PROD1 - BACSU - GREMLIN Contacts

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PROD1 - Proline dehydrogenase 1

UniProt:	O32179	Sequences: MLRHVFLFLSQNKTLTKFAKAYGTRLGARRFVAGDTIESAVKTVKRLNRSGLCATIDYLGEYAASEKEANQVAEECKKAIQAIAEHQLNSELSLKLTSIGLDLSEELALTHLRAILSVAKQYDVAVTIDMEDYSHYEQTLSIYRQCKQEFEKLGTVIQAYLYRAAEDIRKMRDLKPNLRLVKGAYKESAAVAFPDKRGTDLHFQSLIKLQLLSGNYTAVATHDDDIIAFTKQLVAEHQIPASQFEFQMLYGIRPERQKELAKEGYRMRVYVPYGTDWFSYFMRRIAERPANAAFVLKGILKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	302 (280)
Sequences:	2805 (1756)
Seq/√Len:	104.9

ECOLI - PUTA
BACSU - PROD1 PROD2
HALSA - Q9HNG0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
113_R	149_E	5.719	1.00
81_Q	118_V	5.424	1.00
169_R	209_L	4.497	1.00
196_K	200_D	3.935	1.00
109_L	145_Q	3.654	1.00
204_Q	229_F	3.443	1.00
73_A	114_A	3.322	1.00
207_I	219_V	3.320	1.00
219_V	230_T	3.297	1.00
157_I	164_A	3.097	1.00
74_E	78_K	2.763	1.00
36_T	39_S	2.688	1.00
77_K	118_V	2.679	1.00
128_I	143_Y	2.649	1.00
118_V	121_Q	2.633	1.00
35_D	39_S	2.615	1.00
117_S	121_Q	2.610	1.00
208_K	233_L	2.606	1.00
116_L	126_V	2.457	1.00
50_S	258_K	2.418	1.00
168_I	206_L	2.390	1.00
70_N	111_H	2.310	1.00
159_A	206_L	2.269	1.00
207_I	230_T	2.265	1.00
148_Q	172_R	2.264	1.00
193_F	202_H	2.258	1.00
99_I	115_I	2.252	1.00
137_E	141_S	2.221	1.00
84_A	122_Y	2.133	1.00
197_R	201_L	2.130	1.00
113_R	117_S	2.091	1.00
81_Q	122_Y	2.066	1.00
204_Q	225_D	2.065	1.00
165_A	205_S	2.032	1.00
127_T	156_V	2.025	1.00
66_E	70_N	1.993	1.00
106_E	110_T	1.986	1.00
70_N	74_E	1.957	1.00
75_E	273_Y	1.924	1.00
244_F	265_Y	1.924	1.00
75_E	78_K	1.912	1.00
234_V	244_F	1.906	1.00
66_E	111_H	1.887	1.00
212_L	237_H	1.775	1.00
77_K	114_A	1.755	1.00
109_L	142_I	1.753	1.00
105_E	141_S	1.752	1.00
80_I	124_V	1.742	1.00
118_V	122_Y	1.734	1.00
208_K	212_L	1.663	1.00
165_A	169_R	1.637	1.00
260_L	267_M	1.622	1.00
208_K	229_F	1.580	1.00
270_Y	280_Y	1.571	1.00
130_M	139_T	1.541	1.00
157_I	168_I	1.522	1.00
195_D	198_G	1.487	1.00
117_S	150_F	1.482	1.00
165_A	202_H	1.473	1.00
109_L	146_C	1.446	1.00
95_K	98_S	1.436	1.00
163_R	167_D	1.421	1.00
66_E	107_L	1.415	1.00
38_E	78_K	1.413	1.00
224_D	256_R	1.404	1.00
143_Y	155_T	1.402	1.00
221_T	226_I	1.375	1.00
246_F	265_Y	1.362	1.00
165_A	209_L	1.360	1.00
52_L	258_K	1.357	1.00
198_G	201_L	1.350	0.99
97_T	135_H	1.348	0.99
194_P	198_G	1.337	0.99
53_C	266_R	1.328	0.99
166_E	169_R	1.326	0.99
204_Q	226_I	1.309	0.99
38_E	82_A	1.308	0.99
34_G	39_S	1.300	0.99
43_T	46_R	1.286	0.99
91_E	127_T	1.283	0.99
115_I	126_V	1.269	0.99
65_S	68_E	1.267	0.99
193_F	198_G	1.267	0.99
74_E	77_K	1.265	0.99
257_Q	267_M	1.215	0.99
221_T	227_I	1.208	0.99
109_L	149_E	1.207	0.99
77_K	81_Q	1.201	0.99
232_Q	236_E	1.192	0.99
