YPDF - ECOLI - GREMLIN Contacts

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YPDF - Aminopeptidase YpdF

UniProt:	P76524	Sequences: MTLLASLRDWLKAQQLDAVLLSSRQNKQPHLGISTGSGYVVISRESAHILVDSRYYVEVEARAQGYQLHLLDATNTLTTIVNQIIADEQLQTLGFEGQQVSWETAHRWQSELNAKLVSATPDVLRQIKTPEEVEKIRLACGIADRGAEHIRRFIQAGMSEREIAAELEWFMRQQGAEKASFDTIVASGWRGALPHGKASDKIVAAGEFVTLDFGALYQGYCSDMTRTLLVNGEGVSAESHLLFNVYQIVLQAQLAAISAIRPGVRCQQVDDAARRVITEAGYGDYFGHNTGHAIGIEVHEDPRFSPRDTTTLQPGMLLTVEPGIYLPGQGGVRIEDVVLVTPQGAEVLYAMPKTVLLTGEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14153
Length:	361 (341)
Sequences:	11024 (8051)
Seq/√Len:	436.0

ECOLI - YPDF AMPP PEPQ MAP1
BACSU - YKVY YQHT MAP11 MAP12
HALSA - Q9HRF6 Q9HQC0 Q9HMB3 Q9HP03
SULSO - Q980E9 Q981D7

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
137_R	346_E	5.580	1.00
314_P	342_P	4.510	1.00
260_I	340_V	3.239	1.00
133_V	339_L	3.038	1.00
237_A	329_Q	2.725	1.00
138_L	141_G	2.567	1.00
247_Q	251_Q	2.534	1.00
145_R	174_Q	2.472	1.00
25_Q	297_E	2.452	1.00
235_V	238_E	2.400	1.00
149_H	170_F	2.353	1.00
189_W	201_K	2.349	1.00
270_D	274_R	2.348	1.00
248_I	280_A	2.326	1.00
169_W	173_Q	2.303	1.00
265_R	268_Q	2.295	1.00
255_A	276_V	2.282	1.00
267_Q	309_T	2.272	1.00
237_A	244_N	2.256	1.00
166_E	169_W	2.245	1.00
16_L	94_G	2.243	1.00
254_L	258_S	2.232	1.00
256_A	273_A	2.190	1.00
159_S	202_I	2.174	1.00
236_S	244_N	2.170	1.00
136_I	317_L	2.150	1.00
31_L	40_V	2.138	1.00
127_I	313_Q	2.134	1.00
341_T	346_E	2.132	1.00
275_R	279_E	2.127	1.00
106_H	109_Q	2.121	1.00
294_I	337_V	2.105	1.00
259_A	272_A	2.072	1.00
137_R	141_G	1.983	1.00
92_T	113_N	1.933	1.00
50_L	80_I	1.922	1.00
10_W	13_A	1.863	1.00
203_V	230_V	1.846	1.00
255_A	258_S	1.841	1.00
135_K	218_Q	1.828	1.00
168_E	172_R	1.809	1.00
52_D	55_Y	1.797	1.00
204_A	207_E	1.795	1.00
245_V	332_V	1.787	1.00
76_T	79_T	1.771	1.00
247_Q	355_V	1.764	1.00
12_K	44_R	1.747	1.00
153_F	166_E	1.740	1.00
245_V	330_G	1.711	1.00
276_V	280_A	1.706	1.00
161_R	200_D	1.688	1.00
144_D	351_M	1.688	1.00
170_F	173_Q	1.677	1.00
201_K	207_E	1.675	1.00
249_V	332_V	1.671	1.00
341_T	344_G	1.644	1.00
212_D	223_D	1.636	1.00
320_V	338_V	1.628	1.00
151_R	228_L	1.622	1.00
251_Q	255_A	1.602	1.00
223_D	335_E	1.600	1.00
170_F	174_Q	1.597	1.00
265_R	311_T	1.591	1.00
92_T	115_K	1.580	1.00
271_D	275_R	1.577	1.00
277_I	324_I	1.573	1.00
229_L	234_G	1.571	1.00
339_L	348_L	1.553	1.00
334_I	353_K	1.537	1.00
257_I	338_V	1.536	1.00
239_S	247_Q	1.530	1.00
251_Q	280_A	1.526	1.00
319_T	337_V	1.517	1.00
185_V	209_V	1.510	1.00
208_F	238_E	1.500	1.00
7_L	30_H	1.487	1.00
313_Q	316_M	1.481	1.00
159_S	162_E	1.474	1.00
