YOCD - BACSU - GREMLIN Contacts

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YOCD - Putative carboxypeptidase YocD

UniProt:	O35046	Sequences: MYASKLKKGDEIRIVSPATSMSILSNEAKIQAKTALERLGYRVTIAEHANECNEFDSSSIESRVHDLHAAFFDPGVKAILTTLGGFNSNQLLRYLDYEKIKRHPKILCGYSDITALCNAIYQKTGLVTYSGPHFSTFAMKKGLDYTEEYFLSCCASDDPFEIHPSSEWSDDRWFLDQENRRFYPNNGPVVIQEGYAEGTLIGGNLCTLNLLQGTEYFPETEHTILLIEDDYMSDIHMFDRDLQSLIHLPAFSHVKAILIGRFQKASNVSIDLVKAMIETKKELSGIPIIANINAGHTSPIATFPIGGTCRIEAISGTSRIWIDKH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	325 (293)
Sequences:	2945 (2277)
Seq/√Len:	133.0

ECOLI - LDCA
BACSU - YOCD LDC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
197_E	310_R	4.761	1.00
10_D	77_K	4.047	1.00
13_R	70_A	3.883	1.00
11_E	42_R	3.643	1.00
18_A	88_S	3.540	1.00
51_E	62_S	3.139	1.00
59_S	62_S	3.116	1.00
221_E	253_H	3.003	1.00
60_I	90_Q	2.964	1.00
11_E	44_T	2.941	1.00
16_S	82_T	2.865	1.00
44_T	73_D	2.848	1.00
41_Y	155_A	2.813	1.00
197_E	308_T	2.746	1.00
12_I	41_Y	2.515	1.00
14_I	82_T	2.361	1.00
68_H	99_K	2.214	1.00
64_V	94_Y	2.208	1.00
222_H	255_K	2.194	1.00
246_I	283_L	2.194	1.00
200_L	303_F	2.191	1.00
33_K	37_E	2.165	1.00
224_I	309_C	2.140	1.00
195_Y	312_E	2.126	1.00
256_A	311_I	2.113	1.00
195_Y	310_R	2.110	1.00
44_T	76_V	2.098	1.00
65_H	69_A	2.088	1.00
78_A	106_I	2.075	1.00
199_T	223_T	2.063	1.00
217_F	250_A	2.040	1.00
48_H	66_D	2.040	1.00
48_H	51_E	1.960	1.00
254_V	257_I	1.912	1.00
74_P	103_H	1.852	1.00
227_I	259_I	1.850	1.00
37_E	42_R	1.829	1.00
257_I	286_I	1.819	1.00
64_V	68_H	1.799	1.00
4_S	77_K	1.784	1.00
13_R	76_V	1.780	1.00
225_L	254_V	1.767	1.00
39_L	151_L	1.730	1.00
32_A	134_F	1.706	1.00
34_T	38_R	1.689	1.00
148_E	152_S	1.688	1.00
258_L	292_I	1.668	1.00
34_T	37_E	1.663	1.00
45_I	49_A	1.644	1.00
193_E	314_I	1.642	1.00
15_V	70_A	1.607	1.00
68_H	72_F	1.602	1.00
41_Y	151_L	1.593	1.00
33_K	45_I	1.591	1.00
11_E	75_G	1.588	1.00
61_E	94_Y	1.571	1.00
226_L	305_I	1.561	1.00
67_L	71_F	1.544	1.00
145_Y	301_A	1.540	1.00
127_V	307_G	1.528	1.00
47_E	69_A	1.527	1.00
200_L	309_C	1.523	1.00
143_L	299_P	1.514	1.00
11_E	76_V	1.505	1.00
72_F	99_K	1.500	1.00
258_L	311_I	1.489	1.00
33_K	43_V	1.476	1.00
199_T	308_T	1.412	1.00
16_S	49_A	1.407	1.00
272_L	275_A	1.400	1.00
