POTF - ECOLI - GREMLIN Contacts

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POTF - Putrescine-binding periplasmic protein

UniProt:	P31133	Sequences: MTALNKKWLSGLVAGALMAVSVGTLAAEQKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11629
Length:	370 (323)
Sequences:	36515 (29200)
Seq/√Len:	1624.7

ECOLI - POTF POTD YDCS YCJN MALE UGPB YNJB THIB
BACSU - CYCB MDXE ARAN YURO YESO YTCQ LIPO MSME
HALSA - Q9HP00 Q9HR87 Q9HHQ8 Q9HMT5 Q9HNZ3 Q9HR04
SULSO - Q97ZC3 Q97VC2 Q97YY1 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
31_T	58_V	3.768	1.00
144_V	265_S	3.644	1.00
33_H	58_V	3.267	1.00
99_Q	289_K	3.248	1.00
164_L	216_K	2.946	1.00
31_T	56_K	2.925	1.00
145_D	263_N	2.821	1.00
100_P	127_N	2.802	1.00
159_S	162_L	2.464	1.00
67_V	71_K	2.456	1.00
55_I	291_E	2.445	1.00
53_T	294_Q	2.427	1.00
50_E	56_K	2.419	1.00
48_N	298_Y	2.397	1.00
301_R	304_V	2.331	1.00
216_K	220_N	2.312	1.00
215_L	219_P	2.279	1.00
48_N	51_K	2.257	1.00
212_D	216_K	2.237	1.00
142_Y	265_S	2.230	1.00
204_D	209_P	2.220	1.00
168_N	220_N	2.202	1.00
294_Q	297_N	2.187	1.00
33_H	60_D	2.114	1.00
306_A	310_D	2.053	1.00
144_V	148_K	2.044	1.00
102_D	127_N	2.031	1.00
48_N	307_H	2.023	1.00
80_D	288_N	2.020	1.00
47_A	51_K	2.000	1.00
153_E	166_P	1.992	1.00
30_K	291_E	1.971	1.00
48_N	52_E	1.967	1.00
288_N	291_E	1.953	1.00
146_K	239_C	1.936	1.00
209_P	212_D	1.932	1.00
98_F	281_A	1.921	1.00
44_D	47_A	1.902	1.00
130_A	279_V	1.882	1.00
165_K	168_N	1.880	1.00
213_L	216_K	1.860	1.00
111_N	320_A	1.824	1.00
207_T	212_D	1.795	1.00
49_F	294_Q	1.789	1.00
162_L	165_K	1.787	1.00
104_S	293_Y	1.769	1.00
147_V	240_V	1.755	1.00
46_V	295_F	1.748	1.00
123_H	128_K	1.744	1.00
290_D	294_Q	1.726	1.00
46_V	50_E	1.723	1.00
302_P	306_A	1.717	1.00
82_V	283_P	1.714	1.00
29_Q	56_K	1.713	1.00
304_V	307_H	1.700	1.00
99_Q	284_A	1.699	1.00
49_F	53_T	1.697	1.00
168_N	172_L	1.696	1.00
165_K	169_L	1.656	1.00
50_E	53_T	1.641	1.00
307_H	311_H	1.633	1.00
232_D	237_D	1.625	1.00
161_D	164_L	1.601	1.00
289_K	293_Y	1.600	1.00
291_E	294_Q	1.599	1.00
164_L	217_L	1.598	1.00
155_A	158_D	1.586	1.00
52_E	301_R	1.583	1.00
164_L	168_N	1.582	1.00
145_D	149_A	1.575	1.00
114_P	118_K	1.549	1.00
44_D	48_N	1.547	1.00
164_L	220_N	1.543	1.00
178_S	238_I	1.535	1.00
142_Y	267_S	1.531	1.00
36_N	59_Y	1.522	1.00
143_N	146_K	1.521	1.00
144_V	263_N	1.517	1.00
47_A	50_E	1.511	1.00
169_L	173_K	1.503	1.00
30_K	288_N	1.495	1.00
231_N	235_N	1.474	1.00
