PHNP - ECOLI - GREMLIN Contacts

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PHNP - Phosphoribosyl 1,2-cyclic phosphodiesterase

UniProt:	P16692	Sequences: MSLTLTLTGTGGAQGVPAWGCECAACARARRSPQYRRQPCSGVVKFNDAITLIDAGLHDLADRWSPGSFQQFLLTHYHMDHVQGLFPLRWGVGDPIPVYGPPDEQGCDDLFKHPGLLDFSHTVEPFVVFDLQGLQVTPLPLNHSKLTFGYLLETAHSRVAWLSDTAGLPEKTLKFLRNNQPQVMVMDCSHPPRADAPRNHCDLNTVLALNQVIRSPRVILTHISHQFDAWLMENALPSGFEVGFDGMEIGVA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10725
Length:	252 (222)
Sequences:	8732 (6620)
Seq/√Len:	444.3

ECOLI - PHNP RBN
BACSU - YHFI YYCJ RNZ
HALSA - Q9HNK7 Q9HPR7 RNZ
SULSO - Q981E1 RNZ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
160_A	181_P	4.572	1.00
151_L	158_R	3.490	1.00
173_L	212_V	3.409	1.00
182_Q	216_P	3.289	1.00
217_R	241_E	3.034	1.00
97_P	121_H	2.687	1.00
45_K	50_I	2.623	1.00
97_P	119_F	2.381	1.00
210_N	218_V	2.315	1.00
192_P	204_N	2.312	1.00
183_V	219_I	2.290	1.00
53_I	152_L	2.228	1.00
130_D	135_Q	2.207	1.00
49_A	70_Q	2.192	1.00
43_V	50_I	2.186	1.00
141_L	149_G	2.107	1.00
57_L	61_A	2.022	1.00
185_V	221_T	1.985	1.00
139_L	175_F	1.943	1.00
160_A	176_L	1.899	1.00
141_L	147_T	1.874	1.00
71_Q	97_P	1.867	1.00
208_A	212_V	1.844	1.00
73_L	136_V	1.834	1.00
124_E	127_V	1.814	1.00
186_M	201_C	1.799	1.00
178_N	214_R	1.749	1.00
58_H	61_A	1.736	1.00
174_K	177_R	1.728	1.00
205_T	208_A	1.691	1.00
159_V	185_V	1.685	1.00
128_V	137_T	1.684	1.00
135_Q	153_E	1.678	1.00
73_L	150_Y	1.654	1.00
217_R	239_G	1.638	1.00
102_P	122_T	1.606	1.00
158_R	181_P	1.597	1.00
59_D	62_D	1.590	1.00
55_A	74_L	1.582	1.00
58_H	62_D	1.571	1.00
51_T	71_Q	1.565	1.00
137_T	153_E	1.515	1.00
105_Q	109_D	1.514	1.00
219_I	241_E	1.498	1.00
158_R	182_Q	1.489	1.00
153_E	158_R	1.443	1.00
162_L	186_M	1.440	1.00
151_L	160_A	1.421	1.00
57_L	60_L	1.414	1.00
74_L	85_L	1.410	1.00
40_C	161_W	1.408	1.00
141_L	162_L	1.399	1.00
176_L	181_P	1.397	1.00
157_S	182_Q	1.385	1.00
142_N	166_A	1.363	1.00
46_F	133_G	1.335	1.00
25_A	243_G	1.335	1.00
128_V	135_Q	1.332	1.00
101_P	148_F	1.311	1.00
23_C	26_C	1.310	1.00
38_Q	59_D	1.309	1.00
210_N	215_S	1.301	1.00
147_T	163_S	1.297	1.00
115_G	118_D	1.290	1.00
71_Q	99_Y	1.283	1.00
241_E	247_M	1.268	1.00
244_F	247_M	1.264	1.00
53_I	73_L	1.255	1.00
202_D	205_T	1.250	1.00
162_L	165_T	1.243	1.00
203_L	207_L	1.236	1.00
177_R	214_R	1.231	1.00
99_Y	121_H	1.228	1.00
49_A	132_Q	1.226	1.00
107_C	111_F	1.215	1.00
151_L	181_P	1.199	1.00
95_P	119_F	1.193	1.00
219_I	243_G	1.181	1.00
112_K	115_G	1.165	1.00
173_L	209_L	1.160	1.00
188_C	220_L	1.156	1.00
75_T	150_Y	1.153	1.00
137_T	175_F	1.151	1.00
44_V	152_L	1.145	1.00
107_C	113_H	1.144	1.00
237_P	240_F	1.139	1.00
114_P	117_L	1.137	1.00
176_L	213_I	1.133	1.00
109_D	112_K	1.132	1.00
106_G	110_L	1.130	1.00
51_T	136_V	1.111	1.00
53_I	150_Y	1.103	1.00
173_L	177_R	1.102	1.00
208_A	211_Q	1.098	1.00
138_P	150_Y	1.086	1.00
221_T	243_G	1.085	1.00
81_H	222_H	1.079	1.00
171_K	174_K	1.079	1.00
72_F	85_L	1.070	1.00
