OPPD - ECOLI - GREMLIN Contacts

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OPPD - Oligopeptide transport ATP-binding protein OppD

UniProt:	P76027	Sequences: MSVIETATVPLAQQQADALLNVKDLRVTFSTPDGDVTAVNDLNFSLRAGETLGIVGESGSGKSQTAFALMGLLAANGRIGGSATFNGREILNLPEHELNKLRAEQISMIFQDPMTSLNPYMRVGEQLMEVLMLHKNMSKAEAFEESVRMLDAVKMPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLLIADEPTTALDVTVQAQIMTLLNELKREFNTAIIMITHDLVVVAGICDKVLVMYAGRTMEYGNARDVFYQPVHPYSIGLLNAVPRLDAEGETMLTIPGNPPNLLRLPKGCPFQPRCPHAMEICSSAPPLEEFTPGRLRACFKPVEELL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10677
Length:	337 (273)
Sequences:	49533 (30772)
Seq/√Len:	1862.4

ECOLI - OPPD POTG DDPD OPPF PROV FBPC POTA METN DPPF DPPD CYSA MALK YCJV SAPD UGPC YDCT GSIA YEHX DDPF MODC YADG ARAG YHES MACB RBSA UUP MDLB FEPC MLAF MDLA CYDC SAPF TAUB NIKE HISP YTFR SSUB CYDD MSBA YOJI LSRA FHUC FECE YECC YHDZ GLNQ PHNC PHNK ETTA YPHE GLTL LPTB ZNUC XYLG MODF LIVG ALSA SUFC PSTB MGLA FTSE ARTP LOLD LIVF THIQ BTUD NIKD YEJF YBBA FETA PHNL YDDA CCMA YBHF YNJD YBIT YHIH
BACSU - OPUCA OPUAA DPPD APPD OPUBA YVRA OPPD MSMX APPF METN YURJ YKFD YKPA TAGH OPPF YHCH YCBN YFMM YXLF YFIL YHAQ YVFR YDBJ YHEH SUNT YDIF ECFA1 RBSA YUSV YFMR YFMF YTRB YFIB YFIC FHUC TCYN YGAD BMRA YKNV YHEI YWJA YKNU CYDD YTLC CYDC YLMA ECFA2 YCLP BCEA SUFC YXDL YKOD NATA ECSA YXEO YVCR SKFE GLNQ YJKB ARTM PSTB2 PSTB1 SSUB FTSE TCYC MNTB YVRO YKNY EXPZ ALBC YTHP YUFO YHCG ZNUC YYBJ YCLH YYDI YTRE
HALSA - Q9HMX3 Q9HMW0 Q9HMX2 Q9HNZ9 BTUDA Q9HR06 Q9HHQ5 Q9HMT3 Q9HMG1 Q9HRJ6 Q9HMU8 Q9HSQ7 Q9HRH8 PSTB2 PHNC Q9HHM2 Q9HMG6 Q9HNY3 PSTB1 Q9HRZ9 Q9HRV7 Y2317 Y1631 Q9HHR7 Q9HR96 Q9HS04 Q9HT03 Q9HQA8 Q9HR21 Q9HMC1 Q9HMW1
SULSO - Q97VK8 Q97UF2 Q97UH3 Q97YP7 Q97YP3 Q97YY4 Q97UY8 Q97VF5 Q97YP8 Q97ZC0 Q97VC1 Q97UJ9 Q97VF4 Q97VK9 Q7LX64 Q97VH6 Q97YK2 Q97UD4 Q97X18 Q97YQ7 Q97Z03 Q97U54 Q97UH4 Q980W0 Y1893 Y2030 PSTB Q97W42 Q7LXM4 Q7LY07 Q97V01 Q97VY4 Q97V00 Q97VM2 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
50_E	238_K	4.287	1.00
105_Q	188_K	3.597	1.00
24_D	41_D	3.388	1.00
21_N	45_S	3.375	1.00
23_K	82_S	3.271	1.00
37_T	40_N	2.932	1.00
27_V	68_A	2.909	1.00
52_L	240_L	2.826	1.00
82_S	89_E	2.739	1.00
252_N	255_D	2.616	1.00
53_G	236_C	2.576	1.00
47_R	50_E	2.555	1.00
86_N	188_K	2.505	1.00
238_K	250_Y	2.486	1.00
240_L	247_T	2.400	1.00
21_N	84_T	2.389	1.00
28_T	37_T	2.377	1.00
