OPPD - BACSU - GREMLIN Contacts

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OPPD - Oligopeptide transport ATP-binding protein OppD

UniProt:	P24136	Sequences: MIRVTRLLEVKDLAISFKTYGGEVQAIRGVNFHLDKGETLAIVGESGSGKSVTSQAIMKLIPMPPGYFKRGEILFEGKDLVPLSEKEMQNVRGKEIGMIFQDPMTSLNPTMKVGKQITEVLFKHEKISKEAAKKRAVELLELVGIPMPEKRVNQFPHEFSGGMRQRVVIAMALAANPKLLIADEPTTALDVTIQAQILELMKDLQKKIDTSIIFITHDLGVVANVADRVAVMYAGQIVETGTVDEIFYDPRHPYTWGLLASMPTLESSGEEELTAIPGTPPDLTNPPKGDAFALRSSYAMKIDFEQEPPMFKVSDTHYVKSWLLHPDAPKVEPPEAVKAKMRKLANTFEKPVLVREVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	358 (298)
Sequences:	26346 (18685)
Seq/√Len:	1082.4

ECOLI - PROV FBPC CYSA POTG DPPF POTA METN MALK YCJV YDCT UGPC OPPD DPPD YHES DDPD SAPD OPPF GSIA MODC YEHX DDPF YADG UUP ARAG MACB RBSA FEPC MLAF MDLA CYDC MSBA MDLB SAPF CYDD ETTA NIKE HISP TAUB YECC FECE YOJI SSUB FHUC PHNC YTFR GLNQ LSRA PHNK YHDZ GLTL LPTB ZNUC SUFC ARTP MODF FTSE LIVG LOLD THIQ LIVF YPHE PSTB BTUD NIKD YBBA FETA XYLG YBHF ALSA YEJF MGLA PHNL YDDA CCMA YNJD YBIT
BACSU - OPPD OPUCA OPUBA DPPD OPUAA METN MSMX APPD YVRA YURJ YKFD APPF YDIF YHCH YKPA OPPF TAGH YFIL YCBN YXLF YDBJ YVFR YHAQ YFMM YFMR YHEH ECFA1 SUNT YUSV YFIC YFIB YTRB RBSA YKNV BMRA YWJA YHEI YKNU YGAD YFMF TCYN FHUC CYDD CYDC YCLP BCEA YLMA YTLC YKOD YXDL SUFC ECFA2 YXEO ECSA SKFE NATA YVCR FTSE SSUB YJKB ARTM GLNQ YVRO TCYC PSTB1 YKNY EXPZ ALBC MNTB YTHP PSTB2 YYBJ YCLH ZNUC YHCG YTRE YUFO YYDI
HALSA - Q9HMX3 Q9HMX2 Q9HMW0 BTUDA Q9HNZ9 Q9HHQ5 Q9HMT3 Q9HR06 Q9HRJ6 Q9HMU8 Q9HMG1 Q9HSQ7 PSTB2 Q9HRH8 Q9HHM2 PHNC Q9HMG6 Q9HNY3 Q9HRV7 Q9HRZ9 Y1631 Y2317 Q9HR96 PSTB1 Q9HHR7 Q9HS04 Q9HT03 Q9HQA8 Q9HMC1 Q9HR21 Q9HMW1
SULSO - Q97UF2 Q97UH3 Q97ZC0 Q97YP3 Q97YY4 Q97UY8 Q97VK8 Q97VF5 Q7LX64 Q97VC1 Q97UJ9 Q97VF4 Q97YP8 Q97VK9 Q97VH6 Q97YP7 Q97YK2 Q97X18 Q97UD4 Q97YQ7 Q980W0 Q97U54 Q97Z03 Q97UH4 Y1893 PSTB Q97W42 Y2030 Q7LY07 Q97V01 Q7LXM4 Q97V00 Q97VM2 Q97VY4 Q97UG5 Q7LX80 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
38_E	228_R	4.218	1.00
95_E	178_K	3.558	1.00
9_E	33_H	3.339	1.00
11_K	72_E	3.298	1.00
12_D	29_G	3.192	1.00
15_I	56_A	3.108	1.00
76_E	178_K	2.954	1.00
72_E	79_D	2.772	1.00
40_L	230_A	2.720	1.00
41_A	226_A	2.669	1.00
242_T	245_E	2.639	1.00
25_Q	28_R	2.533	1.00
14_A	70_R	2.505	1.00
230_A	237_I	2.489	1.00
35_D	38_E	2.468	1.00
228_R	240_T	2.415	1.00
10_V	13_L	2.399	1.00
135_R	138_E	2.391	1.00
79_D	82_P	2.328	1.00
241_G	246_I	2.326	1.00
139_L	174_A	2.307	1.00
151_R	154_Q	2.283	1.00
16_S	25_Q	2.276	1.00
9_E	74_L	2.219	1.00
36_K	178_K	2.216	1.00