61_E	65_H	1.385	1.00
225_L	251_F	1.375	1.00
220_T	250_A	1.370	1.00
117_C	128_T	1.367	1.00
151_L	155_A	1.365	1.00
212_Q	248_L	1.360	1.00
77_K	103_H	1.350	1.00
130_S	204_N	1.337	1.00
226_L	303_F	1.336	1.00
251_F	286_I	1.310	1.00
13_R	44_T	1.310	1.00
71_F	100_I	1.305	1.00
190_V	313_A	1.297	1.00
110_Y	136_T	1.297	1.00
48_H	62_S	1.296	1.00
97_Y	119_A	1.285	1.00
257_I	281_K	1.281	1.00
121_Y	305_I	1.278	1.00
243_Q	280_K	1.276	1.00
71_F	126_L	1.266	1.00
26_N	30_I	1.265	1.00
80_L	108_C	1.264	1.00
130_S	300_I	1.264	1.00
117_C	305_I	1.257	1.00
106_I	129_Y	1.251	1.00
196_A	256_A	1.243	1.00
129_Y	302_T	1.234	1.00
254_V	286_I	1.230	1.00
117_C	130_S	1.216	1.00
88_S	116_L	1.210	1.00
261_R	293_N	1.209	1.00
93_R	247_H	1.204	1.00
150_F	154_C	1.195	0.99
120_I	124_T	1.186	0.99
15_V	95_L	1.184	0.99
7_K	10_D	1.178	0.99
30_I	33_K	1.173	0.99
35_A	39_L	1.173	0.99
212_Q	217_F	1.161	0.99
259_I	262_F	1.155	0.99
17_P	113_I	1.154	0.99
46_A	66_D	1.147	0.99
45_I	50_N	1.137	0.99
202_G	226_L	1.121	0.99
209_N	212_Q	1.120	0.99
274_K	290_A	1.113	0.99
312_E	315_S	1.113	0.99
100_I	124_T	1.108	0.99
92_L	115_A	1.102	0.99
13_R	46_A	1.100	0.99
235_I	276_M	1.089	0.99
161_E	319_R	1.085	0.99
90_Q	239_D	1.079	0.99
189_V	290_A	1.077	0.99
37_E	43_V	1.071	0.99
117_C	121_Y	1.071	0.99
108_C	131_G	1.070	0.99
98_E	101_K	1.068	0.99
14_I	134_F	1.061	0.99
233_S	237_M	1.058	0.99
229_D	262_F	1.051	0.99
107_L	120_I	1.047	0.99
108_C	302_T	1.046	0.99
216_Y	247_H	1.029	0.98
81_T	113_I	1.023	0.98
233_S	241_D	1.014	0.98
120_I	128_T	1.004	0.98
261_R	297_T	1.002	0.98
64_V	95_L	0.999	0.98
226_L	294_A	0.999	0.98
310_R	319_R	0.998	0.98
312_E	318_S	0.997	0.98
123_K	215_E	0.995	0.98
30_I	34_T	0.992	0.98
71_F	103_H	0.990	0.98
115_A	207_T	0.985	0.98
11_E	43_V	0.980	0.98
64_V	91_L	0.979	0.98
62_S	65_H	0.975	0.98
212_Q	244_S	0.971	0.98
46_A	70_A	0.967	0.98
148_E	151_L	0.966	0.98
208_L	227_I	0.959	0.98
220_T	253_H	0.956	0.97
118_N	208_L	0.953	0.97
83_L	87_N	0.950	0.97
248_L	251_F	0.949	0.97
257_I	288_I	0.936	0.97
107_L	113_I	0.935	0.97
136_T	300_I	0.935	0.97
224_I	256_A	0.932	0.97
281_K	288_I	0.927	0.97
42_R	75_G	0.924	0.97
12_I	43_V	0.922	0.97
289_I	313_A	0.919	0.97
127_V	304_P	0.918	0.97
68_H	95_L	0.917	0.97
44_T	75_G	0.917	0.97