40_N	246_R	2.338	1.00
161_R	164_M	2.336	1.00
22_V	25_L	2.241	1.00
138_S	141_E	2.229	1.00
26_R	80_G	2.224	1.00
26_R	41_D	2.196	1.00
66_A	225_I	2.127	1.00
233_A	254_R	2.102	1.00
89_E	92_N	2.087	1.00
48_A	188_K	2.037	1.00
251_G	256_V	2.023	1.00
23_K	84_T	2.009	1.00
145_E	148_R	2.004	1.00
149_M	184_L	1.997	1.00
29_F	64_Q	1.931	1.00
121_M	125_E	1.916	1.00
226_T	232_V	1.864	1.00
145_E	186_R	1.836	1.00
147_V	162_M	1.776	1.00
66_A	191_I	1.762	1.00
71_G	98_L	1.747	1.00
26_R	37_T	1.736	1.00
18_A	21_N	1.731	1.00
53_G	232_V	1.709	1.00
240_L	250_Y	1.699	1.00
18_A	47_R	1.677	1.00
143_F	147_V	1.640	1.00
148_R	152_A	1.639	1.00
157_E	160_K	1.634	1.00
27_V	73_L	1.633	1.00
22_V	44_F	1.600	1.00
164_M	168_E	1.590	1.00
29_F	38_A	1.568	1.00
128_M	142_A	1.554	1.00
25_L	75_A	1.553	1.00
212_N	215_K	1.545	1.00
251_G	255_D	1.540	1.00
28_T	35_D	1.531	1.00
86_N	105_Q	1.529	1.00
124_G	163_K	1.526	1.00
24_D	43_N	1.525	1.00
255_D	259_Q	1.493	1.00
214_L	220_T	1.490	1.00
124_G	162_M	1.477	1.00
132_M	142_A	1.476	1.00
212_N	234_G	1.465	1.00
161_R	169_F	1.460	1.00
51_T	215_K	1.441	1.00
98_L	102_R	1.440	1.00
128_M	146_S	1.426	1.00
149_M	152_A	1.420	1.00
26_R	40_N	1.412	1.00
27_V	76_N	1.411	1.00
114_M	174_R	1.398	1.00
192_A	222_I	1.386	1.00
122_R	125_E	1.365	1.00
22_V	69_L	1.357	1.00
46_L	52_L	1.350	1.00
127_L	150_L	1.339	1.00
156_P	160_K	1.317	1.00
17_D	48_A	1.305	1.00
208_M	231_V	1.303	1.00
144_E	148_R	1.302	1.00
124_G	143_F	1.300	1.00
109_I	192_A	1.283	1.00
44_F	240_L	1.278	1.00
23_K	45_S	1.277	1.00
44_F	65_T	1.276	1.00
124_G	128_M	1.275	1.00
160_K	164_M	1.263	1.00
51_T	222_I	1.255	1.00
28_T	76_N	1.253	1.00
169_F	177_V	1.251	1.00
143_F	162_M	1.249	1.00
50_E	237_D	1.245	1.00
71_G	74_A	1.232	1.00
73_L	76_N	1.229	1.00
266_I	270_N	1.226	1.00
141_E	144_E	1.223	1.00
148_R	151_D	1.211	1.00
211_L	222_I	1.209	1.00
70_M	108_M	1.208	1.00
18_A	45_S	1.199	1.00
51_T	236_C	1.195	1.00
122_R	163_K	1.194	1.00
88_R	93_L	1.174	1.00
42_L	65_T	1.171	1.00
23_K	43_N	1.171	1.00
125_E	128_M	1.167	1.00
48_A	86_N	1.163	1.00
52_L	238_K	1.160	1.00
126_Q	181_M	1.149	1.00
186_R	220_T	1.147	1.00
54_I	223_I	1.143	1.00
254_R	258_Y	1.140	1.00
297_K	302_Q	1.133	1.00
142_A	146_S	1.122	1.00
84_T	89_E	1.112	1.00
93_L	98_L	1.106	1.00
152_A	213_E	1.105	1.00
263_P	266_I	1.091	1.00
137_M	141_E	1.090	1.00
52_L	250_Y	1.089	1.00
65_T	242_M	1.085	1.00
120_Y	167_H	1.076	1.00
