APPD - BACSU - GREMLIN Contacts

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APPD - Oligopeptide transport ATP-binding protein AppD

UniProt:	P42064	Sequences: MSTLLEVNNLKTYFFRKKEPIPAVDGVDFHISKGETVALVGESGSGKSITSLSIMGLVQSSGGKIMDGSIKLEDKDLTSFTENDYCKIRGNEVSMIFQEPMTSLNPVLTIGEQITEVLIYHKNMKKKEARQRAVELLQMVGFSRAEQIMKEYPHRLSGGMRQRVMIAIALSCNPKLLIADEPTTALDVTIQAQVLELMKDLCQKFNTSILLITHDLGVVSEAADRVIVMYCGQVVENATVDDLFLEPLHPYTEGLLTSIPVIDGEIDKLNAIKGSVPTPDNLPPGCRFAPRCPKAMDKCWTNQPSLLTHKSGRTVRCFLYEEEGAEQS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	328 (267)
Sequences:	55548 (34596)
Seq/√Len:	2117.2

ECOLI - DPPD OPPD DDPD PROV YDCT CYSA POTG FBPC DPPF YCJV MALK METN SAPD POTA UGPC YADG OPPF YEHX GSIA DDPF MODC MACB RBSA YHES ARAG UUP FEPC MLAF SAPF NIKE PHNC TAUB MDLB MDLA FECE HISP FHUC YECC YTFR GLNQ CYDC SSUB MSBA CYDD XYLG YHDZ PHNK YOJI LPTB ETTA ZNUC GLTL LSRA YPHE SUFC MODF LIVG THIQ NIKD FTSE ARTP PSTB LOLD ALSA BTUD LIVF MGLA YBBA FETA YEJF PHNL CCMA YDDA YNJD YBHF YBIT YHIH
BACSU - APPD DPPD OPUBA OPPD OPUCA OPUAA YVRA MSMX METN YURJ APPF YKFD YHCH YCBN OPPF YHAQ YDBJ YVFR YFIL YXLF YKPA TAGH YFMM YHEH YUSV YDIF YTRB RBSA ECFA1 FHUC YFMF SUNT TCYN YFMR YXDL YFIC YFIB YCLP YKNV BMRA YLMA YGAD YKNU YWJA BCEA YKOD YTLC CYDD YHEI YXEO SUFC CYDC ECSA SKFE GLNQ YTHP ARTM YVCR NATA ECFA2 TCYC SSUB FTSE YJKB MNTB YVRO PSTB1 ALBC YKNY PSTB2 YUFO YHCG YCLH ZNUC EXPZ YYBJ YYDI YTRE
HALSA - Q9HMX3 Q9HMW0 Q9HMX2 BTUDA Q9HNZ9 Q9HHQ5 Q9HMT3 Q9HR06 Q9HRJ6 Q9HMG1 Q9HMU8 Q9HRH8 Q9HSQ7 PHNC Q9HMG6 PSTB2 Q9HHM2 Q9HNY3 Q9HRZ9 Q9HRV7 Y2317 Y1631 PSTB1 Q9HR96 Q9HHR7 Q9HS04 Q9HT03 Q9HQA8 Q9HR21 Q9HMC1 Q9HMW1
SULSO - Q97UH3 Q97UF2 Q97YP3 Q97YY4 Q97VF5 Q97UY8 Q97YP7 Q97ZC0 Q97VK8 Q97VC1 Q97VF4 Q97YP8 Q97VH6 Q97UJ9 Q97VK9 Q7LX64 Q97YK2 Q97UD4 Q97X18 Q97YQ7 Q97U54 Q97Z03 Y1893 Q980W0 Q97UH4 Y2030 Q97W42 PSTB Q7LY07 Q97V01 Q97V00 Q97UG5 Q7LXM4 Q97VM2 Q97VY4 Q7LX80 Q97Z56 Q97YP4 Q97Z96 Q97UC2 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
35_E	225_R	4.182	1.00
92_E	175_K	3.504	1.00
9_N	26_G	3.397	1.00
6_E	30_H	3.202	1.00
8_N	69_S	3.165	1.00
22_P	25_D	2.897	1.00
12_T	53_S	2.888	1.00
37_V	227_I	2.788	1.00
69_S	76_D	2.593	1.00
239_T	242_D	2.576	1.00
38_A	223_A	2.531	1.00
25_D	233_Q	2.483	1.00
32_S	35_E	2.447	1.00
225_R	237_N	2.403	1.00
148_I	151_E	2.386	1.00
227_I	234_V	2.374	1.00
