POTD - ECOLI - GREMLIN Contacts

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POTD - Spermidine/putrescine-binding periplasmic protein

UniProt:	P0AFK9	Sequences: MKKWSRHLLAAGALALGMSAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10752
Length:	348 (307)
Sequences:	37728 (30197)
Seq/√Len:	1723.4

ECOLI - POTD POTF YDCS MALE YNJB YCJN UGPB THIB
BACSU - CYCB YESO MDXE ARAN YURO LIPO YTCQ MSME YVGL
HALSA - Q9HP00 Q9HR87 Q9HNZ3 Q9HMT5 Q9HHQ8 Q9HR04
SULSO - Q97ZC3 Q97YY1 Q97VC2 Q97UZ1 Q97UF5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_T	55_I	3.796	1.00
140_G	244_D	3.545	1.00
30_Y	55_I	3.270	1.00
97_Q	268_K	3.199	1.00
28_T	53_K	2.861	1.00
141_D	242_P	2.826	1.00
98_K	123_N	2.805	1.00
155_W	201_K	2.768	1.00
52_I	270_G	2.572	1.00
200_K	204_P	2.525	1.00
47_T	53_K	2.479	1.00
45_Q	277_F	2.415	1.00
50_T	273_K	2.400	1.00
280_R	283_V	2.354	1.00
150_S	153_D	2.249	1.00
197_N	201_K	2.186	1.00
273_K	276_N	2.176	1.00
45_Q	48_K	2.176	1.00
190_K	194_A	2.136	1.00
138_V	244_D	2.126	1.00
30_Y	57_S	2.116	1.00
64_T	68_K	2.102	1.00
140_G	144_D	2.065	1.00
45_Q	49_E	2.047	1.00
285_K	289_E	2.001	1.00
142_A	224_N	1.999	1.00
100_D	123_N	1.991	1.00
44_E	48_K	1.983	1.00
27_N	270_G	1.968	1.00
96_I	260_A	1.964	1.00
78_D	267_N	1.963	1.00
45_Q	286_Q	1.961	1.00
194_A	197_N	1.958	1.00
267_N	270_G	1.906	1.00
198_E	201_K	1.896	1.00
47_T	50_T	1.861	1.00
143_V	225_L	1.850	1.00
126_S	258_S	1.844	1.00
193_E	197_N	1.828	1.00
119_F	124_D	1.821	1.00
206_V	209_F	1.812	1.00
46_F	50_T	1.812	1.00
109_N	299_A	1.811	1.00
210_N	213_N	1.800	1.00
43_L	47_T	1.798	1.00
46_F	273_K	1.794	1.00
141_D	145_P	1.777	1.00
43_L	274_L	1.760	1.00
281_P	285_K	1.753	1.00
116_N	119_F	1.750	1.00
26_N	53_K	1.734	1.00
153_D	156_K	1.711	1.00
80_V	262_P	1.682	1.00
97_Q	263_A	1.676	1.00
269_E	273_K	1.666	1.00
217_P	222_E	1.665	1.00
283_V	286_Q	1.664	1.00
157_P	161_G	1.614	1.00
112_P	116_N	1.606	1.00
268_K	272_L	1.606	1.00
270_G	273_K	1.604	1.00
149_T	153_D	1.589	1.00
286_Q	290_T	1.570	1.00
159_Y	163_L	1.567	1.00
265_A	268_K	1.567	1.00
49_E	280_R	1.556	1.00
139_N	142_A	1.546	1.00
44_E	47_T	1.525	1.00
152_A	155_W	1.499	1.00
306_P	310_N	1.476	1.00
65_M	68_K	1.470	1.00
27_N	267_N	1.468	1.00
33_N	56_Y	1.465	1.00
197_N	200_K	1.464	1.00
140_G	242_P	1.454	1.00
286_Q	289_E	1.452	1.00