307_H	310_D	1.464	1.00
213_L	217_L	1.456	1.00
212_D	215_L	1.454	1.00
205_D	209_P	1.445	1.00
286_A	289_K	1.445	1.00
118_K	123_H	1.440	1.00
164_L	213_L	1.426	1.00
81_L	292_A	1.410	1.00
49_F	295_F	1.404	1.00
327_A	331_E	1.382	1.00
282_M	296_L	1.359	1.00
67_V	70_G	1.354	1.00
140_I	267_S	1.353	1.00
24_T	27_A	1.349	1.00
170_E	239_C	1.341	1.00
161_D	165_K	1.327	1.00
139_G	266_F	1.324	1.00
17_L	20_V	1.324	1.00
166_P	169_L	1.313	1.00
336_Y	340_D	1.309	1.00
221_I	224_F	1.305	1.00
225_H	228_Q	1.304	1.00
49_F	298_Y	1.304	1.00
108_E	297_N	1.303	1.00
93_L	129_F	1.290	1.00
158_D	162_L	1.275	1.00
327_A	330_R	1.264	1.00
204_D	207_T	1.245	1.00
35_Y	71_K	1.241	1.00
100_P	103_K	1.234	1.00
232_D	238_I	1.229	1.00
293_Y	297_N	1.229	1.00
320_A	323_P	1.227	1.00
122_K	279_V	1.224	1.00
146_K	170_E	1.220	1.00
46_V	59_Y	1.215	1.00
49_F	55_I	1.213	1.00
233_L	264_V	1.208	1.00
290_D	293_Y	1.208	1.00
286_A	292_A	1.203	1.00
282_M	292_A	1.186	1.00
111_N	318_N	1.185	1.00
228_Q	231_N	1.184	1.00
153_E	169_L	1.165	1.00
302_P	320_A	1.163	1.00
55_I	294_Q	1.147	1.00
151_L	170_E	1.145	1.00
303_D	306_A	1.138	1.00
259_K	262_V	1.135	1.00
81_L	295_F	1.135	1.00
141_G	243_G	1.134	1.00
140_I	240_V	1.133	1.00
100_P	128_K	1.131	1.00
216_K	219_P	1.123	1.00
21_S	24_T	1.120	1.00
84_P	281_A	1.113	1.00
14_A	18_M	1.113	1.00
16_A	19_A	1.109	1.00
113_D	319_K	1.098	1.00
318_N	321_A	1.089	1.00
32_L	295_F	1.087	1.00
80_D	286_A	1.086	1.00
143_N	262_V	1.078	1.00
209_P	213_L	1.071	1.00
48_N	303_D	1.070	1.00
114_P	117_L	1.068	1.00
52_E	298_Y	1.064	1.00
49_F	291_E	1.059	1.00
298_Y	304_V	1.057	1.00
44_D	307_H	1.054	1.00
34_I	280_F	1.053	1.00
167_E	240_V	1.052	1.00
197_D	200_S	1.049	1.00
147_V	166_P	1.049	1.00
151_L	173_K	1.048	1.00
143_N	263_N	1.039	1.00
50_E	54_G	1.038	1.00
96_G	284_A	1.031	1.00
145_D	262_V	1.029	1.00
250_Q	253_N	1.027	1.00
107_P	110_K	1.025	1.00
166_P	240_V	1.024	1.00
158_D	270_K	1.023	1.00
303_D	307_H	1.021	1.00
92_Q	98_F	1.020	1.00
46_V	57_V	1.013	1.00
169_L	172_L	1.011	1.00
146_K	151_L	1.010	1.00
17_L	21_S	1.008	1.00
82_V	281_A	1.007	1.00
295_F	299_L	1.007	1.00
90_E	94_T	0.994	1.00
282_M	286_A	0.989	1.00
147_V	153_E	0.989	1.00
197_D	201_T	0.988	1.00
284_A	289_K	0.984	1.00
283_P	286_A	0.980	1.00
302_P	318_N	0.979	1.00
52_E	303_D	0.977	1.00
282_M	293_Y	0.975	1.00
243_G	247_D	0.973	1.00
249_W	253_N	0.973	1.00
338_P	341_V	0.966	1.00
93_L	124_D	0.957	1.00
45_T	48_N	0.956	1.00
