DPPD - ECOLI - GREMLIN Contacts

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DPPD - Dipeptide transport ATP-binding protein DppD

UniProt:	P0AAG0	Sequences: MALLNVDKLSVHFGDESAPFRAVDRISYSVKQGEVVGIVGESGSGKSVSSLAIMGLIDYPGRVMAEKLEFNGQDLQRISEKERRNLVGAEVAMIFQDPMTSLNPCYTVGFQIMEAIKVHQGGNKSTRRQRAIDLLNQVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACRPKLLIADEPTTALDVTIQAQIIELLLELQQKENMALVLITHDLALVAEAAHKIIVMYAGQVVETGDAHAIFHAPRHPYTQALLRALPEFAQDKERLASLPGVVPGKYDRPNGCLLNPRCPYATDRCRAEEPALNMLADGRQSKCHYPLDDAGRPTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12627
Length:	327 (268)
Sequences:	51960 (32410)
Seq/√Len:	1979.8

ECOLI - DPPD MALK SAPD UGPC YCJV PROV POTG POTA FBPC CYSA OPPD DDPD DPPF METN YDCT YEHX OPPF DDPF MODC YADG GSIA ARAG YHES RBSA UUP FEPC YECC MACB MLAF MDLA SAPF CYDC MDLB NIKE CYDD MSBA LPTB TAUB HISP FHUC FECE YOJI YTFR GLNQ PHNC SSUB LSRA GLTL PHNK YHDZ ETTA SUFC YPHE ZNUC LIVG ARTP BTUD PSTB MODF XYLG ALSA FTSE LIVF THIQ LOLD NIKD MGLA FETA YEJF YBBA CCMA PHNL YDDA YNJD YBHF YBIT YHIH
BACSU - OPUCA DPPD OPUBA APPD MSMX YURJ OPUAA YVRA OPPD APPF YKFD METN OPPF YHCH YFMM TAGH YKPA YHAQ YVFR YXLF YFIL YDBJ YCBN FHUC YHEH YFMF YUSV RBSA ECFA1 SUNT YDIF YFIC YTRB TCYN BMRA YGAD YHEI BCEA YFIB YKNU ECSA YVCR YKNV YTLC YWJA YCLP YFMR SKFE YLMA CYDD YXEO ECFA2 ALBC CYDC YKOD MNTB ARTM SUFC YXDL TCYC NATA GLNQ FTSE YJKB PSTB1 YCLH YVRO SSUB YKNY PSTB2 ZNUC YTHP EXPZ YHCG YUFO YYBJ YTRE YYDI
HALSA - Q9HMX3 Q9HMX2 Q9HMW0 Q9HHQ5 BTUDA Q9HMT3 Q9HNZ9 Q9HR06 Q9HMU8 Q9HMG1 Q9HRJ6 Q9HSQ7 PHNC Q9HRH8 PSTB2 Q9HMG6 Q9HHM2 Q9HRV7 Q9HNY3 Y1631 Y2317 Q9HRZ9 PSTB1 Q9HHR7 Q9HR96 Q9HT03 Q9HR21 Q9HS04 Q9HQA8 Q9HMC1 Q9HMW1
SULSO - Q97UF2 Q97YY4 Q97UY8 Q97UH3 Q97VF5 Q97YP3 Q97VK8 Q97YP7 Q97VC1 Q97ZC0 Q97VK9 Q97UJ9 Q97VF4 Q97VH6 Q97YP8 Q97UD4 Q7LX64 Q97YK2 Q97X18 Y1893 Q97Z03 Y2030 Q97YQ7 Q97U54 Q97UH4 Q97V01 Q980W0 PSTB Q97W42 Q7LY07 Q97V00 Q7LXM4 Q97VY4 Q97VM2 Q97UG5 Q97Z56 Q7LX80 Q97Z96 Q97YP4 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
34_E	223_K	4.187	1.00
90_E	173_K	3.493	1.00
8_K	25_R	3.303	1.00
5_N	29_S	3.179	1.00
7_D	67_K	3.163	1.00
21_R	24_D	2.982	1.00
36_V	225_I	2.913	1.00
11_V	52_A	2.830	1.00
137_Q	203_E	2.627	1.00
37_G	221_A	2.611	1.00
67_K	74_D	2.607	1.00
237_D	240_A	2.560	1.00
71_N	173_K	2.512	1.00
31_K	34_E	2.483	1.00
225_I	232_V	2.406	1.00