155_W	202_L	1.449	1.00
46_F	274_L	1.435	1.00
13_A	16_L	1.433	1.00
138_V	246_V	1.433	1.00
216_N	220_E	1.432	1.00
261_I	275_I	1.429	1.00
191_E	194_A	1.424	1.00
64_T	67_A	1.413	1.00
155_W	198_E	1.413	1.00
65_M	70_K	1.413	1.00
118_P	258_S	1.410	1.00
68_K	72_Y	1.410	1.00
79_L	271_A	1.395	1.00
198_E	202_L	1.394	1.00
152_A	156_K	1.378	1.00
306_P	309_A	1.352	1.00
91_R	125_Y	1.351	1.00
148_V	153_D	1.344	1.00
46_F	277_F	1.344	1.00
18_M	21_A	1.322	1.00
136_I	246_V	1.317	1.00
46_F	52_I	1.308	1.00
217_P	223_V	1.304	1.00
190_K	193_E	1.296	1.00
299_A	302_K	1.285	1.00
104_L	107_F	1.274	1.00
160_K	163_L	1.274	1.00
269_E	272_L	1.266	1.00
201_K	204_P	1.244	1.00
14_L	17_G	1.244	1.00
135_A	245_V	1.234	1.00
213_N	216_N	1.227	1.00
43_L	56_Y	1.226	1.00
272_L	276_N	1.217	1.00
265_A	271_A	1.216	1.00
201_K	205_N	1.205	1.00
281_P	299_A	1.201	1.00
98_K	101_K	1.195	1.00
52_I	273_K	1.192	1.00
218_Y	243_I	1.185	1.00
106_N	276_N	1.184	1.00
109_N	297_N	1.181	1.00
261_I	271_A	1.179	1.00
157_P	205_N	1.179	1.00
67_A	70_K	1.172	1.00
79_L	274_L	1.163	1.00
112_P	115_L	1.158	1.00
98_K	124_D	1.155	1.00
178_R	183_S	1.144	1.00
137_G	228_I	1.144	1.00
159_Y	162_S	1.142	1.00
82_P	260_A	1.137	1.00
155_W	205_N	1.136	1.00
149_T	249_K	1.135	1.00
282_D	285_K	1.125	1.00
105_T	108_S	1.117	1.00
158_E	162_S	1.109	1.00
141_D	241_T	1.105	1.00
43_L	54_V	1.100	1.00
102_S	272_L	1.099	1.00
194_A	198_E	1.098	1.00
139_N	242_P	1.095	1.00
136_I	225_L	1.092	1.00
139_N	241_T	1.088	1.00
297_N	300_A	1.086	1.00
46_F	270_G	1.077	1.00
94_G	263_A	1.069	1.00
261_I	272_L	1.065	1.00
45_Q	282_D	1.062	1.00
31_F	259_L	1.060	1.00
259_L	275_I	1.055	1.00
111_D	298_L	1.054	1.00
78_D	265_A	1.051	1.00
49_E	277_F	1.047	1.00
11_A	15_A	1.046	1.00
29_L	274_L	1.045	1.00
89_K	93_E	1.044	1.00
26_N	51_G	1.043	1.00
157_P	160_K	1.041	1.00
142_A	146_K	1.038	1.00
88_D	92_K	1.035	1.00
205_N	209_F	1.034	1.00
49_E	282_D	1.030	1.00
76_A	262_P	1.025	1.00
186_T	189_P	1.025	1.00
205_N	208_A	1.024	1.00
80_V	260_A	1.023	1.00
10_A	14_L	1.018	1.00
90_M	96_I	1.018	1.00
103_K	106_N	1.015	1.00
282_D	286_Q	1.012	1.00
274_L	278_L	1.011	1.00
281_P	297_N	1.010	1.00
277_F	283_V	1.009	1.00
60_E	64_T	0.999	1.00
142_A	145_P	0.993	1.00
235_V	238_Q	0.990	1.00
91_R	120_D	0.987	1.00
285_K	300_A	0.983	1.00
29_L	270_G	0.981	1.00
36_E	39_P	0.980	1.00