81_L	296_L	0.953	1.00
280_F	296_L	0.952	1.00
78_G	283_P	0.952	1.00
32_L	291_E	0.951	1.00
146_K	149_A	0.948	1.00
16_A	20_V	0.944	1.00
45_T	304_V	0.943	1.00
70_G	74_A	0.941	1.00
163_I	240_V	0.940	1.00
170_E	174_S	0.937	1.00
133_Y	280_F	0.936	1.00
91_R	95_A	0.933	1.00
106_L	109_W	0.933	1.00
44_D	311_H	0.928	1.00
163_I	167_E	0.919	1.00
215_L	218_R	0.915	1.00
15_G	19_A	0.911	1.00
105_K	108_E	0.911	1.00
13_V	17_L	0.908	1.00
148_K	156_P	0.908	1.00
48_N	304_V	0.905	1.00
194_L	209_P	0.905	1.00
188_A	192_N	0.903	1.00
99_Q	293_Y	0.901	1.00
7_K	10_S	0.898	1.00
292_A	296_L	0.895	1.00
295_F	298_Y	0.894	1.00
203_A	207_T	0.893	1.00
306_A	321_A	0.889	1.00
145_D	148_K	0.881	1.00
157_V	162_L	0.878	1.00
13_V	16_A	0.875	1.00
35_Y	79_F	0.871	1.00
112_L	300_L	0.865	1.00
130_A	281_A	0.862	1.00
328_E	331_E	0.860	1.00
176_G	239_C	0.860	1.00
202_K	205_D	0.860	1.00
106_L	297_N	0.859	1.00
115_E	118_K	0.856	1.00
123_H	126_D	0.854	1.00
203_A	206_Y	0.852	1.00
221_I	225_H	0.849	1.00
171_K	174_S	0.847	1.00
160_W	164_L	0.837	1.00
35_Y	62_F	0.835	1.00
142_Y	156_P	0.831	1.00
9_L	12_L	0.826	1.00
336_Y	339_A	0.819	1.00
18_M	21_S	0.819	1.00
122_K	128_K	0.817	1.00
231_N	234_A	0.806	1.00
190_V	194_L	0.802	1.00
75_G	285_D	0.798	1.00
38_S	42_A	0.794	1.00
187_F	191_L	0.788	1.00
260_N	264_V	0.788	1.00
155_A	162_L	0.777	1.00
111_N	302_P	0.775	1.00
39_D	43_P	0.773	1.00
166_P	170_E	0.772	1.00
66_E	70_G	0.760	1.00
151_L	169_L	0.760	1.00
156_P	162_L	0.758	1.00
297_N	301_R	0.755	1.00
12_L	15_G	0.754	1.00
229_Y	241_A	0.753	1.00
12_L	16_A	0.753	1.00
57_V	295_F	0.752	1.00
326_S	330_R	0.750	1.00
331_E	334_G	0.747	1.00
117_L	128_K	0.746	1.00
100_P	129_F	0.745	1.00
189_T	192_N	0.744	1.00
50_E	57_V	0.743	1.00
30_K	55_I	0.741	1.00
98_F	129_F	0.741	1.00
14_A	17_L	0.738	1.00
337_P	341_V	0.737	1.00
112_L	117_L	0.737	1.00
339_A	342_R	0.737	1.00
105_K	293_Y	0.737	1.00
280_F	299_L	0.736	1.00
185_E	189_T	0.736	1.00
38_S	41_I	0.735	1.00
153_E	170_E	0.734	1.00
319_K	323_P	0.734	1.00
167_E	171_K	0.733	1.00
93_L	98_F	0.733	1.00
20_V	24_T	0.723	1.00
72_L	97_V	0.722	1.00
211_T	215_L	0.721	1.00
28_E	31_T	0.719	1.00
332_N	335_I	0.715	1.00
99_Q	103_K	0.715	1.00
99_Q	283_P	0.715	1.00
141_G	248_V	0.715	1.00
99_Q	282_M	0.713	1.00
186_V	190_V	0.712	1.00
69_E	73_M	0.711	1.00
14_A	20_V	0.711	1.00
40_Y	43_P	0.709	1.00
83_V	280_F	0.707	1.00
85_S	88_F	0.707	1.00
227_S	230_I	0.707	1.00
20_V	23_G	0.706	1.00
