DPPD - BACSU - GREMLIN Contacts

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DPPD - Dipeptide transport ATP-binding protein DppD

UniProt:	P26905	Sequences: MEKVLSVQNLHVSFTTYGGTVQAVRGVSFDLYKGETFAIVGESGCGKSVTSQSIMGLLPPYSAKVTDGRILFKNKDLCRLSDKEMRGIRGADISMIFQDPMTALNPTLTVGDQLGEALLRHKKMSKKAARKEVLSMLSLVGIPDPGERLKQYPHQFSGGMRQRIVIAMALICEPDILIADEPTTALDVTIQAQILELFKEIQRKTDVSVILITHDLGVVAQVADRVAVMYAGKMAEIGTRKDIFYQPQHPYTKGLLGSVPRLDLNGAELTPIDGTPPDLFSPPPGCPFAARCPNRMVVCDRVYPGQTIRSDSHTVNCWLQDQRAEHAVLSGDAKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	335 (278)
Sequences:	45446 (28586)
Seq/√Len:	1714.5

ECOLI - DPPD PROV OPPD DDPD YDCT DPPF FBPC POTG POTA METN YCJV CYSA MALK UGPC SAPD OPPF YEHX YADG MODC GSIA DDPF RBSA YHES MACB ARAG UUP MDLA MDLB FEPC SAPF CYDC MLAF CYDD PHNC MSBA NIKE TAUB HISP FHUC YECC FECE YOJI ETTA ZNUC YTFR SSUB GLNQ YHDZ PHNK LSRA LPTB GLTL XYLG SUFC MODF YPHE LIVG NIKD LOLD BTUD PSTB THIQ FTSE ARTP LIVF ALSA MGLA YEJF FETA YBBA PHNL YDDA YBHF CCMA YNJD YBIT YHIH
BACSU - DPPD APPD OPPD OPUBA OPUCA OPUAA YVRA MSMX METN YURJ YKFD APPF YHCH YCBN OPPF YKPA TAGH YVFR YXLF YDBJ YHAQ YFIL YFMM YHEH YDIF SUNT YUSV YFIC YFMR RBSA ECFA1 FHUC YFIB BMRA YGAD YFMF YTRB YKNV YKNU YWJA YXDL TCYN YHEI CYDC YCLP YKOD YLMA CYDD BCEA YTLC ECFA2 YXEO PSTB1 YVCR ARTM SUFC SSUB ECSA GLNQ YJKB SKFE YTHP TCYC NATA FTSE YVRO PSTB2 YKNY ALBC EXPZ MNTB YUFO YCLH ZNUC YHCG YYBJ YTRE YYDI
HALSA - Q9HMX3 Q9HMX2 Q9HMW0 BTUDA Q9HNZ9 Q9HHQ5 Q9HMT3 Q9HR06 Q9HRJ6 Q9HMG1 Q9HSQ7 Q9HMU8 PSTB2 Q9HRH8 PHNC Q9HMG6 Q9HHM2 Q9HNY3 Q9HRV7 Q9HRZ9 PSTB1 Y1631 Y2317 Q9HR96 Q9HHR7 Q9HT03 Q9HS04 Q9HQA8 Q9HMC1 Q9HR21 Q9HMW1
SULSO - Q97UH3 Q97UF2 Q97YY4 Q97YP3 Q97UY8 Q97VF5 Q97VK8 Q97YP7 Q97UJ9 Q97ZC0 Q97VC1 Q97VF4 Q97VK9 Q97YP8 Q97VH6 Q7LX64 Q97YK2 Q97X18 Q97UD4 Q97YQ7 Q97U54 Q97Z03 Y1893 Q980W0 Q97UH4 PSTB Y2030 Q97W42 Q97V01 Q97UG5 Q97V00 Q7LXM4 Q7LY07 Q97VM2 Q97VY4 Q7LX80 Q97Z56 Q97YP4 Q97UC2 Q97Z96 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
35_E	225_R	4.405	1.00
92_D	175_D	3.630	1.00
9_N	26_G	3.556	1.00
8_Q	69_R	3.361	1.00
6_S	30_D	3.297	1.00
12_V	53_S	3.004	1.00
22_Q	25_R	2.930	1.00
37_F	227_A	2.829	1.00
69_R	76_D	2.645	1.00
239_T	242_D	2.626	1.00
38_A	223_A	2.513	1.00
73_K	175_D	2.486	1.00
227_A	234_M	2.432	1.00
32_Y	35_E	2.430	1.00
7_V	10_L	2.414	1.00
148_R	151_Q	2.382	1.00
220_A	241_K	2.374	1.00
225_R	237_I	2.354	1.00
76_D	79_R	2.326	1.00