262_P	265_A	0.971	1.00
42_L	45_Q	0.970	1.00
234_F	238_Q	0.962	1.00
261_I	265_A	0.950	1.00
21_A	24_D	0.945	1.00
263_A	268_K	0.936	1.00
171_E	175_M	0.933	1.00
97_Q	272_L	0.918	1.00
162_S	224_N	0.918	1.00
168_D	171_E	0.918	1.00
79_L	275_I	0.917	1.00
129_Y	259_L	0.913	1.00
103_K	272_L	0.913	1.00
141_D	144_D	0.901	1.00
104_L	276_N	0.900	1.00
274_L	277_F	0.895	1.00
154_L	225_L	0.894	1.00
307_E	310_N	0.893	1.00
66_Y	70_K	0.892	1.00
228_I	232_S	0.888	1.00
142_A	159_Y	0.887	1.00
45_Q	283_V	0.887	1.00
187_T	192_I	0.886	1.00
32_Y	77_Y	0.879	1.00
70_K	93_E	0.878	1.00
10_A	13_A	0.877	1.00
42_L	283_V	0.871	1.00
66_Y	69_L	0.868	1.00
146_K	162_S	0.868	1.00
271_A	275_I	0.866	1.00
12_G	16_L	0.862	1.00
189_P	193_E	0.855	1.00
138_V	147_S	0.851	1.00
27_N	51_G	0.846	1.00
185_N	188_D	0.845	1.00
216_N	219_M	0.845	1.00
188_D	191_E	0.840	1.00
200_K	203_M	0.836	1.00
32_Y	59_Y	0.836	1.00
214_P	226_G	0.828	1.00
151_W	155_W	0.828	1.00
305_S	309_A	0.826	1.00
126_S	260_A	0.823	1.00
110_L	279_L	0.823	1.00
111_D	114_M	0.821	1.00
98_K	125_Y	0.819	1.00
54_V	274_L	0.818	1.00
65_M	69_L	0.818	1.00
158_E	161_G	0.816	1.00
312_K	315_Y	0.816	1.00
96_I	125_Y	0.810	1.00
168_D	172_V	0.810	1.00
110_L	115_L	0.809	1.00
298_L	302_K	0.803	1.00
180_L	194_A	0.802	1.00
14_L	18_M	0.800	1.00
97_Q	262_P	0.800	1.00
164_L	167_D	0.800	1.00
47_T	54_V	0.798	1.00
6_R	13_A	0.797	1.00
189_P	192_I	0.794	1.00
118_P	124_D	0.787	1.00
115_L	124_D	0.782	1.00
199_L	203_M	0.782	1.00
173_F	177_L	0.780	1.00
212_D	215_A	0.777	1.00
167_D	170_R	0.775	1.00
219_M	239_A	0.766	1.00
167_D	171_E	0.765	1.00
171_E	174_Q	0.765	1.00
180_L	183_S	0.763	1.00
259_L	278_L	0.761	1.00
9_L	13_A	0.760	1.00
27_N	52_I	0.759	1.00
97_Q	265_A	0.756	1.00
235_V	239_A	0.751	1.00
132_G	255_W	0.750	1.00
91_R	96_I	0.746	1.00
276_N	280_R	0.743	1.00
109_N	281_P	0.741	1.00
51_G	273_K	0.740	1.00
97_Q	101_K	0.740	1.00
138_V	143_V	0.740	1.00
81_V	259_L	0.736	1.00
173_F	176_A	0.736	1.00
13_A	17_G	0.736	1.00
17_G	20_A	0.736	1.00
167_D	172_V	0.734	1.00
159_Y	224_N	0.733	1.00
196_Y	200_K	0.731	1.00
24_D	27_N	0.731	1.00
29_L	267_N	0.727	1.00
41_G	44_E	0.726	1.00
113_D	116_N	0.725	1.00
307_E	311_D	0.722	1.00
143_V	146_K	0.719	1.00
137_G	233_A	0.718	1.00
166_T	171_E	0.716	1.00
212_D	216_N	0.715	1.00
165_L	168_D	0.714	1.00
65_M	72_Y	0.713	1.00
47_T	52_I	0.712	1.00