175_C	178_S	0.706	1.00
72_L	78_G	0.705	1.00
113_D	116_L	0.703	1.00
69_E	91_R	0.701	1.00
101_L	296_L	0.701	1.00
39_D	42_A	0.699	1.00
337_P	340_D	0.698	1.00
148_K	263_N	0.697	1.00
164_L	167_E	0.697	1.00
99_Q	286_A	0.696	1.00
29_Q	54_G	0.692	1.00
171_K	176_G	0.691	1.00
32_L	288_N	0.686	1.00
230_I	234_A	0.683	1.00
196_K	199_N	0.679	1.00
141_G	266_F	0.679	1.00
102_D	128_K	0.678	1.00
104_S	290_D	0.676	1.00
50_E	55_I	0.675	1.00
60_D	79_F	0.674	1.00
141_G	264_V	0.672	1.00
45_T	307_H	0.672	1.00
10_S	14_A	0.669	1.00
151_L	174_S	0.668	1.00
114_P	319_K	0.668	1.00
71_K	77_T	0.667	1.00
202_K	206_Y	0.666	1.00
330_R	334_G	0.665	1.00
111_N	319_K	0.665	1.00
56_K	59_Y	0.664	1.00
68_L	71_K	0.661	1.00
196_K	205_D	0.660	1.00
33_H	80_D	0.660	1.00
89_L	130_A	0.660	1.00
136_A	276_F	0.658	1.00
192_N	197_D	0.657	1.00
156_P	267_S	0.657	1.00
8_W	11_G	0.657	1.00
34_I	81_L	0.656	1.00
71_K	74_A	0.655	1.00
338_P	342_R	0.654	1.00
171_K	175_C	0.651	1.00
191_L	196_K	0.650	1.00
294_Q	298_Y	0.650	1.00
198_P	201_T	0.650	1.00
18_M	22_V	0.648	1.00
328_E	332_N	0.647	1.00
66_E	69_E	0.646	1.00
249_W	252_S	0.641	1.00
191_L	206_Y	0.641	1.00
227_S	231_N	0.639	1.00
248_V	252_S	0.634	1.00
228_Q	232_D	0.634	1.00
143_N	236_G	0.633	1.00
15_G	18_M	0.631	1.00
45_T	298_Y	0.630	1.00
222_R	226_S	0.630	1.00
82_V	98_F	0.629	1.00
196_K	206_Y	0.629	1.00
10_S	13_V	0.628	1.00
11_G	15_G	0.628	1.00
102_D	293_Y	0.626	1.00
22_V	25_L	0.625	1.00
145_D	236_G	0.624	1.00
289_K	292_A	0.618	1.00
70_G	73_M	0.617	1.00
163_I	177_V	0.616	1.00
181_D	184_E	0.614	1.00
34_I	59_Y	0.613	1.00
24_T	28_E	0.613	1.00
80_D	292_A	0.613	1.00
32_L	292_A	0.611	1.00
194_L	213_L	0.610	1.00
7_K	19_A	0.608	1.00
142_Y	147_V	0.607	1.00
222_R	225_H	0.607	1.00
160_W	213_L	0.607	1.00
210_A	214_L	0.606	1.00
232_D	235_N	0.605	1.00
30_K	33_H	0.605	1.00
35_Y	60_D	0.603	1.00
69_E	72_L	0.601	1.00
89_L	93_L	0.601	1.00
156_P	166_P	0.601	1.00
103_K	127_N	0.601	1.00
330_R	333_P	0.599	1.00
313_F	316_N	0.598	1.00
23_G	26_A	0.598	1.00
319_K	322_T	0.597	1.00
148_K	151_L	0.596	1.00
112_L	116_L	0.596	1.00
13_V	20_V	0.595	1.00
333_P	336_Y	0.594	1.00
147_V	170_E	0.594	1.00
113_D	322_T	0.592	1.00
142_Y	240_V	0.592	1.00
80_D	287_K	0.591	1.00
93_L	96_G	0.590	1.00
88_F	91_R	0.589	1.00
326_S	329_V	0.589	1.00
53_T	291_E	0.588	1.00
230_I	243_G	0.587	1.00
9_L	20_V	0.586	1.00
148_K	152_G	0.586	1.00
202_K	207_T	0.586	1.00
168_N	171_K	0.585	1.00
162_L	166_P	0.585	1.00