99_K	103_H	0.916	0.97
294_A	303_F	0.915	0.97
152_S	156_S	0.910	0.97
206_C	233_S	0.909	0.97
39_L	147_E	0.907	0.97
217_F	220_T	0.906	0.97
212_Q	245_L	0.902	0.96
12_I	78_A	0.898	0.96
14_I	33_K	0.895	0.96
89_N	247_H	0.888	0.96
149_Y	302_T	0.885	0.96
250_A	253_H	0.885	0.96
195_Y	314_I	0.884	0.96
201_I	223_T	0.880	0.96
206_C	229_D	0.880	0.96
210_L	244_S	0.875	0.96
87_N	239_D	0.875	0.96
289_I	311_I	0.873	0.96
196_A	311_I	0.873	0.96
21_M	82_T	0.872	0.96
153_C	302_T	0.869	0.96
309_C	320_I	0.868	0.96
52_C	58_S	0.867	0.96
220_T	223_T	0.865	0.95
60_I	239_D	0.861	0.95
18_A	113_I	0.860	0.95
204_N	262_F	0.860	0.95
86_F	236_H	0.859	0.95
205_L	245_L	0.858	0.95
232_M	264_K	0.857	0.95
83_L	133_H	0.851	0.95
36_L	80_L	0.849	0.95
229_D	233_S	0.848	0.95
152_S	157_D	0.847	0.95
189_V	274_K	0.847	0.95
29_K	33_K	0.846	0.95
121_Y	201_I	0.833	0.94
67_L	95_L	0.832	0.94
60_I	64_V	0.830	0.94
89_N	207_T	0.830	0.94
205_L	241_D	0.828	0.94
73_D	105_K	0.825	0.94
87_N	90_Q	0.815	0.94
209_N	244_S	0.814	0.94
15_V	66_D	0.811	0.94
209_N	241_D	0.810	0.94
259_I	290_A	0.809	0.94
47_E	65_H	0.809	0.94
39_L	155_A	0.806	0.93
201_I	218_P	0.806	0.93
233_S	236_H	0.805	0.93
278_E	282_E	0.804	0.93
206_C	210_L	0.804	0.93
71_F	107_L	0.802	0.93
53_N	59_S	0.802	0.93
149_Y	153_C	0.799	0.93
68_H	97_Y	0.795	0.93
214_T	244_S	0.794	0.93
93_R	216_Y	0.791	0.93
96_D	100_I	0.790	0.93
256_A	313_A	0.790	0.93
218_P	250_A	0.784	0.92
30_I	50_N	0.782	0.92
4_S	7_K	0.782	0.92
104_P	126_L	0.781	0.92
243_Q	279_T	0.779	0.92
15_V	79_I	0.776	0.92
100_I	126_L	0.776	0.92
149_Y	152_S	0.776	0.92
234_D	237_M	0.775	0.92
32_A	36_L	0.775	0.92
110_Y	300_I	0.769	0.92
31_Q	34_T	0.767	0.92
6_L	10_D	0.764	0.92
119_A	216_Y	0.763	0.91
81_T	107_L	0.762	0.91
68_H	96_D	0.761	0.91
11_E	77_K	0.760	0.91
89_N	210_L	0.753	0.91
115_A	211_L	0.745	0.90
194_G	313_A	0.745	0.90
238_F	273_V	0.743	0.90
95_L	100_I	0.743	0.90
92_L	216_Y	0.741	0.90
83_L	231_Y	0.739	0.90
304_P	307_G	0.738	0.90
60_I	87_N	0.737	0.90
246_I	280_K	0.736	0.90
30_I	37_E	0.733	0.90
89_N	243_Q	0.733	0.90
274_K	278_E	0.733	0.90
219_E	223_T	0.733	0.90
67_L	91_L	0.732	0.90
67_L	107_L	0.732	0.90
45_I	48_H	0.732	0.90
207_T	210_L	0.730	0.90
192_Q	278_E	0.728	0.89
312_E	316_G	0.727	0.89
281_K	284_S	0.726	0.89