25_R	233_K	2.320	1.00
13_S	22_Q	2.275	1.00
6_S	71_L	2.257	1.00
238_G	243_I	2.223	1.00
51_S	212_I	2.209	1.00
11_H	67_D	2.208	1.00
11_H	26_G	2.172	1.00
132_E	135_S	2.156	1.00
33_K	175_D	2.154	1.00
136_M	171_I	2.146	1.00
81_S	84_E	2.026	1.00
132_E	173_E	2.013	1.00
125_S	128_A	2.012	1.00
14_F	49_V	1.996	1.00
56_G	85_M	1.954	1.00
138_S	146_G	1.869	1.00
38_A	219_V	1.857	1.00
8_Q	71_L	1.828	1.00
75_K	84_E	1.805	1.00
213_T	219_V	1.778	1.00
108_L	112_D	1.751	1.00
134_L	149_L	1.748	1.00
51_S	178_I	1.715	1.00
151_Q	155_Q	1.689	1.00
201_I	207_V	1.663	1.00
14_F	23_A	1.650	1.00
199_K	202_Q	1.629	1.00
9_N	28_S	1.624	1.00
12_V	58_L	1.617	1.00
7_V	29_F	1.596	1.00
11_H	22_Q	1.579	1.00
115_G	133_V	1.566	1.00
134_L	146_G	1.543	1.00
13_S	66_T	1.542	1.00
115_G	129_A	1.536	1.00
242_D	246_Q	1.535	1.00
135_S	139_L	1.525	1.00
73_K	92_D	1.489	1.00
119_L	129_A	1.482	1.00
148_R	156_F	1.481	1.00
12_V	66_T	1.475	1.00
13_S	20_T	1.475	1.00
10_L	60_P	1.473	1.00
227_A	237_I	1.467	1.00
7_V	54_I	1.462	1.00
80_L	84_E	1.454	1.00
199_K	221_Q	1.453	1.00
15_T	20_T	1.442	1.00
143_P	147_E	1.441	1.00
111_G	150_K	1.436	1.00
130_R	134_L	1.435	1.00
111_G	149_L	1.430	1.00
36_T	202_Q	1.418	1.00
109_T	112_D	1.406	1.00
11_H	25_R	1.386	1.00
198_F	209_V	1.378	1.00
195_L	218_V	1.365	1.00
286_C	292_C	1.362	1.00
31_L	37_F	1.360	1.00
96_I	179_A	1.350	1.00
101_M	161_R	1.349	1.00
114_L	137_L	1.322	1.00
8_Q	30_D	1.295	1.00
112_D	115_G	1.279	1.00
179_A	209_V	1.276	1.00
36_T	209_V	1.274	1.00
8_Q	28_S	1.272	1.00
156_F	164_I	1.268	1.00
238_G	242_D	1.267	1.00
29_F	50_T	1.248	1.00
39_I	210_I	1.240	1.00
35_E	224_D	1.240	1.00
29_F	227_A	1.239	1.00
147_E	151_Q	1.238	1.00
253_K	257_G	1.229	1.00
75_K	80_L	1.227	1.00
107_T	154_H	1.205	1.00
109_T	150_K	1.204	1.00
55_M	95_M	1.200	1.00
130_R	149_L	1.197	1.00
80_L	85_M	1.179	1.00
56_G	59_P	1.179	1.00
111_G	115_G	1.179	1.00
113_Q	168_M	1.176	1.00
9_N	67_D	1.173	1.00
129_A	133_V	1.165	1.00
131_K	135_S	1.152	1.00
31_L	176_I	1.128	1.00
108_L	116_E	1.127	1.00
241_K	245_Y	1.125	1.00
37_F	225_R	1.120	1.00
211_L	222_V	1.113	1.00
33_K	73_K	1.111	1.00
53_S	60_P	1.109	1.00
27_V	50_T	1.106	1.00
114_L	171_I	1.092	1.00
37_F	237_I	1.089	1.00
284_P	289_A	1.086	1.00
94_S	169_A	1.078	1.00
128_A	131_K	1.069	1.00
124_M	129_A	1.066	1.00
137_L	149_L	1.066	1.00
71_L	76_D	1.061	1.00
226_V	240_R	1.054	1.00
177_L	207_V	1.047	1.00
33_K	206_D	1.047	1.00
139_L	200_E	1.043	1.00