139_M	205_F	2.369	1.00
73_E	175_K	2.298	1.00
200_D	204_K	2.282	1.00
7_V	10_L	2.278	1.00
13_Y	22_P	2.272	1.00
6_E	71_K	2.251	1.00
51_S	212_I	2.204	1.00
11_K	26_G	2.198	1.00
33_K	175_K	2.135	1.00
76_D	79_S	2.105	1.00
238_A	243_L	2.088	1.00
139_M	204_K	2.084	1.00
132_R	135_E	2.077	1.00
220_S	241_D	2.043	1.00
136_L	171_S	2.027	1.00
132_R	173_N	2.020	1.00
213_T	219_V	1.977	1.00
125_K	128_E	1.935	1.00
14_F	49_I	1.924	1.00
8_N	71_K	1.827	1.00
134_V	149_M	1.759	1.00
38_A	219_V	1.733	1.00
11_K	22_P	1.732	1.00
51_S	178_I	1.684	1.00
108_L	112_E	1.652	1.00
9_N	28_D	1.624	1.00
12_T	58_V	1.603	1.00
115_T	129_A	1.598	1.00
151_E	155_R	1.597	1.00
227_I	237_N	1.596	1.00
148_I	156_L	1.556	1.00
14_F	23_A	1.542	1.00
115_T	133_A	1.542	1.00
7_V	29_F	1.538	1.00
238_A	242_D	1.521	1.00
135_E	139_M	1.513	1.00
173_N	205_F	1.512	1.00
111_G	150_K	1.496	1.00
11_K	62_G	1.493	1.00
199_K	221_E	1.479	1.00
199_K	202_C	1.475	1.00
130_R	134_V	1.469	1.00
144_R	147_Q	1.467	1.00
119_I	129_A	1.457	1.00
12_T	61_S	1.447	1.00
111_G	149_M	1.434	1.00
10_L	60_S	1.429	1.00
179_A	209_I	1.426	1.00
11_K	25_D	1.417	1.00
242_D	246_E	1.417	1.00
73_E	92_E	1.402	1.00
13_Y	20_P	1.385	1.00
36_T	202_C	1.372	1.00
134_V	144_R	1.348	1.00
96_I	179_A	1.345	1.00
35_E	224_D	1.341	1.00
15_F	20_P	1.338	1.00
101_M	161_R	1.336	1.00
7_V	54_I	1.333	1.00
143_S	147_Q	1.333	1.00
156_L	164_V	1.329	1.00
8_N	30_H	1.320	1.00
139_M	200_D	1.318	1.00
109_T	112_E	1.305	1.00
195_L	218_V	1.305	1.00
147_Q	151_E	1.298	1.00
75_K	80_F	1.292	1.00
31_I	37_V	1.276	1.00
111_G	115_T	1.266	1.00
114_I	137_L	1.258	1.00
8_N	28_D	1.231	1.00
36_T	209_I	1.227	1.00
13_Y	61_S	1.224	1.00
56_G	59_Q	1.219	1.00
29_F	227_I	1.204	1.00
250_P	253_E	1.201	1.00
253_E	257_T	1.200	1.00
55_M	95_M	1.199	1.00
29_F	50_T	1.194	1.00
130_R	149_M	1.184	1.00
137_L	149_M	1.176	1.00
37_V	237_N	1.169	1.00
131_Q	135_E	1.168	1.00
112_E	115_T	1.159	1.00
39_L	210_L	1.154	1.00
36_T	223_A	1.152	1.00
71_K	76_D	1.138	1.00
241_D	245_L	1.135	1.00
109_T	150_K	1.134	1.00
37_V	225_R	1.133	1.00
27_V	50_T	1.125	1.00
128_E	131_Q	1.110	1.00
111_G	130_R	1.101	1.00
32_S	225_R	1.099	1.00
198_M	209_I	1.099	1.00
113_Q	168_I	1.086	1.00
53_S	60_S	1.080	1.00
114_I	171_S	1.079	1.00
226_V	240_V	1.068	1.00
50_T	229_M	1.066	1.00
111_G	133_A	1.066	1.00
33_K	206_N	1.066	1.00
33_K	73_E	1.061	1.00
177_L	207_T	1.060	1.00