78_A	154_C	0.721	0.89
12_I	80_L	0.719	0.89
121_Y	128_T	0.719	0.89
17_P	116_L	0.718	0.89
236_H	239_D	0.718	0.89
54_E	58_S	0.713	0.88
26_N	50_N	0.713	0.88
227_I	242_L	0.707	0.88
246_I	252_S	0.705	0.88
106_I	127_V	0.702	0.88
19_T	83_L	0.698	0.87
110_Y	130_S	0.698	0.87
97_Y	124_T	0.696	0.87
8_K	151_L	0.692	0.87
33_K	134_F	0.689	0.87
190_V	289_I	0.689	0.87
29_K	45_I	0.689	0.87
214_T	217_F	0.689	0.87
206_C	241_D	0.685	0.86
100_I	120_I	0.684	0.86
113_I	116_L	0.684	0.86
261_R	291_N	0.679	0.86
36_L	43_V	0.676	0.86
227_I	257_I	0.671	0.85
225_L	250_A	0.667	0.85
214_T	247_H	0.666	0.85
70_A	76_V	0.665	0.85
205_L	238_F	0.662	0.84
11_E	73_D	0.659	0.84
244_S	248_L	0.658	0.84
92_L	119_A	0.658	0.84
199_T	222_H	0.657	0.84
152_S	160_F	0.655	0.84
245_L	250_A	0.652	0.84
144_D	148_E	0.651	0.83
313_A	318_S	0.649	0.83
106_I	154_C	0.648	0.83
189_V	291_N	0.648	0.83
32_A	138_A	0.644	0.83
119_A	124_T	0.644	0.83
49_A	82_T	0.643	0.83
17_P	67_L	0.643	0.83
147_E	151_L	0.642	0.83
60_I	91_L	0.639	0.82
97_Y	100_I	0.639	0.82
188_P	293_N	0.636	0.82
243_Q	247_H	0.635	0.82
151_L	154_C	0.633	0.82
192_Q	286_I	0.632	0.82
101_K	124_T	0.631	0.82
146_T	299_P	0.630	0.81
88_S	115_A	0.628	0.81
87_N	229_D	0.628	0.81
69_A	73_D	0.626	0.81
27_E	31_Q	0.625	0.81
238_F	265_A	0.624	0.81
136_T	139_M	0.623	0.81
108_C	150_F	0.623	0.81
93_R	246_I	0.622	0.81
96_D	104_P	0.621	0.81
118_N	218_P	0.620	0.80
246_I	279_T	0.619	0.80
13_R	73_D	0.619	0.80
152_S	158_D	0.619	0.80
193_E	313_A	0.617	0.80
206_C	237_M	0.616	0.80
73_D	76_V	0.616	0.80
68_H	100_I	0.616	0.80
129_Y	304_P	0.614	0.80
56_D	90_Q	0.613	0.80
22_S	28_A	0.613	0.80
88_S	107_L	0.612	0.80
233_S	238_F	0.612	0.80
14_I	45_I	0.608	0.79
237_M	241_D	0.604	0.79
134_F	138_A	0.601	0.78
246_I	284_S	0.601	0.78
5_K	157_D	0.599	0.78
8_K	42_R	0.597	0.78
136_T	146_T	0.597	0.78
312_E	317_T	0.595	0.78
98_E	102_R	0.595	0.78
242_L	280_K	0.594	0.78
86_F	239_D	0.594	0.78
312_E	319_R	0.593	0.77
7_K	77_K	0.592	0.77
228_E	260_G	0.589	0.77
128_T	305_I	0.589	0.77
106_I	302_T	0.588	0.77
12_I	155_A	0.588	0.77
14_I	32_A	0.587	0.77
311_I	320_I	0.586	0.77
252_S	284_S	0.585	0.76
87_N	236_H	0.583	0.76
235_I	265_A	0.583	0.76
6_L	106_I	0.582	0.76
205_L	239_D	0.581	0.76
88_S	113_I	0.579	0.76