204_N	208_A	1.070	1.00
51_T	134_L	1.068	1.00
111_F	114_P	1.061	1.00
43_V	52_L	1.056	1.00
219_I	249_I	1.054	1.00
215_S	218_V	1.053	1.00
183_V	217_R	1.052	1.00
73_L	129_F	1.052	1.00
243_G	247_M	1.050	1.00
100_G	104_E	1.049	1.00
79_M	83_Q	1.039	1.00
136_V	152_L	1.036	1.00
170_E	212_V	1.036	1.00
188_C	206_V	1.034	1.00
108_D	112_K	1.032	1.00
166_A	205_T	1.025	1.00
50_I	70_Q	1.024	1.00
46_F	49_A	1.024	1.00
109_D	113_H	1.023	1.00
114_P	118_D	1.022	1.00
188_C	203_L	1.019	1.00
50_I	68_S	1.006	1.00
149_G	162_L	1.002	1.00
186_M	206_V	0.997	1.00
44_V	53_I	0.991	1.00
165_T	172_T	0.981	1.00
207_L	210_N	0.978	1.00
37_R	245_D	0.970	1.00
108_D	111_F	0.966	1.00
42_G	221_T	0.965	1.00
106_G	113_H	0.962	1.00
106_G	114_P	0.961	1.00
42_G	185_V	0.960	1.00
24_A	248_E	0.959	1.00
105_Q	108_D	0.958	1.00
108_D	115_G	0.956	1.00
172_T	175_F	0.954	1.00
111_F	115_G	0.947	1.00
170_E	173_L	0.942	1.00
154_T	157_S	0.935	1.00
70_Q	94_D	0.935	1.00
177_R	212_V	0.930	1.00
65_S	68_S	0.929	1.00
151_L	175_F	0.920	1.00
110_L	114_P	0.918	1.00
186_M	209_L	0.914	1.00
123_V	129_F	0.901	1.00
219_I	247_M	0.901	1.00
191_P	203_L	0.899	1.00
211_Q	237_P	0.897	1.00
191_P	194_A	0.897	1.00
46_F	134_L	0.896	1.00
139_L	172_T	0.893	1.00
113_H	116_L	0.887	1.00
190_H	195_D	0.885	1.00
181_P	215_S	0.882	1.00
184_M	210_N	0.878	1.00
49_A	134_L	0.878	1.00
166_A	201_C	0.877	1.00
103_D	122_T	0.865	1.00
25_A	42_G	0.860	1.00
77_Y	104_E	0.856	1.00
123_V	150_Y	0.856	1.00
153_E	156_H	0.856	1.00
189_S	224_S	0.853	1.00
106_G	109_D	0.850	1.00
130_D	133_G	0.841	1.00
105_Q	112_K	0.841	1.00
102_P	124_E	0.838	1.00
51_T	73_L	0.837	1.00
49_A	133_G	0.833	1.00
210_N	220_L	0.832	1.00
112_K	117_L	0.832	1.00
110_L	113_H	0.830	1.00
204_N	235_A	0.826	1.00
112_K	118_D	0.826	1.00
107_C	110_L	0.825	1.00
72_F	96_I	0.825	1.00
173_L	213_I	0.817	1.00
24_A	45_K	0.817	1.00
162_L	172_T	0.807	1.00
235_A	238_S	0.806	1.00
159_V	183_V	0.806	1.00
127_V	138_P	0.803	1.00
77_Y	103_D	0.801	1.00
125_P	140_P	0.800	1.00
49_A	131_L	0.796	1.00
24_A	27_A	0.796	1.00
52_L	55_A	0.793	1.00
137_T	151_L	0.781	1.00
86_F	90_W	0.780	1.00
53_I	161_W	0.779	1.00
178_N	181_P	0.778	1.00
109_D	114_P	0.773	1.00
144_S	199_N	0.772	1.00
113_H	117_L	0.771	1.00
191_P	235_A	0.766	1.00
190_H	198_R	0.755	1.00
139_L	149_G	0.751	1.00
207_L	240_F	0.742	1.00
74_L	104_E	0.741	1.00
107_C	115_G	0.739	1.00
167_G	205_T	0.739	1.00
223_I	242_V	0.738	1.00
162_L	184_M	0.737	1.00
44_V	159_V	0.734	1.00
26_C	41_S	0.734	1.00
25_A	219_I	0.730	1.00
206_V	210_N	0.730	1.00
169_P	172_T	0.726	1.00
139_L	151_L	0.726	1.00
49_A	71_Q	0.723	1.00
123_V	148_F	0.719	1.00
106_G	111_F	0.717	1.00
77_Y	82_V	0.717	1.00
166_A	199_N	0.714	1.00
108_D	118_D	0.714	1.00
108_D	113_H	0.713	1.00
112_K	116_L	0.713	1.00
78_H	143_H	0.711	1.00
123_V	138_P	0.710	1.00
223_I	227_F	0.710	1.00
73_L	99_Y	0.704	1.00
52_L	69_F	0.703	1.00
106_G	116_L	0.701	1.00
85_L	98_V	0.699	1.00
55_A	72_F	0.699	1.00
101_P	104_E	0.692	1.00