58_V	61_S	1.056	1.00
202_C	209_I	1.055	1.00
127_K	131_Q	1.052	1.00
129_A	133_A	1.051	1.00
54_I	210_L	1.043	1.00
24_V	53_S	1.042	1.00
124_M	129_A	1.037	1.00
107_V	154_H	1.024	1.00
115_T	119_I	1.020	1.00
141_G	200_D	1.018	1.00
202_C	224_D	1.015	1.00
31_I	176_L	1.009	1.00
13_Y	25_D	1.000	1.00
173_N	207_T	0.996	1.00
138_Q	143_S	0.995	1.00
186_L	194_V	0.991	1.00
138_Q	144_R	0.988	1.00
211_L	222_A	0.979	1.00
177_L	209_I	0.975	1.00
108_L	116_E	0.966	1.00
143_S	148_I	0.964	1.00
240_V	244_F	0.958	1.00
55_M	178_I	0.956	1.00
45_S	229_M	0.955	1.00
191_Q	218_V	0.951	1.00
32_S	208_S	0.950	1.00
93_V	176_L	0.939	1.00
12_T	49_I	0.926	1.00
88_I	93_V	0.925	1.00
115_T	130_R	0.925	1.00
134_V	138_Q	0.924	1.00
39_L	227_I	0.922	1.00
94_S	174_P	0.920	1.00
52_L	57_L	0.913	1.00
135_E	138_Q	0.911	1.00
118_L	171_S	0.909	1.00
250_P	254_G	0.903	1.00
254_G	258_S	0.898	1.00
94_S	169_A	0.892	1.00
242_D	245_L	0.890	1.00
7_V	70_I	0.889	1.00
110_I	156_L	0.889	1.00
39_L	50_T	0.886	1.00
75_K	92_E	0.886	1.00
53_S	70_I	0.875	1.00
244_F	247_P	0.873	1.00
126_K	129_A	0.871	1.00
12_T	24_V	0.871	1.00
179_A	198_M	0.870	1.00
15_F	19_E	0.868	1.00
10_L	53_S	0.862	1.00
24_V	27_V	0.859	1.00
125_K	129_A	0.855	1.00
218_V	222_A	0.853	1.00
191_Q	215_D	0.852	1.00
96_I	166_I	0.851	1.00
109_T	152_Y	0.851	1.00
23_A	49_I	0.849	1.00
249_H	252_T	0.847	1.00
279_P	282_L	0.843	1.00
4_L	73_E	0.839	1.00
108_L	113_Q	0.830	1.00
142_F	148_I	0.829	1.00
104_L	161_R	0.828	1.00
132_R	136_L	0.828	1.00
276_V	279_P	0.825	1.00
243_L	252_T	0.825	1.00
72_L	92_E	0.823	1.00
9_N	12_T	0.823	1.00
234_V	237_N	0.823	1.00
4_L	72_L	0.822	1.00
52_L	58_V	0.819	1.00
136_L	167_A	0.814	1.00
36_T	199_K	0.813	1.00
128_E	132_R	0.812	1.00
76_D	80_F	0.811	1.00
110_I	164_V	0.808	1.00
136_L	139_M	0.803	1.00
124_M	128_E	0.799	1.00
277_P	283_P	0.799	1.00
152_Y	155_R	0.795	1.00
58_V	63_G	0.794	1.00
83_N	87_K	0.787	1.00
5_L	54_I	0.785	1.00
53_S	58_V	0.784	1.00
261_V	264_G	0.784	1.00
130_R	150_K	0.783	1.00
176_L	210_L	0.779	1.00
196_E	221_E	0.779	1.00
141_G	193_Q	0.779	1.00
223_A	226_V	0.777	1.00
31_I	208_S	0.774	1.00
26_G	233_Q	0.774	1.00
133_A	149_M	0.767	1.00
181_E	214_H	0.767	1.00
40_V	219_V	0.763	1.00
274_G	277_P	0.761	1.00
254_G	257_T	0.759	1.00
9_N	62_G	0.759	1.00
117_V	172_C	0.758	1.00
144_R	149_M	0.755	1.00
263_D	266_I	0.755	1.00
122_K	132_R	0.754	1.00