140_A	144_E	1.065	1.00
190_L	220_T	1.064	1.00
47_R	238_K	1.060	1.00
215_K	222_I	1.053	1.00
127_L	184_L	1.053	1.00
121_M	129_E	1.050	1.00
135_K	145_E	1.048	1.00
239_V	253_A	1.045	1.00
46_L	189_L	1.044	1.00
199_L	207_I	1.038	1.00
68_A	75_A	1.015	1.00
24_D	80_G	1.014	1.00
215_K	237_D	1.012	1.00
107_S	187_P	1.006	1.00
150_L	162_M	1.006	1.00
224_M	235_I	0.999	1.00
131_L	184_L	0.995	1.00
22_V	83_A	0.978	1.00
48_A	219_N	0.977	1.00
145_E	149_M	0.977	1.00
124_G	146_S	0.975	1.00
101_L	106_I	0.969	1.00
128_M	143_F	0.967	1.00
47_R	221_A	0.957	1.00
28_T	40_N	0.952	1.00
106_I	189_L	0.947	1.00
40_N	300_P	0.945	1.00
54_I	240_L	0.937	1.00
70_M	191_I	0.933	1.00
69_L	223_I	0.931	1.00
190_L	222_I	0.930	1.00
255_D	258_Y	0.926	1.00
296_P	302_Q	0.924	1.00
19_L	86_N	0.923	1.00
246_R	300_P	0.920	1.00
107_S	182_A	0.917	1.00
143_F	163_K	0.912	1.00
54_I	65_T	0.898	1.00
117_L	174_R	0.897	1.00
204_Q	228_D	0.894	1.00
39_V	68_A	0.892	1.00
128_M	132_M	0.890	1.00
139_K	142_A	0.888	1.00
247_T	250_Y	0.884	1.00
154_K	213_E	0.884	1.00
147_V	151_D	0.881	1.00
27_V	64_Q	0.877	1.00
60_S	242_M	0.870	1.00
25_L	68_A	0.870	1.00
192_A	211_L	0.869	1.00
67_F	72_L	0.865	1.00
156_P	161_R	0.864	1.00
147_V	157_E	0.863	1.00
204_Q	231_V	0.860	1.00
85_F	105_Q	0.855	1.00
263_P	267_G	0.851	1.00
144_E	147_V	0.851	1.00
212_N	235_I	0.850	1.00
257_F	260_P	0.849	1.00
109_I	179_I	0.847	1.00
154_K	206_Q	0.841	1.00
20_L	69_L	0.839	1.00
253_A	264_Y	0.839	1.00
265_S	269_L	0.836	1.00
149_M	153_V	0.835	1.00
274_R	277_A	0.834	1.00
18_A	48_A	0.829	1.00
68_A	83_A	0.826	1.00
295_L	300_P	0.824	1.00
151_D	157_E	0.824	1.00
253_A	257_F	0.824	1.00
298_G	301_F	0.819	1.00
122_R	165_Y	0.816	1.00
298_G	302_Q	0.816	1.00
141_E	145_E	0.812	1.00
270_N	283_L	0.811	1.00
194_E	227_H	0.806	1.00
68_A	73_L	0.805	1.00
121_M	126_Q	0.802	1.00
38_A	64_Q	0.802	1.00
231_V	235_I	0.801	1.00
256_V	265_S	0.801	1.00
51_T	212_N	0.794	1.00
67_F	73_L	0.792	1.00
27_V	39_V	0.789	1.00
130_V	181_M	0.787	1.00
123_V	169_F	0.786	1.00
55_V	232_V	0.786	1.00
155_M	161_R	0.785	1.00
46_L	223_I	0.785	1.00
46_L	221_A	0.781	1.00
42_L	247_T	0.776	1.00
88_R	105_Q	0.775	1.00
41_D	246_R	0.771	1.00
243_Y	248_M	0.767	1.00
19_L	85_F	0.764	1.00
205_A	209_T	0.762	1.00
292_L	295_L	0.761	1.00
137_M	142_A	0.761	1.00
123_V	177_V	0.761	1.00
210_L	213_E	0.760	1.00
104_E	135_K	0.759	1.00
118_N	121_M	0.756	1.00