302_I	306_Q	2.153	1.00
54_S	215_I	2.133	1.00
137_V	152_V	2.057	1.00
141_E	149_E	2.050	1.00
6_R	9_E	2.040	1.00
6_R	35_D	1.988	1.00
223_A	244_D	1.980	1.00
14_A	29_G	1.951	1.00
16_S	23_E	1.914	1.00
128_S	131_A	1.896	1.00
11_K	74_L	1.894	1.00
154_Q	158_E	1.885	1.00
41_A	222_V	1.885	1.00
59_K	88_M	1.833	1.00
111_M	115_K	1.833	1.00
137_V	149_E	1.831	1.00
135_R	176_N	1.830	1.00
76_E	95_E	1.822	1.00
293_A	304_F	1.803	1.00
17_F	52_V	1.771	1.00
16_S	69_K	1.730	1.00
122_F	132_A	1.724	1.00
28_R	236_Q	1.717	1.00
138_E	142_L	1.712	1.00
6_R	33_H	1.674	1.00
18_K	23_E	1.672	1.00
114_G	152_V	1.640	1.00
10_V	32_F	1.636	1.00
12_D	31_N	1.629	1.00
88_M	92_R	1.603	1.00
202_K	205_Q	1.596	1.00
299_A	304_F	1.594	1.00
146_P	150_K	1.589	1.00
216_T	222_V	1.584	1.00
54_S	181_I	1.553	1.00
312_K	315_D	1.534	1.00
118_T	136_A	1.533	1.00
236_Q	307_E	1.532	1.00
15_I	69_K	1.495	1.00
133_K	152_V	1.452	1.00
230_A	240_T	1.451	1.00
114_G	153_N	1.432	1.00
15_I	61_I	1.428	1.00
42_I	213_I	1.418	1.00
10_V	57_I	1.417	1.00
201_M	212_I	1.410	1.00
78_K	83_L	1.409	1.00
133_K	137_V	1.405	1.00
39_T	205_Q	1.405	1.00
32_F	53_T	1.395	1.00
104_M	164_R	1.384	1.00
30_V	53_T	1.374	1.00
14_A	28_R	1.372	1.00
17_F	26_A	1.366	1.00
198_L	221_V	1.356	1.00
13_L	63_M	1.354	1.00
112_K	153_N	1.338	1.00
159_F	167_V	1.320	1.00
91_V	96_I	1.303	1.00
115_K	118_T	1.295	1.00
112_K	115_K	1.295	1.00
118_T	132_A	1.294	1.00
36_K	76_E	1.294	1.00
151_R	159_F	1.292	1.00
110_T	157_H	1.290	1.00
312_K	316_T	1.288	1.00
301_K	304_F	1.285	1.00
114_G	118_T	1.270	1.00
83_L	88_M	1.269	1.00
245_E	249_D	1.259	1.00
202_K	224_N	1.257	1.00
117_I	140_L	1.247	1.00
99_I	182_A	1.246	1.00
204_L	210_T	1.242	1.00
34_L	40_L	1.241	1.00
214_F	225_V	1.227	1.00
14_A	25_Q	1.215	1.00
11_K	31_N	1.212	1.00
36_K	209_D	1.207	1.00
32_F	230_A	1.204	1.00
291_A	307_E	1.198	1.00
288_K	293_A	1.196	1.00
260_A	274_T	1.196	1.00
256_W	260_A	1.192	1.00
16_S	28_R	1.189	1.00
74_L	79_D	1.185	1.00
236_Q	291_A	1.177	1.00
130_E	134_K	1.176	1.00
12_D	70_R	1.171	1.00
290_D	296_S	1.170	1.00
134_K	138_E	1.168	1.00
111_M	119_E	1.167	1.00
40_L	240_T	1.166	1.00
133_K	153_N	1.165	1.00
11_K	33_H	1.161	1.00
301_K	305_E	1.161	1.00
34_L	179_L	1.149	1.00
244_D	248_Y	1.146	1.00
182_A	212_I	1.145	1.00
241_G	245_E	1.136	1.00
55_Q	60_L	1.122	1.00
118_T	122_F	1.121	1.00
131_A	134_K	1.120	1.00
40_L	228_R	1.112	1.00
142_L	203_D	1.097	1.00
121_L	174_A	1.096	1.00
146_P	151_R	1.096	1.00
229_V	243_V	1.093	1.00
117_I	174_A	1.087	1.00
256_W	298_Y	1.087	1.00
39_T	212_I	1.079	1.00
118_T	133_K	1.075	1.00