156_L	160_M	0.753	1.00
279_P	283_P	0.753	1.00
27_V	234_V	0.748	1.00
199_K	222_A	0.748	1.00
104_L	164_V	0.736	1.00
36_T	222_A	0.735	1.00
96_I	169_A	0.732	1.00
273_K	276_V	0.731	1.00
272_I	276_V	0.730	1.00
240_V	243_L	0.727	1.00
271_A	275_S	0.724	1.00
176_L	208_S	0.724	1.00
140_V	167_A	0.723	1.00
121_H	172_C	0.719	1.00
77_L	88_I	0.714	1.00
37_V	210_L	0.710	1.00
153_P	164_V	0.710	1.00
24_V	50_T	0.707	1.00
82_E	87_K	0.707	1.00
252_T	256_L	0.707	1.00
274_G	279_P	0.706	1.00
87_K	91_N	0.706	1.00
36_T	224_D	0.706	1.00
178_I	210_L	0.705	1.00
197_L	200_D	0.701	1.00
211_L	223_A	0.701	1.00
119_I	126_K	0.700	1.00
278_T	283_P	0.699	1.00
183_T	218_V	0.699	1.00
136_L	170_L	0.698	1.00
278_T	281_N	0.697	1.00
15_F	18_K	0.697	1.00
91_N	122_K	0.696	1.00
117_V	120_Y	0.695	1.00
105_N	108_L	0.692	1.00
196_E	199_K	0.692	1.00
102_T	161_R	0.692	1.00
144_R	148_I	0.691	1.00
54_I	70_I	0.690	1.00
274_G	278_T	0.690	1.00
40_V	228_V	0.689	1.00
117_V	168_I	0.685	1.00
230_Y	235_V	0.685	1.00
223_A	240_V	0.684	1.00
173_N	204_K	0.684	1.00
109_T	113_Q	0.683	1.00
199_K	203_Q	0.683	1.00
114_I	133_A	0.682	1.00
216_L	244_F	0.682	1.00
122_K	129_A	0.681	1.00
4_L	176_L	0.680	1.00
148_I	160_M	0.676	1.00
77_L	93_V	0.675	1.00
122_K	125_K	0.675	1.00
278_T	282_L	0.673	1.00
192_A	196_E	0.672	1.00
201_L	207_T	0.669	1.00
80_F	88_I	0.668	1.00
5_L	72_L	0.667	1.00
52_L	95_M	0.663	1.00
243_L	247_P	0.659	1.00
69_S	78_T	0.658	1.00
258_S	261_V	0.657	1.00
235_V	249_H	0.655	1.00
31_I	210_L	0.655	1.00
230_Y	254_G	0.652	1.00
118_L	123_N	0.652	1.00
72_L	88_I	0.652	1.00
14_F	58_V	0.651	1.00
72_L	77_L	0.649	1.00
270_N	274_G	0.648	1.00
228_V	247_P	0.648	1.00
48_S	52_L	0.648	1.00
111_G	114_I	0.647	1.00
280_D	283_P	0.644	1.00
272_I	275_S	0.643	1.00
99_E	102_T	0.642	1.00
111_G	134_V	0.641	1.00
230_Y	233_Q	0.638	1.00
251_Y	254_G	0.638	1.00
241_D	244_F	0.638	1.00
72_L	176_L	0.633	1.00
57_L	97_F	0.633	1.00
219_V	226_V	0.632	1.00
71_K	74_D	0.631	1.00
35_E	237_N	0.630	1.00
33_K	208_S	0.625	1.00
276_V	283_P	0.624	1.00
104_L	113_Q	0.624	1.00
34_G	208_S	0.623	1.00
7_V	50_T	0.620	1.00
196_E	200_D	0.619	1.00
259_I	263_D	0.618	1.00
42_E	230_Y	0.617	1.00
5_L	176_L	0.615	1.00
142_F	160_M	0.615	1.00
69_S	79_S	0.613	1.00
170_L	207_T	0.607	1.00
158_G	163_R	0.605	1.00
131_Q	138_Q	0.603	1.00
228_V	243_L	0.602	1.00
70_I	78_T	0.601	1.00