254_L	354_T	1.472	1.00
187_S	201_K	1.469	1.00
180_S	221_C	1.463	1.00
256_A	269_V	1.462	1.00
156_A	205_A	1.450	1.00
212_D	335_E	1.443	1.00
165_A	169_W	1.442	1.00
261_R	264_V	1.426	1.00
126_Q	316_M	1.405	1.00
250_L	254_L	1.388	1.00
149_H	174_Q	1.376	1.00
163_I	203_V	1.375	1.00
252_A	276_V	1.369	1.00
130_P	134_E	1.354	1.00
208_F	229_L	1.344	1.00
216_L	221_C	1.336	1.00
339_L	346_E	1.335	1.00
9_D	13_A	1.330	1.00
148_E	152_R	1.328	1.00
187_S	203_V	1.326	1.00
251_Q	279_E	1.324	1.00
149_H	152_R	1.320	1.00
134_E	138_L	1.311	1.00
245_V	326_L	1.303	1.00
17_D	91_Q	1.300	1.00
28_Q	219_G	1.299	1.00
58_E	62_R	1.278	1.00
253_Q	257_I	1.266	1.00
264_V	268_Q	1.259	1.00
162_E	173_Q	1.254	1.00
16_L	115_K	1.242	1.00
10_W	14_Q	1.241	1.00
80_I	83_Q	1.239	1.00
273_A	290_T	1.235	1.00
262_P	314_P	1.234	1.00
236_S	239_S	1.225	1.00
257_I	347_V	1.224	1.00
312_L	318_L	1.206	1.00
123_V	313_Q	1.200	1.00
254_L	353_K	1.198	1.00
147_A	224_M	1.191	1.00
166_E	170_F	1.190	1.00
127_I	316_M	1.189	1.00
253_Q	353_K	1.182	1.00
143_A	224_M	1.167	1.00
30_H	124_L	1.152	1.00
268_Q	271_D	1.151	1.00
164_A	168_E	1.151	1.00
136_I	140_C	1.149	1.00
163_I	209_V	1.149	1.00
208_F	227_T	1.140	1.00
312_L	340_V	1.138	1.00
253_Q	336_D	1.137	1.00
141_G	145_R	1.130	1.00
267_Q	271_D	1.124	1.00
8_R	43_S	1.121	1.00
166_E	173_Q	1.117	1.00
251_Q	276_V	1.115	1.00
142_I	176_A	1.110	1.00
244_N	280_A	1.108	1.00
142_I	219_G	1.105	1.00
260_I	269_V	1.094	1.00
246_Y	334_I	1.093	1.00
255_A	272_A	1.087	1.00
138_L	217_Y	1.081	1.00
256_A	272_A	1.076	1.00
248_I	277_I	1.066	1.00
26_N	96_E	1.066	1.00
246_Y	353_K	1.065	1.00
11_L	16_L	1.063	1.00
190_R	196_G	1.059	1.00
105_A	109_Q	1.055	1.00
270_D	290_T	1.051	1.00
149_H	166_E	1.048	1.00
244_N	248_I	1.047	1.00
17_D	92_T	1.044	1.00
7_L	19_V	1.043	1.00
264_V	272_A	1.040	1.00
244_N	247_Q	1.037	1.00
201_K	204_A	1.034	1.00
315_G	339_L	1.034	1.00
134_E	137_R	1.029	1.00
102_W	105_A	1.028	1.00
140_C	144_D	1.027	1.00
67_Q	70_L	1.027	1.00
269_V	272_A	1.025	1.00
21_L	30_H	1.022	1.00
149_H	173_Q	1.021	1.00
186_A	196_G	1.021	1.00
131_E	135_K	1.020	1.00
60_E	63_A	1.003	1.00
259_A	264_V	1.002	1.00
317_L	339_L	1.001	1.00
48_H	72_D	0.989	1.00
158_M	166_E	0.989	1.00
27_K	38_G	0.988	1.00
336_D	353_K	0.987	1.00
188_G	207_E	0.987	1.00
94_G	117_V	0.985	1.00
252_A	277_I	0.983	1.00
317_L	348_L	0.982	1.00
191_G	210_T	0.981	1.00
260_I	338_V	0.979	1.00
147_A	228_L	0.977	1.00
8_R	11_L	0.976	1.00
187_S	207_E	0.973	1.00
137_R	339_L	0.972	1.00
338_V	347_V	0.968	1.00
56_Y	60_E	0.968	1.00
267_Q	307_R	0.966	1.00
158_M	162_E	0.965	1.00
148_E	351_M	0.963	1.00
26_N	122_D	0.962	1.00
43_S	47_A	0.953	1.00