146_R	149_V	2.401	1.00
223_K	235_T	2.398	1.00
12_H	21_R	2.378	1.00
24_D	231_Q	2.357	1.00
5_N	69_E	2.297	1.00
10_S	65_A	2.204	1.00
130_R	133_D	2.198	1.00
6_V	9_L	2.177	1.00
10_S	25_R	2.146	1.00
218_A	239_H	2.136	1.00
32_Q	173_K	2.118	1.00
130_R	171_R	2.104	1.00
50_S	210_I	2.077	1.00
74_D	77_R	2.043	1.00
123_N	126_T	2.037	1.00
134_L	169_A	1.976	1.00
236_G	241_I	1.929	1.00
13_F	48_V	1.913	1.00
7_D	69_E	1.909	1.00
79_S	82_E	1.901	1.00
132_I	147_L	1.876	1.00
10_S	21_R	1.823	1.00
106_Y	110_F	1.803	1.00
55_G	83_R	1.752	1.00
211_T	217_V	1.749	1.00
50_S	176_I	1.740	1.00
13_F	22_A	1.717	1.00
37_G	217_V	1.715	1.00
109_G	148_D	1.642	1.00
149_V	153_Q	1.637	1.00
113_M	131_A	1.630	1.00
73_Q	82_E	1.605	1.00
225_I	235_T	1.601	1.00
236_G	240_A	1.582	1.00
11_V	57_I	1.579	1.00
113_M	127_R	1.573	1.00
171_R	203_E	1.551	1.00
133_D	137_Q	1.537	1.00
12_H	64_M	1.529	1.00
109_G	147_L	1.528	1.00
8_K	27_S	1.526	1.00
71_N	90_E	1.526	1.00
11_V	64_M	1.521	1.00
142_D	145_S	1.519	1.00
199_L	205_M	1.515	1.00
197_L	219_E	1.500	1.00
117_K	127_R	1.476	1.00
6_V	28_Y	1.471	1.00
146_R	154_L	1.462	1.00
240_A	244_A	1.457	1.00
128_R	132_I	1.457	1.00
78_I	82_E	1.452	1.00
132_I	142_D	1.420	1.00
9_L	59_Y	1.412	1.00
177_A	207_L	1.408	1.00
10_S	24_D	1.404	1.00
141_P	145_S	1.391	1.00
107_T	110_F	1.360	1.00
109_G	113_M	1.351	1.00
99_M	159_S	1.345	1.00
145_S	149_V	1.299	1.00
112_I	135_L	1.294	1.00
6_V	53_I	1.292	1.00
30_V	36_V	1.289	1.00
35_V	200_Q	1.284	1.00
34_E	222_H	1.274	1.00
94_I	177_A	1.273	1.00
28_Y	49_S	1.272	1.00
193_I	216_L	1.252	1.00
110_F	113_M	1.250	1.00
7_D	29_S	1.250	1.00
7_D	27_S	1.234	1.00
128_R	147_L	1.230	1.00
35_V	207_L	1.222	1.00
54_M	93_M	1.206	1.00
55_G	58_D	1.205	1.00
107_T	148_D	1.205	1.00
73_Q	78_I	1.201	1.00
109_G	128_R	1.198	1.00
105_C	152_H	1.196	1.00
28_Y	225_I	1.195	1.00
36_V	235_T	1.189	1.00
196_L	207_L	1.188	1.00
69_E	74_D	1.183	1.00
26_I	49_S	1.180	1.00
197_L	200_Q	1.176	1.00
78_I	83_R	1.175	1.00
154_L	162_V	1.173	1.00
38_I	208_V	1.164	1.00
251_Q	255_R	1.164	1.00
129_Q	133_D	1.162	1.00
135_L	147_L	1.155	1.00
36_V	223_K	1.153	1.00
32_Q	71_N	1.148	1.00
239_H	243_H	1.142	1.00
31_K	223_K	1.132	1.00
111_Q	166_M	1.124	1.00
106_Y	114_E	1.088	1.00
35_V	221_A	1.080	1.00
224_I	238_A	1.061	1.00
126_T	129_Q	1.058	1.00
52_A	59_Y	1.056	1.00
139_G	198_E	1.040	1.00
122_G	127_R	1.036	1.00
171_R	205_M	1.026	1.00