115_L	119_F	0.712	1.00
86_Y	89_K	0.711	1.00
16_L	19_S	0.706	1.00
97_Q	261_I	0.705	1.00
80_V	96_I	0.704	1.00
147_S	153_D	0.704	1.00
137_G	245_V	0.702	1.00
147_S	246_V	0.702	1.00
164_L	168_D	0.700	1.00
10_A	16_L	0.700	1.00
99_I	275_I	0.698	1.00
146_K	158_E	0.697	1.00
102_S	105_T	0.695	1.00
19_S	22_H	0.692	1.00
112_P	298_L	0.692	1.00
119_F	122_N	0.690	1.00
11_A	14_L	0.689	1.00
110_L	114_M	0.688	1.00
40_P	44_E	0.684	1.00
100_D	124_D	0.683	1.00
144_D	242_P	0.683	1.00
233_A	237_R	0.683	1.00
186_T	191_E	0.679	1.00
109_N	298_L	0.678	1.00
6_R	9_L	0.678	1.00
12_G	15_A	0.675	1.00
169_A	173_F	0.675	1.00
6_R	10_A	0.674	1.00
310_N	313_T	0.665	1.00
215_A	219_M	0.663	1.00
179_K	182_Y	0.662	1.00
234_F	237_R	0.660	1.00
188_D	192_I	0.660	1.00
97_Q	264_N	0.658	1.00
15_A	18_M	0.653	1.00
213_N	217_P	0.650	1.00
31_F	56_Y	0.649	1.00
111_D	115_L	0.647	1.00
164_L	223_V	0.644	1.00
311_D	314_L	0.643	1.00
100_D	272_L	0.643	1.00
178_R	182_Y	0.642	1.00
19_S	23_A	0.640	1.00
8_L	12_G	0.638	1.00
36_E	40_P	0.637	1.00
164_L	169_A	0.637	1.00
57_S	77_Y	0.636	1.00
17_G	21_A	0.635	1.00
64_T	72_Y	0.635	1.00
180_L	184_G	0.634	1.00
20_A	23_A	0.633	1.00
273_K	277_F	0.633	1.00
141_D	221_G	0.631	1.00
180_L	198_E	0.630	1.00
165_L	171_E	0.628	1.00
146_K	159_Y	0.628	1.00
309_A	312_K	0.627	1.00
9_L	16_L	0.626	1.00
191_E	195_A	0.626	1.00
68_K	71_T	0.623	1.00
29_L	271_A	0.623	1.00
67_A	71_T	0.622	1.00
30_Y	78_D	0.621	1.00
25_D	28_T	0.619	1.00
188_D	193_E	0.614	1.00
146_K	224_N	0.614	1.00
150_S	250_E	0.613	1.00
31_F	79_L	0.612	1.00
7_H	11_A	0.610	1.00
87_V	126_S	0.610	1.00
305_S	308_V	0.610	1.00
195_A	199_L	0.608	1.00
137_G	243_I	0.608	1.00
53_K	56_Y	0.608	1.00
87_V	91_R	0.606	1.00
59_Y	68_K	0.605	1.00
268_K	271_A	0.605	1.00
42_L	278_L	0.605	1.00
111_D	301_R	0.601	1.00
27_N	273_K	0.601	1.00
78_D	271_A	0.601	1.00
178_R	181_G	0.599	1.00
215_A	228_I	0.599	1.00
37_Y	40_P	0.599	1.00
133_A	230_N	0.599	1.00
50_T	270_G	0.598	1.00
261_I	268_K	0.597	1.00
9_L	12_G	0.596	1.00
27_N	30_Y	0.596	1.00
174_Q	177_L	0.596	1.00
118_P	126_S	0.594	1.00
42_L	286_Q	0.594	1.00
106_N	109_N	0.594	1.00
7_H	10_A	0.593	1.00
66_Y	89_K	0.593	1.00
139_N	221_G	0.590	1.00
108_S	111_D	0.586	1.00
83_S	86_Y	0.585	1.00
165_L	169_A	0.584	1.00
42_L	277_F	0.584	1.00
79_L	259_L	0.583	1.00
165_L	173_F	0.583	1.00