149_M	180_A	0.756	1.00
39_V	42_L	0.755	1.00
135_K	186_R	0.751	1.00
157_E	161_R	0.750	1.00
161_R	173_M	0.745	1.00
134_H	185_C	0.744	1.00
24_D	27_V	0.736	1.00
130_V	185_C	0.736	1.00
267_G	271_A	0.733	1.00
283_L	287_G	0.732	1.00
89_E	93_L	0.732	1.00
138_S	142_A	0.729	1.00
169_F	173_M	0.728	1.00
289_P	292_L	0.726	1.00
165_Y	168_E	0.725	1.00
236_C	239_V	0.724	1.00
146_S	162_M	0.724	1.00
115_T	174_R	0.723	1.00
151_D	156_P	0.717	1.00
291_N	294_R	0.710	1.00
191_I	223_I	0.707	1.00
100_K	104_E	0.706	1.00
17_D	47_R	0.705	1.00
90_I	101_L	0.701	1.00
262_H	265_S	0.699	1.00
127_L	146_S	0.698	1.00
196_T	231_V	0.698	1.00
140_A	143_F	0.698	1.00
238_K	249_E	0.697	1.00
51_T	235_I	0.695	1.00
171_G	176_R	0.693	1.00
276_D	279_G	0.693	1.00
208_M	234_G	0.692	1.00
132_M	139_K	0.690	1.00
236_C	253_A	0.688	1.00
117_L	177_V	0.687	1.00
224_M	236_C	0.685	1.00
93_L	101_L	0.684	1.00
271_A	274_R	0.683	1.00
287_G	290_P	0.683	1.00
241_V	260_P	0.679	1.00
267_G	270_N	0.679	1.00
82_S	91_L	0.678	1.00
144_E	151_D	0.678	1.00
286_P	289_P	0.674	1.00
166_P	177_V	0.673	1.00
282_M	285_I	0.672	1.00
155_M	173_M	0.672	1.00
297_K	300_P	0.666	1.00
19_L	189_L	0.666	1.00
291_N	296_P	0.666	1.00
136_N	139_K	0.666	1.00
243_Y	246_R	0.666	1.00
290_P	296_P	0.665	1.00
291_N	295_L	0.665	1.00
145_E	152_A	0.661	1.00
70_M	106_I	0.660	1.00
212_N	216_R	0.657	1.00
285_I	289_P	0.657	1.00
52_L	223_I	0.656	1.00
67_F	108_M	0.655	1.00
82_S	92_N	0.654	1.00
85_F	101_L	0.654	1.00
229_L	257_F	0.654	1.00
51_T	237_D	0.653	1.00
299_C	302_Q	0.652	1.00
189_L	223_I	0.652	1.00
18_A	86_N	0.652	1.00
284_T	288_N	0.651	1.00
85_F	189_L	0.650	1.00
209_T	234_G	0.650	1.00
189_L	221_A	0.648	1.00
55_V	241_V	0.648	1.00
128_M	162_M	0.646	1.00
124_G	127_L	0.646	1.00
143_F	146_S	0.645	1.00
149_M	183_L	0.644	1.00
209_T	212_N	0.643	1.00
69_L	83_A	0.641	1.00
19_L	47_R	0.641	1.00
153_V	180_A	0.637	1.00
20_L	85_F	0.637	1.00
117_L	126_Q	0.634	1.00
63_S	67_F	0.631	1.00
292_L	296_P	0.631	1.00
297_K	301_F	0.628	1.00
94_P	98_L	0.627	1.00
272_V	276_D	0.626	1.00
131_L	135_K	0.626	1.00
209_T	213_E	0.626	1.00
28_T	80_G	0.625	1.00
179_I	207_I	0.625	1.00
72_L	110_F	0.624	1.00
29_F	73_L	0.622	1.00
139_K	143_F	0.620	1.00
19_L	45_S	0.618	1.00
41_D	80_G	0.616	1.00
90_I	106_I	0.614	1.00
137_M	140_A	0.613	1.00
243_Y	267_G	0.611	1.00
260_P	265_S	0.610	1.00
84_T	87_G	0.607	1.00
83_A	91_L	0.606	1.00
24_D	81_G	0.606	1.00