58_M	98_M	1.073	1.00
125_E	135_R	1.068	1.00
114_G	133_K	1.057	1.00
42_I	230_A	1.056	1.00
59_K	62_P	1.047	1.00
38_E	227_D	1.043	1.00
28_R	291_A	1.043	1.00
296_S	303_D	1.042	1.00
132_A	136_A	1.033	1.00
289_G	293_A	1.030	1.00
96_I	179_L	1.025	1.00
56_A	63_M	1.024	1.00
139_L	142_L	1.011	1.00
180_L	212_I	1.009	1.00
289_G	292_F	1.004	1.00
138_E	141_E	0.999	1.00
194_Q	218_D	0.997	1.00
127_I	132_A	0.991	1.00
116_Q	171_M	0.991	1.00
97_G	172_A	0.990	1.00
53_T	232_M	0.988	1.00
124_H	127_I	0.986	1.00
313_V	317_H	0.982	1.00
150_K	154_Q	0.980	1.00
58_M	181_I	0.975	1.00
299_A	303_D	0.972	1.00
39_T	226_A	0.964	1.00
180_L	210_T	0.957	1.00
94_K	125_E	0.955	1.00
35_D	211_S	0.948	1.00
205_Q	227_D	0.944	1.00
108_N	111_M	0.931	1.00
42_I	53_T	0.930	1.00
118_T	152_V	0.928	1.00
202_K	225_V	0.928	1.00
205_Q	212_I	0.917	1.00
137_V	141_E	0.914	1.00
27_I	56_A	0.910	1.00
56_A	61_I	0.908	1.00
10_V	73_I	0.908	1.00
292_F	296_S	0.907	1.00
43_V	222_V	0.902	1.00
293_A	299_A	0.901	1.00
35_D	228_R	0.898	1.00
246_I	255_T	0.893	1.00
140_L	152_V	0.892	1.00
245_E	248_Y	0.891	1.00
34_L	213_I	0.889	1.00
314_S	317_H	0.885	1.00
13_L	56_A	0.883	1.00
111_M	116_Q	0.883	1.00
34_L	211_S	0.869	1.00
83_L	91_V	0.868	1.00
7_L	75_F	0.863	1.00
73_I	81_V	0.861	1.00
290_D	293_A	0.860	1.00
237_I	240_T	0.859	1.00
302_I	305_E	0.858	1.00
179_L	213_I	0.855	1.00
39_T	202_K	0.852	1.00
129_K	132_A	0.852	1.00
182_A	201_M	0.847	1.00
136_A	152_V	0.845	1.00
120_V	171_M	0.844	1.00
286_P	291_A	0.844	1.00
282_D	285_N	0.843	1.00
264_T	267_S	0.842	1.00
144_G	203_D	0.841	1.00
48_S	232_M	0.838	1.00
6_R	36_K	0.836	1.00
285_N	288_K	0.832	1.00
113_V	167_V	0.832	1.00
56_A	73_I	0.831	1.00
80_L	91_V	0.830	1.00
139_L	170_A	0.828	1.00
55_Q	61_I	0.826	1.00
296_S	300_M	0.826	1.00
135_R	139_L	0.820	1.00
134_K	141_E	0.820	1.00
131_A	135_R	0.819	1.00
17_F	61_I	0.817	1.00
283_L	286_P	0.815	1.00
255_T	259_L	0.809	1.00
128_S	132_A	0.801	1.00
251_R	313_V	0.799	1.00
80_L	96_I	0.798	1.00
117_I	136_A	0.794	1.00
278_G	281_P	0.792	1.00
99_I	169_I	0.788	1.00
194_Q	221_V	0.787	1.00
287_P	293_A	0.784	1.00
306_Q	309_P	0.783	1.00
15_I	52_V	0.782	1.00
40_L	213_I	0.780	1.00
79_D	83_L	0.779	1.00
75_F	95_E	0.779	1.00
125_E	132_A	0.777	1.00
15_I	27_I	0.776	1.00
7_L	179_L	0.773	1.00
127_I	131_A	0.772	1.00
145_I	163_M	0.768	1.00
189_L	197_I	0.765	1.00
57_I	213_I	0.763	1.00
107_L	167_V	0.761	1.00
176_N	210_T	0.759	1.00
313_V	316_T	0.757	1.00
219_L	247_F	0.757	1.00
247_F	250_P	0.754	1.00
186_T	221_V	0.753	1.00
7_L	76_E	0.753	1.00
97_G	177_P	0.753	1.00