25_R	29_R	1.185	0.99
181_V	184_A	1.179	0.99
73_A	111_H	1.172	0.99
202_H	206_L	1.169	0.99
144_R	170_K	1.160	0.98
211_L	237_H	1.158	0.98
91_E	125_A	1.156	0.98
44_V	56_I	1.156	0.98
95_K	185_Y	1.139	0.98
233_L	237_H	1.127	0.98
73_A	77_K	1.119	0.98
258_K	262_K	1.101	0.98
229_F	233_L	1.098	0.98
57_D	270_Y	1.090	0.98
44_V	54_A	1.089	0.98
37_I	82_A	1.076	0.97
93_S	270_Y	1.074	0.97
212_L	233_L	1.070	0.97
231_K	246_F	1.058	0.97
80_I	92_L	1.053	0.97
105_E	138_Q	1.046	0.97
112_L	146_C	1.040	0.97
82_A	86_H	1.039	0.97
233_L	236_E	1.034	0.97
109_L	113_R	1.030	0.97
162_Y	194_P	1.025	0.97
91_E	177_N	1.022	0.97
208_K	236_E	1.019	0.96
256_R	259_E	1.014	0.96
186_K	194_P	1.012	0.96
112_L	128_I	1.009	0.96
132_D	135_H	1.009	0.96
77_K	115_I	1.003	0.96
80_I	122_Y	1.000	0.96
199_T	290_A	1.000	0.96
86_H	89_N	0.998	0.96
218_A	247_Q	0.996	0.96
26_L	35_D	0.995	0.96
46_R	49_R	0.985	0.96
155_T	178_L	0.983	0.96
97_T	101_L	0.976	0.95
48_N	54_A	0.969	0.95
127_T	177_N	0.968	0.95
106_E	145_Q	0.967	0.95
104_S	107_L	0.964	0.95
81_Q	121_Q	0.961	0.95
211_L	234_V	0.956	0.95
57_D	129_D	0.953	0.95
76_C	92_L	0.952	0.95
178_L	210_Q	0.951	0.95
71_Q	75_E	0.941	0.94
291_N	294_F	0.939	0.94
91_E	95_K	0.930	0.94
164_A	167_D	0.926	0.94
209_L	213_S	0.922	0.94
216_Y	244_F	0.919	0.94
81_Q	84_A	0.919	0.94
52_L	261_A	0.918	0.94
31_F	184_A	0.907	0.93
231_K	265_Y	0.906	0.93
180_L	206_L	0.905	0.93
136_Y	181_V	0.905	0.93
259_E	263_E	0.904	0.93
136_Y	163_R	0.899	0.93
45_K	86_H	0.899	0.93
164_A	206_L	0.895	0.93
117_S	149_E	0.893	0.93
113_R	150_F	0.890	0.93
45_K	49_R	0.884	0.92
199_T	288_R	0.884	0.92
78_K	81_Q	0.881	0.92
67_K	71_Q	0.880	0.92
133_Y	161_L	0.880	0.92
180_L	210_Q	0.880	0.92
49_R	67_K	0.879	0.92
207_I	233_L	0.875	0.92
201_L	204_Q	0.872	0.92
23_G	26_L	0.871	0.92
116_L	153_L	0.865	0.92
165_A	206_L	0.862	0.91
143_Y	153_L	0.860	0.91
66_E	104_S	0.859	0.91
186_K	192_A	0.858	0.91
100_G	107_L	0.857	0.91
245_E	268_R	0.852	0.91
240_P	243_Q	0.851	0.91
62_Y	132_D	0.850	0.91
42_K	45_K	0.849	0.91
48_N	90_S	0.843	0.91
127_T	218_A	0.842	0.90
61_E	184_A	0.841	0.90
37_I	75_E	0.840	0.90
73_A	115_I	0.838	0.90
147_K	172_R	0.834	0.90
52_L	267_M	0.832	0.90
231_K	263_E	0.830	0.90
132_D	188_S	0.830	0.90
147_K	176_P	0.825	0.90
160_Y	202_H	0.816	0.89
71_Q	74_E	0.814	0.89
37_I	78_K	0.814	0.89
278_F	289_P	0.813	0.89
113_R	146_C	0.809	0.89
41_V	82_A	0.804	0.88
111_H	114_A	0.803	0.88
124_V	153_L	0.799	0.88
145_Q	148_Q	0.797	0.88
58_Y	273_Y	0.795	0.88
29_R	236_E	0.794	0.88
59_L	93_S	0.792	0.88
57_D	95_K	0.790	0.87
230_T	234_V	0.790	0.87
278_F	286_A	0.787	0.87
61_E	95_K	0.787	0.87
129_D	283_R	0.785	0.87
168_I	209_L	0.784	0.87
83_I	92_L	0.783	0.87
54_A	271_V	0.779	0.87