49_G	221_A	0.604	1.00
109_I	182_A	0.604	1.00
85_F	90_I	0.604	1.00
183_L	220_T	0.602	1.00
126_Q	166_P	0.602	1.00
22_V	65_T	0.600	1.00
253_A	256_V	0.598	1.00
39_V	65_T	0.598	1.00
295_L	298_G	0.594	1.00
19_L	48_A	0.594	1.00
19_L	221_A	0.594	1.00
241_V	256_V	0.593	1.00
90_I	98_L	0.584	1.00
32_P	35_D	0.583	1.00
251_G	257_F	0.583	1.00
17_D	86_N	0.581	1.00
264_Y	267_G	0.580	1.00
20_L	189_L	0.578	1.00
68_A	76_N	0.577	1.00
122_R	126_Q	0.574	1.00
112_D	115_T	0.571	1.00
296_P	301_F	0.570	1.00
57_E	243_Y	0.569	1.00
164_M	169_F	0.568	1.00
296_P	300_P	0.567	1.00
150_L	153_V	0.564	1.00
256_V	260_P	0.563	1.00
48_A	221_A	0.561	1.00
295_L	301_F	0.559	1.00
94_P	100_K	0.558	1.00
76_N	80_G	0.557	1.00
58_S	194_E	0.557	1.00
50_E	250_Y	0.556	1.00
232_V	236_C	0.556	1.00
208_M	226_T	0.554	1.00
248_M	262_H	0.554	1.00
281_T	285_I	0.554	1.00
294_R	297_K	0.552	1.00
157_E	162_M	0.547	1.00
206_Q	209_T	0.545	1.00
124_G	147_V	0.544	1.00
292_L	298_G	0.543	1.00
28_T	38_A	0.543	1.00
288_N	291_N	0.543	1.00
294_R	298_G	0.541	1.00
293_L	298_G	0.541	1.00
277_A	280_E	0.539	1.00
127_L	130_V	0.539	1.00
248_M	300_P	0.537	1.00
51_T	224_M	0.533	1.00
287_G	291_N	0.533	1.00
289_P	293_L	0.531	1.00
285_I	288_N	0.530	1.00
196_T	207_I	0.528	1.00
292_L	300_P	0.528	1.00
57_E	60_S	0.528	1.00
293_L	300_P	0.527	1.00
88_R	101_L	0.526	1.00
249_E	261_V	0.526	1.00
232_V	239_V	0.526	1.00
226_T	231_V	0.526	1.00
116_S	178_M	0.525	1.00
100_K	105_Q	0.524	1.00
74_A	91_L	0.522	1.00
284_T	289_P	0.520	1.00
281_T	284_T	0.519	1.00
131_L	137_M	0.519	1.00
255_D	261_V	0.517	1.00
293_L	296_P	0.513	1.00
292_L	299_C	0.511	1.00
45_S	250_Y	0.510	1.00
131_L	185_C	0.510	1.00
289_P	295_L	0.510	1.00
291_N	302_Q	0.509	1.00
272_V	275_L	0.507	1.00
139_K	144_E	0.506	1.00
135_K	138_S	0.506	1.00
249_E	260_P	0.504	1.00
285_I	292_L	0.500	1.00
295_L	299_C	0.500	1.00
293_L	297_K	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	0.9021	100	0.206	Contact Map
4fwiB	1	0.9021	100	0.214	Contact Map
4ry2A	2	0.7151	100	0.226	Contact Map
4f4cA	1	0.7151	100	0.236	Contact Map
4ymuJ	2	0.7122	100	0.236	Contact Map
1oxxK	1	0.8961	100	0.237	Contact Map
4u00A	1	0.7151	100	0.237	Contact Map
2yyzA	1	0.8932	100	0.24	Contact Map
2oljA	2	0.7181	100	0.24	Contact Map
1b0uA	2	0.7329	100	0.242	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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