192_I	195_A	0.582	1.00
100_D	119_F	0.580	1.00
108_S	115_L	0.579	1.00
32_Y	57_S	0.579	1.00
91_R	94_G	0.579	1.00
138_V	225_L	0.577	1.00
151_W	198_E	0.576	1.00
182_Y	191_E	0.574	1.00
6_R	17_G	0.567	1.00
178_R	184_G	0.567	1.00
217_P	220_E	0.565	1.00
143_V	159_Y	0.565	1.00
66_Y	86_Y	0.564	1.00
32_Y	72_Y	0.564	1.00
101_K	123_N	0.563	1.00
120_D	123_N	0.563	1.00
11_A	17_G	0.562	1.00
166_T	169_A	0.562	1.00
26_N	52_I	0.561	1.00
41_G	290_T	0.558	1.00
165_L	172_V	0.558	1.00
30_Y	33_N	0.558	1.00
185_N	189_P	0.558	1.00
15_A	19_S	0.558	1.00
298_L	301_R	0.557	1.00
109_N	112_P	0.557	1.00
101_K	272_L	0.554	1.00
186_T	192_I	0.553	1.00
43_L	53_K	0.553	1.00
37_Y	41_G	0.550	1.00
293_Y	296_P	0.549	1.00
258_S	262_P	0.548	1.00
309_A	313_T	0.548	1.00
166_T	170_R	0.545	1.00
16_L	21_A	0.545	1.00
81_V	129_Y	0.544	1.00
5_S	8_L	0.544	1.00
136_I	227_M	0.543	1.00
57_S	68_K	0.542	1.00
38_V	41_G	0.542	1.00
172_V	176_A	0.541	1.00
143_V	224_N	0.540	1.00
8_L	14_L	0.539	1.00
31_F	81_V	0.539	1.00
159_Y	225_L	0.537	1.00
284_A	296_P	0.536	1.00
149_T	154_L	0.535	1.00
114_M	131_W	0.533	1.00
99_I	261_I	0.531	1.00
166_T	172_V	0.529	1.00
232_S	236_A	0.529	1.00
21_A	25_D	0.529	1.00
214_P	223_V	0.528	1.00
132_G	257_D	0.527	1.00
99_I	272_L	0.527	1.00
90_M	95_M	0.524	1.00
232_S	235_V	0.524	1.00
124_D	127_I	0.524	1.00
76_A	264_N	0.523	1.00
169_A	172_V	0.523	1.00
211_S	214_P	0.522	1.00
164_L	172_V	0.520	1.00
193_E	196_Y	0.519	1.00
130_I	257_D	0.519	1.00
47_T	51_G	0.519	1.00
192_I	196_Y	0.519	1.00
272_L	275_I	0.515	1.00
82_P	90_M	0.514	1.00
167_D	176_A	0.512	1.00
103_K	269_E	0.509	1.00
215_A	235_V	0.507	1.00
103_K	276_N	0.506	1.00
164_L	170_R	0.505	1.00
195_A	198_E	0.505	1.00
165_L	170_R	0.503	1.00
50_T	277_F	0.502	1.00
27_N	31_F	0.502	1.00
88_D	91_R	0.500	1.00
241_T	244_D	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
3uorA	1	0.9195	100	0.255	Contact Map
4gl0A	1	0.9195	100	0.256	Contact Map
1potA	1	0.9253	100	0.259	Contact Map
4mfiA	1	0.9167	100	0.267	Contact Map
4eqbA	1	0.9195	100	0.269	Contact Map
2v84A	1	0.8994	100	0.271	Contact Map
4r9fA	1	0.9167	100	0.272	Contact Map
3ttmA	1	0.9253	100	0.275	Contact Map
4r2fA	1	0.9109	100	0.277	Contact Map
4jdfA	1	0.9224	100	0.284	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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