175_L	205_M	1.025	1.00
109_G	131_A	1.024	1.00
8_K	65_A	1.019	1.00
136_N	141_P	1.013	1.00
30_V	174_L	1.012	1.00
240_A	243_H	1.010	1.00
112_I	169_A	1.009	1.00
23_V	52_A	1.008	1.00
125_S	129_Q	1.008	1.00
53_I	208_V	1.005	1.00
113_M	117_K	1.003	1.00
49_S	227_M	0.999	1.00
136_N	142_D	0.995	1.00
141_P	146_R	0.989	1.00
51_L	56_L	0.985	1.00
127_R	131_A	0.980	1.00
137_Q	198_E	0.975	1.00
184_L	192_I	0.973	1.00
116_I	169_A	0.971	1.00
175_L	207_L	0.968	1.00
32_Q	204_N	0.960	1.00
248_P	251_Q	0.959	1.00
209_L	220_A	0.952	1.00
31_K	206_A	0.946	1.00
92_A	167_A	0.943	1.00
132_I	136_N	0.942	1.00
200_Q	207_L	0.940	1.00
133_D	136_N	0.934	1.00
113_M	128_R	0.930	1.00
22_A	48_V	0.915	1.00
54_M	176_I	0.913	1.00
91_V	174_L	0.913	1.00
11_V	48_V	0.909	1.00
130_R	134_L	0.907	1.00
6_V	68_L	0.906	1.00
277_K	280_R	0.904	1.00
106_Y	111_Q	0.904	1.00
24_D	285_L	0.903	1.00
122_G	126_T	0.903	1.00
12_H	24_D	0.902	1.00
231_Q	285_L	0.895	1.00
94_I	164_I	0.894	1.00
38_I	49_S	0.889	1.00
120_Q	130_R	0.884	1.00
134_L	137_Q	0.881	1.00
44_S	227_M	0.878	1.00
92_A	172_P	0.876	1.00
80_E	83_R	0.871	1.00
197_L	220_A	0.866	1.00
52_A	68_L	0.865	1.00
126_T	130_R	0.865	1.00
189_Q	213_D	0.863	1.00
51_L	57_I	0.862	1.00
124_K	127_R	0.861	1.00
274_V	277_K	0.858	1.00
35_V	197_L	0.855	1.00
177_A	196_L	0.854	1.00
3_L	71_N	0.851	1.00
38_I	225_I	0.850	1.00
70_F	90_E	0.847	1.00
241_I	250_T	0.846	1.00
189_Q	216_L	0.844	1.00
150_Y	153_Q	0.843	1.00
74_D	78_I	0.842	1.00
139_G	191_Q	0.842	1.00
123_N	127_R	0.839	1.00
134_L	165_A	0.839	1.00
259_E	262_Q	0.838	1.00
107_T	150_Y	0.838	1.00
238_A	242_F	0.833	1.00
73_Q	90_E	0.830	1.00
108_V	162_V	0.829	1.00
102_L	159_S	0.824	1.00
200_Q	222_H	0.822	1.00
128_R	148_D	0.818	1.00
232_V	235_T	0.816	1.00
23_V	26_I	0.813	1.00
15_D	20_F	0.810	1.00
9_L	52_A	0.807	1.00
138_V	165_A	0.804	1.00
142_D	147_L	0.802	1.00
252_A	256_A	0.802	1.00
216_L	220_A	0.800	1.00
195_L	198_E	0.798	1.00
59_Y	64_M	0.795	1.00
52_A	57_I	0.795	1.00
280_R	285_L	0.791	1.00
108_V	154_L	0.791	1.00
3_L	70_F	0.788	1.00
194_E	219_E	0.784	1.00
11_V	23_V	0.783	1.00
35_V	220_A	0.779	1.00
39_V	217_V	0.778	1.00
131_A	147_L	0.777	1.00
89_A	120_Q	0.775	1.00
221_A	224_I	0.774	1.00
103_N	106_Y	0.762	1.00
140_I	146_R	0.760	1.00
117_K	124_K	0.759	1.00
26_I	232_V	0.757	1.00
94_I	167_A	0.756	1.00
248_P	252_A	0.756	1.00
30_V	206_A	0.752	1.00
193_I	219_E	0.752	1.00
