1.00
241_L	245_S	0.720	1.00
93_L	102_I	0.720	1.00
105_E	109_I	0.716	1.00
44_T	209_M	0.709	1.00
24_K	61_L	0.709	1.00
130_G	180_Q	0.706	1.00
215_V	230_V	0.701	1.00
117_Q	133_P	0.700	1.00
143_F	147_Q	0.693	1.00
131_I	135_Y	0.692	1.00
245_S	248_A	0.690	1.00
56_S	60_Q	0.690	1.00
242_L	246_L	0.690	1.00
23_G	69_S	0.689	1.00
104_T	112_R	0.688	1.00
75_R	81_I	0.685	1.00
240_R	243_L	0.678	1.00
63_M	82_M	0.678	1.00
106_P	159_S	0.677	1.00
203_V	231_L	0.675	1.00
170_T	205_V	0.674	1.00
51_S	177_V	0.673	1.00
217_Y	237_P	0.668	1.00
106_P	155_R	0.667	1.00
233_A	237_P	0.665	1.00
241_L	244_D	0.664	1.00
60_Q	84_M	0.658	1.00
17_A	37_L	0.658	1.00
30_H	34_G	0.655	1.00
251_K	254_E	0.655	1.00
230_V	234_P	0.654	1.00
111_K	121_L	0.654	1.00
135_Y	147_Q	0.651	1.00
25_T	30_H	0.650	1.00
170_T	181_I	0.650	1.00
180_Q	183_N	0.649	1.00
23_G	26_T	0.645	1.00
87_Q	145_G	0.643	1.00
130_G	133_P	0.641	1.00
104_T	107_L	0.640	1.00
65_M	86_F	0.637	1.00
134_E	137_D	0.635	1.00
119_R	122_A	0.634	1.00
243_L	247_P	0.633	1.00
125_L	129_V	0.632	1.00
122_A	136_L	0.630	1.00
75_R	163_V	0.630	1.00
32_I	58_L	0.630	1.00
119_R	137_D	0.628	1.00
163_V	197_V	0.627	1.00
210_S	227_A	0.627	1.00
59_A	63_M	0.625	1.00
200_S	205_V	0.625	1.00
22_L	57_T	0.617	1.00
44_T	211_D	0.617	1.00
207_R	227_A	0.617	1.00
50_E	53_C	0.611	1.00
125_L	157_L	0.607	1.00
85_V	149_Q	0.606	1.00
103_I	117_Q	0.605	1.00
206_I	210_S	0.603	1.00
108_W	115_E	0.599	1.00
223_E	239_T	0.598	1.00
62_L	73_Y	0.597	1.00
238_Y	241_L	0.596	1.00
38_Q	224_L	0.596	1.00
207_R	231_L	0.596	1.00
23_G	28_H	0.595	1.00
234_P	243_L	0.595	1.00
17_A	27_E	0.592	1.00
51_S	168_E	0.592	1.00
17_A	62_L	0.580	1.00
162_D	194_L	0.578	1.00
189_Q	194_L	0.567	1.00
216_M	221_I	0.565	1.00
100_W	103_I	0.565	1.00
189_Q	192_H	0.562	1.00
183_N	208_H	0.562	1.00
117_Q	126_A	0.561	1.00
34_G	70_H	0.559	1.00
68_P	73_Y	0.559	1.00
252_P	256_E	0.558	1.00
51_S	173_L	0.558	1.00
144_S	147_Q	0.558	1.00
107_L	113_S	0.556	1.00
23_G	70_H	0.555	1.00
244_D	247_P	0.554	1.00
80_R	159_S	0.553	1.00
233_A	236_H	0.551	1.00
103_I	122_A	0.549	1.00
43_E	224_L	0.548	1.00
42_G	195_T	0.547	1.00
120_A	123_E	0.546	1.00
80_R	111_K	0.544	1.00
238_Y	242_L	0.542	1.00
93_L	151_I	0.542	1.00
153_I	181_I	0.540	1.00
113_S	121_L	0.537	1.00
202_N	205_V	0.533	1.00
26_T	31_A	0.532	1.00
120_A	127_V	0.530	1.00
231_L	242_L	0.529	1.00
235_A	240_R	0.529	1.00
131_I	134_E	0.528	1.00
121_L	128_Q	0.526	1.00
20_N	23_G	0.521	1.00
137_D	140_P	0.520	1.00
104_T	113_S	0.520	1.00
30_H	70_H	0.520	1.00
175_I	179_A	0.516	1.00
206_I	213_V	0.516	1.00
106_P	110_A	0.513	1.00
33_N	218_L	0.513	1.00
217_Y	236_H	0.513	1.00
100_W	113_S	0.513	1.00
95_P	148_R	0.512	1.00
74_I	77_G	0.512	1.00
227_A	230_V	0.510	1.00
41_R	195_T	0.509	1.00
206_I	227_A	0.506	1.00
48_V	203_V	0.505	1.00
37_L	45_L	0.505	1.00
99_V	103_I	0.503	1.00
157_L	194_L	0.502	1.00
149_Q	172_A	0.502	1.00
228_Q	231_L	0.501	1.00
212_R	226_D	0.500	1.00
51_S	150_R	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
4ry2A	2	0.7532	100	0.254	Contact Map
3tuiC	2	0.9318	100	0.259	Contact Map
1oxxK	1	0.9351	100	0.26	Contact Map
4fwiB	1	0.9286	100	0.26	Contact Map
4f4cA	1	0.737	100	0.261	Contact Map
4yerA	2	0.8539	100	0.262	Contact Map
4mkiB	2	0.8799	100	0.264	Contact Map
4u00A	1	0.7468	100	0.266	Contact Map
3fvqA	2	0.9448	100	0.267	Contact Map
2yyzA	1	0.9416	100	0.268	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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