36_K	211_S	0.752	1.00
290_D	303_D	0.747	1.00
43_V	231_V	0.742	1.00
195_A	199_E	0.740	1.00
122_F	129_K	0.739	1.00
243_V	247_F	0.737	1.00
144_G	196_Q	0.735	1.00
277_P	297_S	0.734	1.00
146_P	149_E	0.734	1.00
12_D	15_I	0.731	1.00
125_E	128_S	0.727	1.00
280_P	283_L	0.724	1.00
181_I	213_I	0.719	1.00
112_K	116_Q	0.717	1.00
107_L	164_R	0.717	1.00
18_K	21_G	0.715	1.00
214_F	226_A	0.713	1.00
8_L	57_I	0.713	1.00
78_K	95_E	0.712	1.00
303_D	307_E	0.711	1.00
159_F	163_M	0.710	1.00
127_I	135_R	0.707	1.00
145_I	151_R	0.705	1.00
151_R	163_M	0.705	1.00
291_A	295_R	0.705	1.00
58_M	96_I	0.703	1.00
39_T	225_V	0.700	1.00
134_K	137_V	0.700	1.00
75_F	80_L	0.700	1.00
29_G	236_Q	0.699	1.00
112_K	155_F	0.694	1.00
228_R	239_E	0.694	1.00
72_E	82_P	0.690	1.00
155_F	158_E	0.688	1.00
139_L	173_L	0.688	1.00
233_Y	236_Q	0.687	1.00
143_V	170_A	0.686	1.00
294_L	297_S	0.685	1.00
293_A	297_S	0.684	1.00
106_S	168_V	0.681	1.00
116_Q	156_P	0.679	1.00
16_S	70_R	0.677	1.00
14_A	69_K	0.677	1.00
273_L	276_I	0.677	1.00
121_L	127_I	0.676	1.00
231_V	250_P	0.675	1.00
120_V	175_A	0.674	1.00
286_P	289_G	0.672	1.00
307_E	310_M	0.671	1.00
107_L	116_Q	0.670	1.00
303_D	308_P	0.670	1.00
30_V	237_I	0.667	1.00
18_K	69_K	0.665	1.00
55_Q	98_M	0.664	1.00
310_M	313_V	0.663	1.00
287_P	290_D	0.662	1.00
173_L	210_T	0.659	1.00
289_G	296_S	0.655	1.00
223_A	247_F	0.653	1.00
241_G	247_F	0.653	1.00
75_F	91_V	0.648	1.00
126_K	129_K	0.648	1.00
226_A	243_V	0.647	1.00
27_I	30_V	0.647	1.00
253_P	256_W	0.646	1.00
60_L	100_F	0.644	1.00
252_H	256_W	0.642	1.00
245_E	314_S	0.640	1.00
199_E	203_D	0.639	1.00
125_E	129_K	0.638	1.00
299_A	302_I	0.638	1.00
238_V	291_A	0.638	1.00
202_K	206_K	0.637	1.00
45_E	48_S	0.636	1.00
117_I	171_M	0.634	1.00
300_M	304_F	0.631	1.00
80_L	88_M	0.630	1.00
310_M	317_H	0.628	1.00
125_E	176_N	0.628	1.00
278_G	283_L	0.626	1.00
56_A	69_K	0.626	1.00
129_K	133_K	0.625	1.00
8_L	179_L	0.624	1.00
287_P	294_L	0.624	1.00
226_A	229_V	0.623	1.00
298_Y	301_K	0.622	1.00
281_P	285_N	0.621	1.00
254_Y	258_L	0.619	1.00
59_K	81_V	0.618	1.00
231_V	246_I	0.618	1.00
102_D	105_T	0.616	1.00
39_T	227_D	0.616	1.00
272_E	275_A	0.614	1.00
246_I	250_P	0.613	1.00
290_D	295_R	0.613	1.00
78_K	91_V	0.610	1.00
256_W	259_L	0.607	1.00
29_G	70_R	0.605	1.00
311_F	314_S	0.604	1.00
114_G	136_A	0.603	1.00
23_E	69_K	0.602	1.00
298_Y	302_I	0.602	1.00
300_M	303_D	0.601	1.00
51_S	55_Q	0.600	1.00
121_L	125_E	0.598	1.00
293_A	296_S	0.596	1.00
154_Q	159_F	0.591	1.00
26_A	52_V	0.591	1.00
279_T	282_D	0.590	1.00
221_V	225_V	0.590	1.00
75_F	179_L	0.590	1.00