250_T	254_L	0.749	1.00
8_K	11_V	0.746	1.00
154_L	158_M	0.745	1.00
115_A	166_M	0.742	1.00
247_H	250_T	0.741	1.00
226_V	245_P	0.740	1.00
25_R	231_Q	0.739	1.00
174_L	208_V	0.739	1.00
115_A	170_C	0.738	1.00
142_D	146_R	0.738	1.00
174_L	206_A	0.737	1.00
151_P	162_V	0.736	1.00
209_L	221_A	0.735	1.00
214_L	242_F	0.729	1.00
244_A	247_H	0.721	1.00
276_G	279_D	0.720	1.00
81_K	84_R	0.719	1.00
277_K	281_P	0.719	1.00
4_L	53_I	0.718	1.00
190_A	194_E	0.717	1.00
35_V	222_H	0.711	1.00
256_A	259_E	0.711	1.00
134_L	168_I	0.708	1.00
51_L	93_M	0.707	1.00
221_A	238_A	0.707	1.00
228_Y	231_Q	0.707	1.00
179_E	212_H	0.704	1.00
116_I	120_Q	0.703	1.00
252_A	255_R	0.699	1.00
271_P	274_V	0.697	1.00
176_I	208_V	0.693	1.00
23_V	49_S	0.691	1.00
47_S	51_L	0.691	1.00
275_P	281_P	0.685	1.00
270_L	273_V	0.685	1.00
13_F	57_I	0.681	1.00
228_Y	252_A	0.680	1.00
233_V	247_H	0.680	1.00
146_R	158_M	0.677	1.00
30_V	208_V	0.676	1.00
228_Y	233_V	0.674	1.00
279_D	283_G	0.672	1.00
39_V	226_V	0.670	1.00
276_G	280_R	0.669	1.00
80_E	84_R	0.668	1.00
56_L	95_F	0.667	1.00
226_V	241_I	0.665	1.00
268_A	272_G	0.662	1.00
181_T	216_L	0.661	1.00
36_V	208_V	0.660	1.00
120_Q	171_R	0.657	1.00
75_L	91_V	0.657	1.00
12_H	65_A	0.657	1.00
16_E	20_F	0.656	1.00
112_I	131_A	0.655	1.00
281_P	284_C	0.652	1.00
119_H	170_C	0.651	1.00
4_L	174_L	0.651	1.00
100_T	159_S	0.650	1.00
79_S	83_R	0.650	1.00
270_L	274_V	0.647	1.00
275_P	279_D	0.647	1.00
6_V	49_S	0.646	1.00
255_R	268_A	0.646	1.00
107_T	111_Q	0.645	1.00
194_E	197_L	0.645	1.00
277_K	282_N	0.645	1.00
272_G	275_P	0.643	1.00
276_G	281_P	0.643	1.00
277_K	283_G	0.641	1.00
111_Q	151_P	0.640	1.00
109_G	112_I	0.639	1.00
125_S	128_R	0.633	1.00
238_A	249_Y	0.630	1.00
69_E	72_G	0.629	1.00
279_D	282_N	0.623	1.00
67_K	76_Q	0.623	1.00
70_F	174_L	0.622	1.00
67_K	77_R	0.620	1.00
129_Q	136_N	0.618	1.00
54_M	91_V	0.617	1.00
257_L	261_A	0.616	1.00
242_F	245_P	0.615	1.00
181_T	192_I	0.613	1.00
116_I	121_G	0.612	1.00
25_R	65_A	0.611	1.00
272_G	276_G	0.610	1.00
52_A	64_M	0.610	1.00
102_L	162_V	0.610	1.00
102_L	111_Q	0.608	1.00
278_Y	283_G	0.608	1.00
280_R	283_G	0.608	1.00
33_G	206_A	0.608	1.00
53_I	68_L	0.607	1.00
75_L	78_I	0.607	1.00
272_G	277_K	0.603	1.00
273_V	276_G	0.603	1.00
140_I	158_M	0.602	1.00
8_K	66_E	0.602	1.00
129_Q	132_I	0.600	1.00
41_E	44_S	0.598	1.00
194_E	198_E	0.594	1.00
68_L	76_Q	0.592	1.00