248_I	251_Q	0.952	1.00
239_S	355_V	0.952	1.00
318_L	340_V	0.951	1.00
257_I	320_V	0.950	1.00
248_I	276_V	0.950	1.00
76_T	80_I	0.950	1.00
209_V	230_V	0.947	1.00
260_I	320_V	0.946	1.00
144_D	350_A	0.945	1.00
275_R	278_T	0.945	1.00
131_E	134_E	0.943	1.00
255_A	259_A	0.941	1.00
117_V	120_T	0.939	1.00
262_P	341_T	0.939	1.00
176_A	215_A	0.939	1.00
102_W	106_H	0.937	1.00
168_E	183_T	0.935	1.00
140_C	337_V	0.934	1.00
211_L	228_L	0.930	1.00
154_I	228_L	0.930	1.00
18_A	43_S	0.924	1.00
326_L	329_Q	0.920	1.00
168_E	179_A	0.913	1.00
138_L	218_Q	0.911	1.00
260_I	345_A	0.910	1.00
161_R	165_A	0.909	1.00
8_R	44_R	0.909	1.00
293_A	300_E	0.907	1.00
237_A	326_L	0.906	1.00
11_L	18_A	0.906	1.00
130_P	341_T	0.903	1.00
272_A	275_R	0.899	1.00
77_L	85_I	0.897	1.00
107_R	111_E	0.896	1.00
9_D	12_K	0.893	1.00
30_H	121_P	0.890	1.00
18_A	41_V	0.888	1.00
269_V	312_L	0.888	1.00
294_I	317_L	0.885	1.00
138_L	142_I	0.884	1.00
171_M	215_A	0.879	1.00
293_A	302_P	0.879	1.00
163_I	185_V	0.878	1.00
179_A	183_T	0.873	1.00
43_S	48_H	0.873	1.00
154_I	163_I	0.872	1.00
229_L	238_E	0.870	1.00
277_I	282_Y	0.868	1.00
273_A	286_F	0.867	1.00
340_V	345_A	0.865	1.00
259_A	269_V	0.863	1.00
148_E	352_P	0.858	1.00
304_F	318_L	0.856	1.00
149_H	153_F	0.852	1.00
146_G	170_F	0.851	1.00
212_D	321_E	0.849	1.00
7_L	42_I	0.848	1.00
310_T	313_Q	0.845	1.00
247_Q	250_L	0.843	1.00
272_A	276_V	0.842	1.00
264_V	269_V	0.841	1.00
257_I	345_A	0.840	1.00
190_R	193_L	0.839	1.00
327_P	330_G	0.839	1.00
59_V	63_A	0.838	1.00
155_Q	158_M	0.837	1.00
106_H	110_S	0.833	1.00
182_D	197_K	0.832	1.00
79_T	83_Q	0.826	1.00
167_L	171_M	0.826	1.00
143_A	222_S	0.825	1.00
21_L	121_P	0.823	1.00
49_I	59_V	0.823	1.00
123_V	310_T	0.823	1.00
338_V	345_A	0.822	1.00
305_S	308_D	0.820	1.00
10_W	123_V	0.819	1.00
321_E	335_E	0.819	1.00
186_A	191_G	0.818	1.00
29_P	124_L	0.813	1.00
82_N	86_A	0.811	1.00
234_G	239_S	0.807	1.00
223_D	292_H	0.802	1.00
226_R	336_D	0.802	1.00
266_C	312_L	0.797	1.00
190_R	201_K	0.797	1.00
16_L	19_V	0.797	1.00
262_P	345_A	0.796	1.00
103_E	107_R	0.795	1.00
156_A	230_V	0.794	1.00
237_A	245_V	0.792	1.00
181_F	214_G	0.792	1.00
146_G	171_M	0.791	1.00
292_H	335_E	0.790	1.00
140_C	349_Y	0.786	1.00
245_V	248_I	0.785	1.00
250_L	334_I	0.785	1.00
276_V	279_E	0.784	1.00
160_E	190_R	0.781	1.00
8_R	42_I	0.780	1.00
132_E	220_Y	0.779	1.00
145_R	148_E	0.779	1.00
294_I	319_T	0.778	1.00
262_P	342_P	0.775	1.00
95_F	102_W	0.775	1.00
325_Y	333_R	0.772	1.00
31_L	47_A	0.771	1.00
59_V	62_R	0.769	1.00
17_D	44_R	0.766	1.00
27_K	40_V	0.766	1.00
194_P	288_H	0.766	1.00
262_P	313_Q	0.765	1.00
135_K	138_L	0.763	1.00
100_V	105_A	0.762	1.00