50_T	229_M	1.040	1.00
36_T	223_A	1.037	1.00
127_K	131_K	1.035	1.00
202_Q	209_V	1.031	1.00
52_Q	57_L	1.030	1.00
202_Q	224_D	1.024	1.00
13_S	25_R	1.023	1.00
118_L	171_I	1.021	1.00
135_S	138_S	1.010	1.00
111_G	130_R	1.004	1.00
25_R	287_P	1.000	1.00
143_P	148_R	0.995	1.00
141_G	200_E	0.992	1.00
115_G	119_L	0.987	1.00
55_M	178_I	0.986	1.00
283_P	289_A	0.979	1.00
54_I	210_I	0.978	1.00
45_C	229_M	0.976	1.00
32_Y	225_R	0.970	1.00
7_V	70_I	0.970	1.00
242_D	245_Y	0.968	1.00
261_R	264_L	0.965	1.00
130_R	150_K	0.962	1.00
186_L	194_I	0.960	1.00
126_K	129_A	0.958	1.00
12_V	49_V	0.954	1.00
32_Y	208_S	0.951	1.00
93_I	176_I	0.950	1.00
24_V	53_S	0.949	1.00
177_L	209_V	0.939	1.00
233_K	287_P	0.928	1.00
53_S	70_I	0.921	1.00
115_G	130_R	0.917	1.00
128_A	132_E	0.914	1.00
111_G	133_V	0.907	1.00
23_A	49_V	0.907	1.00
39_I	227_A	0.905	1.00
136_M	139_L	0.904	1.00
134_L	138_S	0.897	1.00
82_D	85_M	0.897	1.00
10_L	53_S	0.894	1.00
125_S	129_A	0.893	1.00
279_L	282_P	0.890	1.00
39_I	50_T	0.887	1.00
72_F	92_D	0.885	1.00
199_K	222_V	0.882	1.00
94_S	174_P	0.880	1.00
191_Q	215_D	0.879	1.00
173_E	207_V	0.879	1.00
4_V	72_F	0.879	1.00
142_I	148_R	0.874	1.00
141_G	193_Q	0.872	1.00
250_P	253_K	0.871	1.00
104_L	161_R	0.870	1.00
234_M	237_I	0.864	1.00
132_E	136_M	0.858	1.00
191_Q	218_V	0.857	1.00
36_T	199_K	0.855	1.00
27_V	234_M	0.854	1.00
108_L	113_Q	0.848	1.00
253_K	294_N	0.847	1.00
136_M	167_A	0.845	1.00
225_R	236_E	0.834	1.00
223_A	226_V	0.831	1.00
122_K	132_E	0.830	1.00
276_P	279_L	0.829	1.00
243_I	252_T	0.826	1.00
31_L	208_S	0.825	1.00
244_F	247_P	0.823	1.00
289_A	295_R	0.816	1.00
75_K	92_D	0.816	1.00
152_Y	155_Q	0.814	1.00
91_A	122_K	0.811	1.00
5_L	54_I	0.810	1.00
26_G	233_K	0.807	1.00
218_V	222_V	0.807	1.00
105_N	108_L	0.806	1.00
12_V	24_V	0.803	1.00
117_A	168_M	0.799	1.00
179_A	198_F	0.799	1.00
53_S	58_L	0.799	1.00
96_I	166_I	0.798	1.00
4_V	73_K	0.797	1.00
40_V	219_V	0.789	1.00
24_V	27_V	0.787	1.00
240_R	244_F	0.782	1.00
52_Q	58_L	0.780	1.00
195_L	221_Q	0.779	1.00
124_M	128_A	0.778	1.00
228_V	247_P	0.778	1.00
285_G	289_A	0.777	1.00
117_A	172_C	0.776	1.00
282_P	287_P	0.775	1.00
283_P	290_A	0.771	1.00
292_C	296_M	0.769	1.00
259_V	263_D	0.765	1.00
287_P	290_A	0.765	1.00
211_L	223_A	0.764	1.00
252_T	256_L	0.762	1.00
109_T	152_Y	0.761	1.00
31_L	210_I	0.760	1.00
176_I	210_I	0.760	1.00
288_F	292_C	0.760	1.00
9_N	12_V	0.758	1.00
156_F	160_M	0.757	1.00
14_F	58_L	0.757	1.00