42_G	161_W	0.690	1.00
23_C	27_A	0.689	1.00
111_F	116_L	0.688	1.00
23_C	185_V	0.686	1.00
128_V	138_P	0.686	1.00
46_F	154_T	0.683	1.00
57_L	62_D	0.682	1.00
138_P	148_F	0.680	1.00
202_D	206_V	0.679	1.00
141_L	165_T	0.678	1.00
41_S	57_L	0.677	1.00
169_P	173_L	0.675	1.00
43_V	64_W	0.674	1.00
27_A	31_R	0.666	1.00
207_L	211_Q	0.664	1.00
89_R	96_I	0.663	1.00
109_D	115_G	0.661	1.00
23_C	44_V	0.658	1.00
51_T	152_L	0.656	1.00
72_F	88_L	0.654	1.00
176_L	184_M	0.652	1.00
230_W	233_E	0.650	1.00
107_C	112_K	0.649	1.00
107_C	117_L	0.643	0.99
168_L	171_K	0.640	0.99
141_L	163_S	0.637	0.99
66_P	88_L	0.634	0.99
162_L	187_D	0.633	0.99
203_L	227_F	0.627	0.99
42_G	53_I	0.626	0.99
106_G	112_K	0.625	0.99
168_L	172_T	0.624	0.99
241_E	244_F	0.622	0.99
103_D	146_L	0.619	0.99
75_T	161_W	0.616	0.99
220_L	240_F	0.615	0.99
228_D	231_L	0.614	0.99
111_F	118_D	0.614	0.99
143_H	164_D	0.613	0.99
108_D	116_L	0.613	0.99
136_V	150_Y	0.611	0.99
128_V	131_L	0.610	0.99
36_R	59_D	0.610	0.99
184_M	215_S	0.609	0.99
51_T	131_L	0.608	0.99
110_L	116_L	0.605	0.99
58_H	87_P	0.604	0.99
27_A	30_R	0.604	0.99
168_L	173_L	0.601	0.99
181_P	184_M	0.597	0.99
71_Q	131_L	0.594	0.99
111_F	117_L	0.586	0.99
187_D	201_C	0.584	0.99
142_N	199_N	0.582	0.99
129_F	138_P	0.582	0.99
165_T	201_C	0.579	0.99
41_S	52_L	0.577	0.99
160_A	184_M	0.575	0.99
142_N	167_G	0.575	0.99
41_S	56_G	0.574	0.99
77_Y	100_G	0.574	0.99
23_C	225_H	0.572	0.99
187_D	200_H	0.572	0.99
194_A	227_F	0.571	0.99
134_L	152_L	0.563	0.99
85_L	89_R	0.562	0.99
161_W	185_V	0.562	0.99
166_A	196_A	0.561	0.99
178_N	216_P	0.556	0.98
160_A	175_F	0.554	0.98
53_I	75_T	0.550	0.98
109_D	118_D	0.550	0.98
206_V	215_S	0.549	0.98
108_D	114_P	0.549	0.98
86_F	89_R	0.549	0.98
76_H	81_H	0.548	0.98
165_T	186_M	0.548	0.98
201_C	209_L	0.547	0.98
76_H	80_D	0.546	0.98
149_G	160_A	0.544	0.98
165_T	187_D	0.543	0.98
170_E	174_K	0.539	0.98
106_G	117_L	0.532	0.98
126_F	171_K	0.531	0.98
167_G	170_E	0.531	0.98
231_L	234_N	0.530	0.98
209_L	212_V	0.527	0.98
167_G	208_A	0.526	0.98
151_L	178_N	0.525	0.98
35_Y	228_D	0.523	0.98
210_N	214_R	0.521	0.98
92_V	96_I	0.521	0.98
101_P	140_P	0.520	0.98
140_P	148_F	0.515	0.97
60_L	246_G	0.514	0.97
126_F	140_P	0.510	0.97
25_A	30_R	0.510	0.97
113_H	118_D	0.509	0.97
108_D	117_L	0.507	0.97
210_N	213_I	0.507	0.97
186_M	218_V	0.506	0.97
140_P	146_L	0.504	0.97
188_C	202_D	0.501	0.97
209_L	213_I	0.501	0.97
52_L	72_F	0.501	0.97
233_E	242_V	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
3g1pA	2	0.9841	100	0.275	Contact Map
3jxpA	2	0.9762	100	0.345	Contact Map
3zwfA	2	0.869	100	0.37	Contact Map
2cbnA	2	0.9087	100	0.384	Contact Map
1y44A	2	0.9087	100	0.387	Contact Map
3md7A	2	0.9563	100	0.389	Contact Map
1zkpA	2	0.9087	100	0.433	Contact Map
4ojvA	2	0.9087	100	0.462	Contact Map
2e7yA	2	0.8532	100	0.477	Contact Map
4qn9A	2	0.9365	100	0.546	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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