288_K	292_F	0.589	1.00
201_M	214_F	0.588	1.00
80_L	83_L	0.588	1.00
41_A	216_T	0.586	1.00
120_V	123_K	0.584	1.00
109_P	157_H	0.583	1.00
222_V	226_A	0.582	1.00
169_I	197_I	0.582	1.00
84_S	88_M	0.579	1.00
130_E	133_K	0.578	1.00
291_A	294_L	0.578	1.00
281_P	287_P	0.578	1.00
257_G	260_A	0.577	1.00
284_T	288_K	0.575	1.00
296_S	299_A	0.575	1.00
114_G	117_I	0.574	1.00
307_E	311_F	0.574	1.00
12_D	71_G	0.570	1.00
309_P	312_K	0.568	1.00
72_E	81_V	0.567	1.00
285_N	289_G	0.567	1.00
121_L	126_K	0.567	1.00
250_P	255_T	0.566	1.00
257_G	276_I	0.564	1.00
283_L	287_P	0.563	1.00
303_D	317_H	0.563	1.00
286_P	290_D	0.563	1.00
262_M	265_L	0.562	1.00
8_L	75_F	0.560	1.00
292_F	295_R	0.559	1.00
200_L	203_D	0.559	1.00
243_V	246_I	0.559	1.00
59_K	79_D	0.558	1.00
89_Q	123_K	0.557	1.00
306_Q	310_M	0.557	1.00
222_V	229_V	0.555	1.00
117_I	120_V	0.553	1.00
156_P	167_V	0.552	1.00
277_P	280_P	0.552	1.00
121_L	175_A	0.552	1.00
302_I	308_P	0.550	1.00
105_T	164_R	0.550	1.00
33_H	228_R	0.549	1.00
198_L	224_N	0.549	1.00
141_E	146_P	0.547	1.00
182_A	185_P	0.544	1.00
42_I	237_I	0.543	1.00
149_E	152_V	0.543	1.00
121_L	135_R	0.543	1.00
116_Q	120_V	0.542	1.00
63_M	69_K	0.539	1.00
306_Q	311_F	0.538	1.00
216_T	226_A	0.537	1.00
120_V	174_A	0.535	1.00
99_I	172_A	0.535	1.00
295_R	299_A	0.534	1.00
57_I	73_I	0.530	1.00
13_L	73_I	0.529	1.00
284_T	287_P	0.529	1.00
99_I	165_Q	0.528	1.00
249_D	253_P	0.527	1.00
184_E	217_H	0.527	1.00
135_R	142_L	0.526	1.00
201_M	225_V	0.525	1.00
212_I	225_V	0.524	1.00
310_M	314_S	0.524	1.00
257_G	261_S	0.520	1.00
240_T	310_M	0.519	1.00
297_S	300_M	0.519	1.00
266_E	269_G	0.518	1.00
10_V	53_T	0.518	1.00
7_L	211_S	0.518	1.00
53_T	56_A	0.515	1.00
312_K	317_H	0.514	1.00
39_T	214_F	0.513	1.00
300_M	317_H	0.513	1.00
20_Y	23_E	0.512	1.00
37_G	211_S	0.510	1.00
267_S	270_E	0.510	1.00
243_V	254_Y	0.508	1.00
294_L	299_A	0.507	1.00
276_I	279_T	0.507	1.00
63_M	73_I	0.504	1.00
300_M	306_Q	0.503	1.00
198_L	225_V	0.502	1.00
205_Q	210_T	0.502	1.00
261_S	264_T	0.501	1.00
102_D	164_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
3tuiC	2	0.9441	100	0.278	Contact Map
4ry2A	2	0.6676	100	0.282	Contact Map
4f4cA	1	0.6508	100	0.283	Contact Map
4ymuJ	2	0.6704	100	0.297	Contact Map
2oljA	2	0.676	100	0.298	Contact Map
1b0uA	2	0.6899	100	0.299	Contact Map
4u00A	1	0.6732	100	0.3	Contact Map
4q9hA	1	0.6872	100	0.301	Contact Map
1v43A	2	0.7682	100	0.303	Contact Map
4mkiB	2	0.7961	100	0.305	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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