83_K	86_R	0.750	1.00
122_K	129_A	0.748	1.00
153_P	164_I	0.747	1.00
133_V	149_L	0.745	1.00
110_V	164_I	0.734	1.00
192_A	196_E	0.732	1.00
76_D	80_L	0.731	1.00
15_T	19_G	0.730	1.00
40_V	228_V	0.730	1.00
176_I	208_S	0.727	1.00
249_H	252_T	0.727	1.00
114_L	133_V	0.726	1.00
122_K	125_S	0.724	1.00
96_I	169_A	0.722	1.00
270_T	274_G	0.721	1.00
36_T	222_V	0.721	1.00
136_M	170_L	0.720	1.00
286_C	289_A	0.720	1.00
289_A	293_P	0.714	1.00
57_L	97_F	0.711	1.00
36_T	224_D	0.711	1.00
52_Q	95_M	0.710	1.00
278_D	282_P	0.707	1.00
273_D	293_P	0.707	1.00
286_C	291_R	0.706	1.00
196_E	200_E	0.705	1.00
140_V	167_A	0.705	1.00
196_E	221_Q	0.705	1.00
288_F	291_R	0.705	1.00
258_S	261_R	0.702	1.00
285_G	288_F	0.700	1.00
148_R	160_M	0.698	1.00
178_I	210_I	0.698	1.00
37_F	210_I	0.696	1.00
72_F	77_L	0.695	1.00
131_K	138_S	0.693	1.00
60_P	66_T	0.693	1.00
197_L	200_E	0.692	1.00
250_P	254_G	0.692	1.00
183_T	218_V	0.690	1.00
138_S	143_P	0.690	1.00
274_G	277_P	0.690	1.00
102_T	161_R	0.689	1.00
69_R	79_R	0.686	1.00
119_L	126_K	0.685	1.00
77_L	93_I	0.684	1.00
254_G	258_S	0.683	1.00
4_V	176_I	0.682	1.00
257_G	270_T	0.682	1.00
181_E	214_H	0.682	1.00
278_D	281_S	0.680	1.00
223_A	240_R	0.679	1.00
277_P	283_P	0.676	1.00
267_A	270_T	0.676	1.00
54_I	70_I	0.675	1.00
115_G	149_L	0.675	1.00
216_L	244_F	0.674	1.00
240_R	251_Y	0.674	1.00
142_I	160_M	0.673	1.00
72_F	176_I	0.668	1.00
13_S	67_D	0.668	1.00
230_Y	233_K	0.667	1.00
5_L	176_I	0.667	1.00
34_G	208_S	0.666	1.00
5_L	72_F	0.663	1.00
263_D	266_G	0.662	1.00
199_K	203_R	0.655	1.00
249_H	253_K	0.654	1.00
55_M	93_I	0.652	1.00
33_K	208_S	0.651	1.00
9_N	68_G	0.650	1.00
121_H	172_C	0.644	1.00
70_I	78_C	0.643	1.00
279_L	283_P	0.642	1.00
293_P	296_M	0.633	1.00
104_L	164_I	0.632	1.00
277_P	290_A	0.631	1.00
48_S	52_Q	0.630	1.00
280_F	283_P	0.628	1.00
282_P	285_G	0.626	1.00
196_E	199_K	0.624	1.00
228_V	243_I	0.623	1.00
111_G	114_L	0.621	1.00
279_L	284_P	0.617	1.00
166_I	194_I	0.615	1.00
271_P	275_T	0.613	1.00
290_A	294_N	0.613	1.00
69_R	78_C	0.612	1.00
242_D	248_Q	0.611	1.00
126_K	130_R	0.609	1.00
281_S	285_G	0.607	1.00
230_Y	235_A	0.607	1.00
273_D	276_P	0.606	1.00
151_Q	156_F	0.603	1.00
286_C	293_P	0.602	1.00
114_L	117_A	0.601	1.00
294_N	297_V	0.600	1.00
42_E	45_C	0.599	1.00
278_D	283_P	0.599	1.00
127_K	130_R	0.598	1.00
24_V	50_T	0.597	1.00
243_I	247_P	0.597	1.00
77_L	80_L	0.596	1.00
284_P	287_P	0.596	1.00
274_G	278_D	0.595	1.00