79_A	273_Y	0.777	0.87
96_L	142_I	0.777	0.87
225_D	228_A	0.775	0.86
66_E	101_L	0.774	0.86
129_D	158_Q	0.770	0.86
138_Q	142_I	0.769	0.86
157_I	178_L	0.767	0.86
210_Q	217_T	0.763	0.86
72_V	76_C	0.763	0.86
30_R	252_I	0.762	0.85
201_L	205_S	0.755	0.85
120_K	151_E	0.754	0.85
280_Y	284_R	0.749	0.85
162_Y	193_F	0.745	0.84
61_E	270_Y	0.734	0.83
225_D	229_F	0.730	0.83
249_L	270_Y	0.729	0.83
283_R	287_E	0.729	0.83
133_Y	188_S	0.727	0.83
101_L	138_Q	0.722	0.82
144_R	174_L	0.720	0.82
44_V	48_N	0.718	0.82
161_L	192_A	0.718	0.82
232_Q	235_A	0.714	0.82
81_Q	85_E	0.714	0.82
290_A	294_F	0.708	0.81
203_F	226_I	0.706	0.81
180_L	207_I	0.704	0.81
177_N	218_A	0.694	0.80
202_H	205_S	0.694	0.80
196_K	226_I	0.692	0.80
74_E	114_A	0.692	0.80
281_F	288_R	0.690	0.79
223_D	226_I	0.689	0.79
143_Y	176_P	0.689	0.79
82_A	85_E	0.689	0.79
36_T	275_T	0.688	0.79
156_V	181_V	0.684	0.79
258_K	261_A	0.684	0.79
170_K	215_N	0.683	0.79
235_A	238_Q	0.681	0.78
140_L	167_D	0.681	0.78
117_S	120_K	0.680	0.78
141_S	145_Q	0.678	0.78
63_A	69_A	0.678	0.78
283_R	288_R	0.669	0.77
52_L	269_V	0.667	0.77
22_Y	27_G	0.667	0.77
146_C	153_L	0.666	0.77
63_A	68_E	0.662	0.76
272_P	280_Y	0.659	0.76
157_I	167_D	0.659	0.76
51_G	56_I	0.659	0.76
70_N	110_T	0.658	0.76
272_P	283_R	0.657	0.76
229_F	232_Q	0.656	0.76
144_R	148_Q	0.655	0.76
106_E	109_L	0.655	0.76
40_A	56_I	0.655	0.76
133_Y	191_V	0.654	0.76
206_L	210_Q	0.653	0.76
95_K	129_D	0.652	0.75
107_L	110_T	0.651	0.75
180_L	219_V	0.650	0.75
179_R	182_K	0.650	0.75
246_F	260_L	0.646	0.75
114_A	118_V	0.646	0.75
23_G	27_G	0.645	0.75
56_I	90_S	0.645	0.75
175_K	243_Q	0.643	0.74
41_V	56_I	0.642	0.74
22_Y	26_L	0.641	0.74
105_E	189_A	0.641	0.74
39_S	42_K	0.641	0.74
81_Q	230_T	0.639	0.74
227_I	260_L	0.639	0.74
228_A	231_K	0.638	0.74
59_L	277_W	0.635	0.73
61_E	249_L	0.634	0.73
187_E	286_A	0.629	0.73
144_R	157_I	0.626	0.72
181_V	199_T	0.625	0.72
227_I	246_F	0.625	0.72
96_L	112_L	0.623	0.72
193_F	199_T	0.623	0.72
195_D	201_L	0.621	0.72
94_L	126_V	0.620	0.72
168_I	181_V	0.619	0.72
211_L	230_T	0.619	0.72
41_V	88_L	0.617	0.71
40_A	44_V	0.617	0.71
260_L	265_Y	0.615	0.71
117_S	148_Q	0.615	0.71
121_Q	151_E	0.614	0.71
261_A	267_M	0.611	0.71
67_K	106_E	0.610	0.70
77_K	145_Q	0.608	0.70
223_D	277_W	0.607	0.70
221_T	230_T	0.607	0.70
95_K	247_Q	0.605	0.70
203_F	230_T	0.604	0.70
48_N	51_G	0.602	0.69
136_Y	139_T	0.601	0.69
84_A	118_V	0.601	0.69
61_E	287_E	0.600	0.69
133_Y	163_R	0.598	0.69
105_E	145_Q	0.597	0.69
214_G	243_Q	0.596	0.69
53_C	89_N	0.596	0.69
31_F	281_F	0.593	0.68
199_T	223_D	0.593	0.68
28_A	277_W	0.592	0.68
105_E	142_I	0.591	0.68
61_E	129_D	0.591	0.68
74_E	81_Q	0.590	0.68
158_Q	249_L	0.588	0.68
53_C	86_H	0.588	0.68
193_F	205_S	0.586	0.67