120_T	123_V	0.756	1.00
256_A	320_V	0.755	1.00
57_V	61_A	0.753	1.00
90_L	93_L	0.752	1.00
261_R	345_A	0.751	1.00
265_R	309_T	0.746	1.00
245_V	282_Y	0.744	1.00
252_A	256_A	0.742	1.00
83_Q	86_A	0.741	1.00
64_Q	68_L	0.739	1.00
19_V	117_V	0.738	1.00
69_H	73_A	0.737	1.00
15_Q	92_T	0.737	1.00
255_A	273_A	0.737	1.00
147_A	351_M	0.735	1.00
28_Q	296_I	0.734	1.00
18_A	93_L	0.733	1.00
259_A	262_P	0.733	1.00
252_A	272_A	0.733	1.00
323_G	333_R	0.732	1.00
66_Y	69_H	0.729	1.00
167_L	211_L	0.729	1.00
64_Q	67_Q	0.727	1.00
215_A	222_S	0.722	1.00
158_M	163_I	0.722	1.00
48_H	52_D	0.719	1.00
223_D	321_E	0.717	1.00
46_S	67_Q	0.717	1.00
142_I	217_Y	0.712	1.00
193_L	196_G	0.705	1.00
206_G	230_V	0.705	1.00
144_D	148_E	0.700	1.00
189_W	328_G	0.699	1.00
97_G	106_H	0.699	1.00
341_T	345_A	0.698	1.00
53_S	56_Y	0.696	1.00
153_F	170_F	0.696	1.00
140_C	222_S	0.694	1.00
152_R	156_A	0.691	1.00
246_Y	250_L	0.691	1.00
135_K	217_Y	0.690	1.00
288_H	299_H	0.689	1.00
48_H	69_H	0.689	1.00
225_T	335_E	0.686	1.00
187_S	230_V	0.685	1.00
55_Y	58_E	0.681	1.00
39_Y	42_I	0.681	1.00
133_V	137_R	0.681	1.00
274_R	286_F	0.680	1.00
126_Q	313_Q	0.679	1.00
191_G	208_F	0.675	1.00
269_V	290_T	0.672	1.00
142_I	174_Q	0.669	1.00
221_C	298_V	0.669	1.00
285_Y	327_P	0.669	1.00
310_T	316_M	0.668	1.00
256_A	259_A	0.663	1.00
234_G	238_E	0.662	1.00
38_G	42_I	0.658	1.00
42_I	45_E	0.657	1.00
141_G	144_D	0.656	1.00
20_L	41_V	0.654	0.99
128_K	132_E	0.653	0.99
167_L	213_F	0.653	0.99
150_I	211_L	0.652	0.99
11_L	19_V	0.648	0.99
195_H	299_H	0.648	0.99
281_G	284_D	0.646	0.99
262_P	340_V	0.644	0.99
70_L	73_A	0.643	0.99
268_Q	272_A	0.636	0.99
206_G	233_E	0.635	0.99
7_L	124_L	0.632	0.99
205_A	233_E	0.632	0.99
16_L	21_L	0.631	0.99
24_R	27_K	0.630	0.99
159_S	200_D	0.628	0.99
212_D	292_H	0.628	0.99
22_S	25_Q	0.627	0.99
25_Q	296_I	0.626	0.99
46_S	52_D	0.626	0.99
130_P	315_G	0.625	0.99
185_V	211_L	0.622	0.99
49_I	52_D	0.621	0.99
146_G	167_L	0.620	0.99
169_W	172_R	0.619	0.99
147_A	213_F	0.618	0.99
98_Q	101_S	0.616	0.99
82_N	85_I	0.615	0.99
8_R	12_K	0.614	0.99
140_C	224_M	0.612	0.99
165_A	172_R	0.612	0.99
314_P	341_T	0.611	0.99
101_S	105_A	0.609	0.99
248_I	324_I	0.609	0.99
325_Y	331_G	0.608	0.99
261_R	343_Q	0.607	0.99
292_H	321_E	0.607	0.99
150_I	163_I	0.607	0.99
179_A	182_D	0.606	0.99
143_A	213_F	0.605	0.99
147_A	150_I	0.603	0.99
140_C	348_L	0.603	0.99
142_I	215_A	0.602	0.99
144_D	349_Y	0.601	0.99
105_A	111_E	0.600	0.99
253_Q	320_V	0.599	0.99
143_A	146_G	0.597	0.99
101_S	104_T	0.596	0.99
164_A	198_A	0.596	0.99
252_A	273_A	0.593	0.99
101_S	107_R	0.593	0.99
69_H	72_D	0.592	0.99
289_N	292_H	0.592	0.99