55_M	93_V	0.601	1.00
242_D	248_L	0.601	1.00
276_V	280_D	0.600	1.00
42_E	251_Y	0.599	1.00
151_E	156_L	0.599	1.00
98_Q	158_G	0.596	1.00
118_L	124_M	0.595	1.00
126_K	130_R	0.593	1.00
275_S	279_P	0.588	1.00
276_V	282_L	0.587	1.00
271_A	276_V	0.587	1.00
130_R	133_A	0.585	1.00
275_S	278_T	0.585	1.00
75_K	88_I	0.584	1.00
274_G	283_P	0.584	1.00
4_L	208_S	0.580	1.00
238_A	247_P	0.579	1.00
103_S	165_M	0.578	1.00
43_S	181_E	0.577	1.00
238_A	244_F	0.577	1.00
132_R	139_M	0.577	1.00
231_C	279_P	0.574	1.00
166_I	194_V	0.572	1.00
123_N	129_A	0.570	1.00
29_F	37_V	0.569	1.00
220_S	240_V	0.567	1.00
230_Y	249_H	0.567	1.00
183_T	194_V	0.566	1.00
53_S	61_S	0.566	1.00
251_Y	255_L	0.564	1.00
195_L	213_T	0.563	1.00
162_Q	185_A	0.563	1.00
133_A	171_S	0.563	1.00
201_L	205_F	0.562	1.00
113_Q	153_P	0.561	1.00
272_I	279_P	0.560	1.00
140_V	197_L	0.559	1.00
131_Q	134_V	0.558	1.00
42_E	45_S	0.558	1.00
22_P	26_G	0.555	1.00
271_A	274_G	0.554	1.00
114_I	117_V	0.553	1.00
116_E	120_Y	0.552	1.00
273_K	277_P	0.549	1.00
56_G	89_R	0.548	1.00
87_K	92_E	0.546	1.00
110_I	114_I	0.546	1.00
115_T	149_M	0.542	1.00
197_L	201_L	0.540	1.00
219_V	223_A	0.539	1.00
269_L	272_I	0.539	1.00
124_M	132_R	0.535	1.00
265_E	268_K	0.532	1.00
118_L	122_K	0.529	1.00
277_P	281_N	0.529	1.00
246_E	249_H	0.527	1.00
13_Y	23_A	0.522	1.00
277_P	280_D	0.519	1.00
118_L	121_H	0.518	1.00
202_C	207_T	0.515	1.00
264_G	267_D	0.514	1.00
255_L	258_S	0.511	1.00
30_H	237_N	0.511	1.00
118_L	172_C	0.510	1.00
104_L	165_M	0.508	1.00
77_L	80_F	0.506	1.00
200_D	203_Q	0.503	1.00
59_Q	62_G	0.503	1.00
135_E	173_N	0.503	1.00
250_P	257_T	0.502	1.00
256_L	260_P	0.502	1.00
136_L	140_V	0.501	1.00
271_A	279_P	0.500	1.00
265_E	269_L	0.500	1.00
99_E	161_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
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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
4fwiB	1	0.9299	100	0.213	Contact Map
3tuiC	2	0.9573	100	0.22	Contact Map
4u00A	1	0.7348	100	0.233	Contact Map
2oljA	2	0.7378	100	0.234	Contact Map
4ry2A	2	0.7287	100	0.235	Contact Map
4yerA	2	0.8567	100	0.242	Contact Map
4ymuJ	2	0.7317	100	0.244	Contact Map
1b0uA	2	0.753	100	0.245	Contact Map
4f4cA	1	0.7012	100	0.245	Contact Map
2yyzA	1	0.9299	100	0.246	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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