74_E	106_E	0.585	0.67
135_H	139_T	0.585	0.67
57_D	93_S	0.584	0.67
252_I	281_F	0.583	0.67
52_L	254_P	0.583	0.67
49_R	71_Q	0.582	0.67
71_Q	262_K	0.581	0.67
67_K	205_S	0.581	0.67
187_E	192_A	0.578	0.66
248_M	254_P	0.578	0.66
57_D	61_E	0.578	0.66
252_I	288_R	0.577	0.66
72_V	252_I	0.576	0.66
236_E	240_P	0.574	0.66
119_A	126_V	0.573	0.66
92_L	116_L	0.572	0.66
55_T	93_S	0.572	0.66
127_T	279_S	0.571	0.65
133_Y	279_S	0.567	0.65
154_G	179_R	0.566	0.65
130_M	248_M	0.566	0.65
136_Y	199_T	0.565	0.65
129_D	160_Y	0.565	0.65
181_V	276_D	0.564	0.64
93_S	247_Q	0.564	0.64
58_Y	75_E	0.564	0.64
114_A	263_E	0.563	0.64
156_V	161_L	0.563	0.64
70_N	78_K	0.562	0.64
18_F	276_D	0.562	0.64
234_V	239_I	0.560	0.64
160_Y	283_R	0.560	0.64
224_D	228_A	0.557	0.64
160_Y	199_T	0.557	0.64
166_E	178_L	0.557	0.64
211_L	233_L	0.556	0.63
207_I	229_F	0.556	0.63
250_Y	286_A	0.556	0.63
184_A	287_E	0.555	0.63
284_R	287_E	0.554	0.63
185_Y	247_Q	0.552	0.63
73_A	126_V	0.552	0.63
181_V	200_D	0.551	0.63
97_T	146_C	0.551	0.63
187_E	289_P	0.551	0.63
91_E	124_V	0.551	0.63
98_S	101_L	0.548	0.62
55_T	268_R	0.547	0.62
40_A	59_L	0.545	0.62
95_K	156_V	0.544	0.62
33_A	43_T	0.543	0.62
94_L	98_S	0.541	0.61
184_A	249_L	0.540	0.61
165_A	275_T	0.535	0.60
184_A	222_H	0.535	0.60
286_A	289_P	0.535	0.60
125_A	177_N	0.535	0.60
90_S	95_K	0.535	0.60
239_I	242_S	0.533	0.60
19_A	23_G	0.529	0.60
58_Y	281_F	0.529	0.60
129_D	185_Y	0.528	0.59
46_R	50_S	0.527	0.59
252_I	290_A	0.526	0.59
237_H	241_A	0.525	0.59
94_L	261_A	0.524	0.59
94_L	112_L	0.524	0.59
200_D	225_D	0.524	0.59
34_G	51_G	0.523	0.59
29_R	85_E	0.522	0.59
165_A	193_F	0.522	0.59
21_A	25_R	0.520	0.58
57_D	272_P	0.520	0.58
234_V	255_E	0.518	0.58
231_K	244_F	0.516	0.58
137_E	163_R	0.516	0.58
113_R	145_Q	0.514	0.57
257_Q	269_V	0.513	0.57
78_K	82_A	0.513	0.57
216_Y	266_R	0.511	0.57
272_P	279_S	0.511	0.57
31_F	295_V	0.508	0.57
47_L	250_Y	0.508	0.57
66_E	110_T	0.507	0.56
169_R	212_L	0.506	0.56
223_D	252_I	0.503	0.56
248_M	257_Q	0.503	0.56
124_V	127_T	0.503	0.56
116_L	146_C	0.502	0.56
220_A	246_F	0.502	0.56
200_D	252_I	0.502	0.56
110_T	113_R	0.500	0.55
57_D	185_Y	0.500	0.55
220_A	282_M	0.500	0.55
282_M	286_A	0.500	0.55

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
2ekgA	2	0.947	100	0.087	Contact Map
4h6qA	1	0.9139	100	0.089	Contact Map
4nm9A	2	0.957	100	0.161	Contact Map
3hazA	3	0.9735	100	0.165	Contact Map
3e2qA	2	0.9603	100	0.168	Contact Map
4o8aA	2	0.9503	100	0.171	Contact Map
3canA	2	0.3808	49.1	0.96	Contact Map
1k77A	1	0.755	37.9	0.962	Contact Map
3cqjA	2	0.7881	27	0.965	Contact Map
1i60A	1	0.7616	26	0.965	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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