256_A	290_T	0.592	0.99
326_L	330_G	0.586	0.99
18_A	21_L	0.583	0.99
126_Q	310_T	0.583	0.99
150_I	153_F	0.583	0.99
308_D	311_T	0.583	0.99
109_Q	112_L	0.583	0.99
14_Q	17_D	0.583	0.99
154_I	230_V	0.581	0.99
8_R	47_A	0.581	0.99
72_D	80_I	0.581	0.99
266_C	304_F	0.578	0.99
311_T	314_P	0.578	0.99
260_I	312_L	0.576	0.99
107_R	110_S	0.574	0.99
26_N	29_P	0.573	0.99
68_L	71_L	0.572	0.99
292_H	295_G	0.571	0.99
134_E	141_G	0.571	0.99
191_G	229_L	0.571	0.99
191_G	331_G	0.571	0.99
154_I	209_V	0.570	0.99
55_Y	59_V	0.570	0.99
238_E	329_Q	0.569	0.99
162_E	165_A	0.567	0.99
51_V	56_Y	0.567	0.99
139_A	143_A	0.566	0.99
207_E	238_E	0.566	0.99
248_I	282_Y	0.564	0.99
71_L	74_T	0.562	0.98
208_F	234_G	0.562	0.98
26_N	121_P	0.561	0.98
10_W	124_L	0.557	0.98
68_L	72_D	0.557	0.98
51_V	55_Y	0.555	0.98
150_I	166_E	0.554	0.98
224_M	349_Y	0.553	0.98
248_I	252_A	0.553	0.98
133_V	317_L	0.552	0.98
212_D	225_T	0.551	0.98
270_D	289_N	0.550	0.98
66_Y	71_L	0.548	0.98
347_V	350_A	0.547	0.98
33_I	58_E	0.547	0.98
65_G	68_L	0.547	0.98
323_G	331_G	0.545	0.98
317_L	337_V	0.544	0.98
191_G	194_P	0.544	0.98
46_S	69_H	0.539	0.98
255_A	275_R	0.539	0.98
263_G	311_T	0.539	0.98
100_V	104_T	0.537	0.98
66_Y	70_L	0.536	0.98
11_L	14_Q	0.536	0.98
273_A	276_V	0.534	0.98
123_V	126_Q	0.534	0.98
97_G	116_L	0.532	0.98
252_A	255_A	0.532	0.98
57_V	60_E	0.530	0.98
38_G	44_R	0.530	0.98
224_M	337_V	0.529	0.98
251_Q	254_L	0.529	0.98
156_A	204_A	0.527	0.98
22_S	216_L	0.526	0.98
263_G	313_Q	0.525	0.98
130_P	314_P	0.524	0.98
43_S	46_S	0.523	0.98
288_H	291_G	0.522	0.98
53_S	287_G	0.520	0.97
23_S	27_K	0.520	0.97
38_G	45_E	0.520	0.97
122_D	301_D	0.519	0.97
229_L	232_G	0.519	0.97
250_L	353_K	0.518	0.97
229_L	235_V	0.518	0.97
28_Q	34_S	0.517	0.97
163_I	211_L	0.517	0.97
54_R	58_E	0.516	0.97
147_A	151_R	0.515	0.97
189_W	192_A	0.514	0.97
41_V	80_I	0.514	0.97
65_G	69_H	0.513	0.97
127_I	314_P	0.510	0.97
146_G	215_A	0.509	0.97
233_E	239_S	0.508	0.97
277_I	286_F	0.508	0.97
303_R	307_R	0.507	0.97
254_L	257_I	0.503	0.97
22_S	27_K	0.503	0.97
245_V	324_I	0.501	0.97
67_Q	71_L	0.500	0.97
91_Q	113_N	0.500	0.97

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
3q6dA	1	0.9723	100	0.135	Contact Map
2zsgA	2	0.9723	100	0.138	Contact Map
4fkcA	2	0.9695	100	0.155	Contact Map
1wn1A	2	0.9584	100	0.166	Contact Map
1wy2A	2	0.9474	100	0.169	Contact Map
4r60A	2	0.9806	100	0.175	Contact Map
4egeA	2	0.9751	100	0.178	Contact Map
3ig4A	4	0.9806	100	0.188	Contact Map
2v3zA	3	0.9806	100	0.201	Contact Map
1kp0A	2	0.8726	100	0.202	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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