53_S	66_T	0.595	1.00
103_A	165_V	0.595	1.00
109_T	113_Q	0.592	1.00
104_L	113_Q	0.592	1.00
286_C	290_A	0.590	1.00
131_K	134_L	0.589	1.00
269_L	272_I	0.585	1.00
26_G	67_D	0.584	1.00
281_S	284_P	0.584	1.00
117_A	120_R	0.581	1.00
99_D	102_T	0.580	1.00
291_R	295_R	0.578	1.00
292_C	295_R	0.577	1.00
272_I	275_T	0.577	1.00
4_V	208_S	0.576	1.00
130_R	133_V	0.574	1.00
11_H	66_T	0.574	1.00
110_V	156_F	0.574	1.00
113_Q	153_P	0.573	1.00
35_E	237_I	0.571	1.00
266_G	270_T	0.568	1.00
132_E	139_L	0.566	1.00
82_D	86_R	0.565	1.00
71_L	74_N	0.565	1.00
238_G	244_F	0.564	1.00
170_L	207_V	0.564	1.00
219_V	223_A	0.564	1.00
247_P	252_T	0.562	1.00
118_L	122_K	0.561	1.00
77_L	85_M	0.560	1.00
283_P	288_F	0.554	1.00
284_P	288_F	0.553	1.00
219_V	226_V	0.552	1.00
280_F	287_P	0.549	1.00
220_A	239_T	0.544	1.00
235_A	287_P	0.543	1.00
289_A	296_M	0.543	1.00
290_A	293_P	0.542	1.00
289_A	292_C	0.542	1.00
272_I	276_P	0.537	1.00
118_L	124_M	0.535	1.00
81_S	85_M	0.533	1.00
285_G	290_A	0.531	1.00
293_P	297_V	0.530	1.00
118_L	123_K	0.529	1.00
285_G	292_C	0.528	1.00
110_V	114_L	0.526	1.00
258_S	262_L	0.525	1.00
290_A	295_R	0.524	1.00
30_D	237_I	0.522	1.00
271_P	276_P	0.522	1.00
257_G	260_P	0.522	1.00
246_Q	250_P	0.522	1.00
274_G	279_L	0.522	1.00
235_A	249_H	0.518	1.00
45_C	276_P	0.515	1.00
240_R	243_I	0.515	1.00
29_F	37_F	0.515	1.00
283_P	287_P	0.515	1.00
118_L	172_C	0.513	1.00
137_L	148_R	0.513	1.00
110_V	137_L	0.511	1.00
275_T	278_D	0.510	1.00
287_P	294_N	0.509	1.00
282_P	286_C	0.508	1.00
230_Y	254_G	0.507	1.00
251_Y	255_L	0.506	1.00
198_F	222_V	0.506	1.00
279_L	285_G	0.505	1.00
259_V	262_L	0.505	1.00
122_K	173_E	0.504	1.00
43_S	181_E	0.504	1.00
276_P	290_A	0.503	1.00
7_V	50_T	0.503	1.00
276_P	283_P	0.501	1.00
162_Q	185_A	0.501	1.00
284_P	290_A	0.501	1.00
276_P	282_P	0.501	1.00
114_L	168_M	0.500	1.00
123_K	129_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)
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	0.7134	100	0.227	Contact Map
3tuiC	2	0.9522	100	0.233	Contact Map
4f4cA	1	0.6866	100	0.24	Contact Map
4fwiB	1	0.9224	100	0.241	Contact Map
4u00A	1	0.7164	100	0.246	Contact Map
2oljA	2	0.7224	100	0.247	Contact Map
4huqB	1	0.8209	100	0.254	Contact Map
4mkiB	2	0.8388	100	0.254	Contact Map
4q9hA	1	0.7254	100	0.255	Contact Map
1b0uA	2	0.7373	100	0.256	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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