223_Y	226_S	0.583	1.00
99_Q	285_D	0.581	1.00
279_V	283_P	0.580	1.00
186_V	194_L	0.578	1.00
99_Q	104_S	0.578	1.00
260_N	263_N	0.578	1.00
151_L	166_P	0.576	1.00
187_F	190_V	0.574	1.00
34_I	83_V	0.573	1.00
68_L	82_V	0.572	1.00
159_S	271_E	0.572	1.00
302_P	305_V	0.572	1.00
60_D	71_K	0.570	1.00
118_K	122_K	0.568	1.00
10_S	15_G	0.564	1.00
28_E	294_Q	0.563	1.00
149_A	174_S	0.562	1.00
81_L	280_F	0.561	1.00
282_M	289_K	0.561	1.00
13_V	19_A	0.558	1.00
313_F	317_A	0.557	1.00
333_P	337_P	0.555	1.00
8_W	12_L	0.554	1.00
10_S	17_L	0.554	1.00
285_D	289_K	0.551	1.00
140_I	242_I	0.550	1.00
110_K	113_D	0.550	1.00
176_G	180_L	0.549	1.00
92_Q	97_V	0.549	1.00
186_V	189_T	0.546	1.00
9_L	16_A	0.545	1.00
332_N	336_Y	0.545	1.00
33_H	36_N	0.544	1.00
108_E	111_N	0.543	1.00
185_E	188_A	0.543	1.00
185_E	191_L	0.542	1.00
104_S	289_K	0.541	1.00
247_D	251_A	0.541	1.00
137_T	245_A	0.540	1.00
111_N	114_P	0.539	1.00
333_P	338_P	0.539	1.00
10_S	20_V	0.539	1.00
19_A	22_V	0.539	1.00
45_T	299_L	0.537	1.00
123_H	127_N	0.537	1.00
191_L	194_L	0.537	1.00
117_L	123_H	0.536	1.00
116_L	135_W	0.536	1.00
71_K	75_G	0.535	1.00
316_N	322_T	0.534	1.00
113_D	117_L	0.534	1.00
170_E	173_K	0.533	1.00
247_D	250_Q	0.532	1.00
9_L	13_V	0.531	1.00
246_G	249_W	0.531	1.00
206_Y	210_A	0.531	1.00
84_P	92_Q	0.530	1.00
337_P	342_R	0.528	1.00
97_V	100_P	0.527	1.00
101_L	282_M	0.527	1.00
106_L	293_Y	0.525	1.00
128_K	131_M	0.524	1.00
72_L	283_P	0.524	1.00
140_I	163_I	0.522	1.00
62_F	67_V	0.522	1.00
168_N	216_K	0.521	1.00
68_L	72_L	0.521	1.00
196_K	200_S	0.519	1.00
38_S	43_P	0.518	1.00
205_D	210_A	0.516	1.00
53_T	295_F	0.515	1.00
30_K	294_Q	0.515	1.00
105_K	290_D	0.513	1.00
22_V	26_A	0.513	1.00
12_L	18_M	0.512	1.00
122_K	130_A	0.512	1.00
305_V	317_A	0.509	1.00
293_Y	296_L	0.507	1.00
279_V	282_M	0.507	1.00
239_C	242_I	0.501	1.00
23_G	27_A	0.501	1.00
14_A	19_A	0.500	1.00
229_Y	238_I	0.500	1.00
83_V	133_Y	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	0.9027	100	0.204	Contact Map
4r2fA	1	0.8811	100	0.23	Contact Map
4mfiA	1	0.8919	100	0.239	Contact Map
4r9fA	1	0.8946	100	0.252	Contact Map
3ttmA	1	0.9216	100	0.266	Contact Map
3vxbA	1	0.8919	100	0.268	Contact Map
3ttnA	1	0.9027	100	0.282	Contact Map
4jdfA	1	0.9189	100	0.283	Contact Map
4g68A	1	0.8892	100	0.29	Contact Map
4r6kA	1	0.8973	100	0.301	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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