277_K	285_L	0.591	1.00
149_V	154_L	0.590	1.00
280_R	284_C	0.589	1.00
109_G	132_I	0.585	1.00
115_A	118_V	0.584	1.00
32_Q	206_A	0.584	1.00
116_I	122_G	0.582	1.00
97_D	100_T	0.581	1.00
3_L	174_L	0.580	1.00
278_Y	282_N	0.578	1.00
261_A	264_K	0.576	1.00
70_F	75_L	0.576	1.00
3_L	206_A	0.573	1.00
269_S	273_V	0.573	1.00
41_E	228_Y	0.572	1.00
4_L	70_F	0.570	1.00
164_I	192_I	0.567	1.00
12_H	22_A	0.567	1.00
267_L	270_L	0.565	1.00
245_P	250_T	0.565	1.00
128_R	131_A	0.562	1.00
130_R	137_Q	0.561	1.00
273_V	277_K	0.561	1.00
34_E	235_T	0.558	1.00
238_A	241_I	0.557	1.00
168_I	205_M	0.556	1.00
274_V	280_R	0.556	1.00
113_M	147_L	0.554	1.00
282_N	285_L	0.554	1.00
134_L	138_V	0.553	1.00
278_Y	285_L	0.553	1.00
236_G	242_F	0.552	1.00
264_K	268_A	0.549	1.00
10_S	64_M	0.549	1.00
217_V	221_A	0.549	1.00
240_A	246_R	0.548	1.00
160_Q	183_A	0.547	1.00
122_G	130_R	0.546	1.00
275_P	278_Y	0.542	1.00
156_G	161_R	0.542	1.00
111_Q	115_A	0.542	1.00
270_L	277_K	0.539	1.00
228_Y	247_H	0.535	1.00
218_A	242_F	0.534	1.00
265_E	268_A	0.533	1.00
12_H	15_D	0.531	1.00
274_V	278_Y	0.525	1.00
241_I	245_P	0.525	1.00
96_Q	156_G	0.522	1.00
200_Q	203_E	0.519	1.00
131_A	169_A	0.519	1.00
236_G	245_P	0.518	1.00
257_L	260_F	0.516	1.00
217_V	224_I	0.516	1.00
275_P	280_R	0.516	1.00
135_L	146_R	0.515	1.00
145_S	148_D	0.514	1.00
193_I	220_A	0.512	1.00
101_S	163_M	0.512	1.00
254_L	257_L	0.511	1.00
21_R	25_R	0.509	1.00
264_K	267_L	0.509	1.00
233_V	285_L	0.507	1.00
274_V	281_P	0.507	1.00
251_Q	254_L	0.506	1.00
112_I	115_A	0.506	1.00
173_K	205_M	0.505	1.00
211_T	216_L	0.505	1.00
116_I	170_C	0.504	1.00
29_S	235_T	0.503	1.00
41_E	249_Y	0.502	1.00
274_V	279_D	0.501	1.00
269_S	274_V	0.500	1.00
121_G	127_R	0.500	1.00
217_V	238_A	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)
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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
3tuiC	2	0.9388	100	0.21	Contact Map
4ry2A	2	0.7309	100	0.22	Contact Map
4f4cA	1	0.7003	100	0.229	Contact Map
2yyzA	1	0.8471	100	0.231	Contact Map
2it1A	1	0.8716	100	0.234	Contact Map
1g291	4	0.8746	100	0.235	Contact Map
1v43A	2	0.9052	100	0.236	Contact Map
4fwiB	1	0.9419	100	0.237	Contact Map
1oxxK	1	0.9266	100	0.239	Contact Map
1z47A	2	0.9388	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.

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