16_S	261_R	0.579	0.76
315_S	319_R	0.573	0.75
246_I	251_F	0.572	0.75
208_L	245_L	0.571	0.75
238_F	241_D	0.569	0.74
273_V	277_I	0.569	0.74
161_E	317_T	0.567	0.74
114_T	245_L	0.565	0.74
90_Q	236_H	0.563	0.74
9_G	78_A	0.563	0.74
135_S	139_M	0.562	0.74
56_D	87_N	0.562	0.74
185_N	188_P	0.562	0.74
275_A	278_E	0.561	0.73
311_I	314_I	0.561	0.73
68_H	94_Y	0.560	0.73
68_H	91_L	0.556	0.73
196_A	313_A	0.555	0.73
224_I	311_I	0.550	0.72
250_A	254_V	0.549	0.72
162_I	301_A	0.548	0.72
87_N	231_Y	0.548	0.72
91_L	94_Y	0.546	0.71
211_L	218_P	0.546	0.71
231_Y	237_M	0.544	0.71
262_F	273_V	0.544	0.71
121_Y	306_G	0.543	0.71
81_T	88_S	0.542	0.71
83_L	236_H	0.534	0.70
21_M	29_K	0.534	0.70
204_N	229_D	0.533	0.70
69_A	102_R	0.533	0.70
201_I	220_T	0.533	0.70
205_L	266_S	0.531	0.69
219_E	253_H	0.531	0.69
31_Q	35_A	0.531	0.69
153_C	160_F	0.530	0.69
6_L	77_K	0.529	0.69
91_L	95_L	0.529	0.69
121_Y	223_T	0.527	0.69
10_D	41_Y	0.527	0.69
210_L	240_R	0.524	0.68
72_F	100_I	0.524	0.68
86_F	233_S	0.524	0.68
15_V	46_A	0.523	0.68
140_K	143_L	0.522	0.68
227_I	247_H	0.519	0.68
132_P	302_T	0.518	0.67
191_I	194_G	0.515	0.67
239_D	280_K	0.515	0.67
119_A	214_T	0.513	0.67
201_I	254_V	0.512	0.67
183_Y	186_N	0.511	0.66
194_G	256_A	0.511	0.66
68_H	128_T	0.510	0.66
56_D	60_I	0.509	0.66
273_V	276_M	0.508	0.66
10_D	78_A	0.507	0.66
16_S	57_S	0.507	0.66
192_Q	285_G	0.507	0.66
46_A	49_A	0.507	0.66
204_N	241_D	0.507	0.66
81_T	133_H	0.507	0.66
239_D	279_T	0.506	0.66
89_N	136_T	0.505	0.66
149_Y	301_A	0.505	0.66
61_E	93_R	0.503	0.65
123_K	216_Y	0.503	0.65
21_M	32_A	0.503	0.65
229_D	239_D	0.502	0.65
47_E	62_S	0.502	0.65
162_I	185_N	0.502	0.65
35_A	147_E	0.501	0.65
118_N	201_I	0.501	0.65
309_C	318_S	0.500	0.65

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
4e5sA	2	0.9969	100	0.061	Contact Map
3tlaA	2	0.9938	100	0.07	Contact Map
4injA	2	0.9815	100	0.074	Contact Map
4jvoA	2	0.9908	100	0.089	Contact Map
1zl0A	1	0.92	100	0.137	Contact Map
4eysA	3	0.9538	100	0.155	Contact Map
3g23A	2	0.8031	100	0.21	Contact Map
2csuA	2	0.4369	90.4	0.946	Contact Map
4z0nA	1	0.5354	84	0.951	Contact Map
3mwdA	2	0.4246	81.8	0.952	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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