RUTB - ECOLI - GREMLIN Contacts

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RUTB - Peroxyureidoacrylate/ureidoacrylate amidohydrolase RutB

UniProt:	P75897	Sequences: MTTLTARPEAITFDPQQSALIVVDMQNAYATPGGYLDLAGFDVSTTRPVIANIQTAVTAARAAGMLIIWFQNGWDEQYVEAGGPGSPNFHKSNALKTMRKQPQLQGKLLAKGSWDYQLVDELVPQPGDIVLPKPRYSGFFNTPLDSILRSRGIRHLVFTGIATNVCVESTLRDGFFLEYFGVVLEDATHQAGPKFAQKAALFNIETFFGWVSDVETFCDALSPTSFAHIA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13858
Length:	230 (180)
Sequences:	7008 (4917)
Seq/√Len:	366.5

ECOLI - RUTB YECD PNCA YCAC
BACSU - YWOC YAAI PNCA YRDC YDDQ
HALSA - Q9HMH5 Q9HQL7
SULSO - Q97VZ5 Q97YW7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
145_D	179_Y	3.124	1.00
145_D	149_R	3.047	1.00
137_S	173_D	2.707	1.00
71_Q	132_P	2.583	1.00
60_A	65_M	2.414	1.00
25_M	53_I	2.402	1.00
155_H	180_F	2.397	1.00
17_Q	154_R	2.357	1.00
204_I	209_G	2.324	1.00
158_F	171_L	2.267	1.00
53_I	159_T	2.265	1.00
145_D	177_L	2.262	1.00
184_L	217_F	2.235	1.00
193_P	198_K	2.146	1.00
28_A	115_D	2.088	1.00
18_S	155_H	1.953	1.00
143_P	147_I	1.953	1.00
174_G	181_G	1.942	1.00
52_N	214_V	1.922	1.00
155_H	182_V	1.919	1.00
59_A	63_A	1.913	1.00
213_D	216_T	1.906	1.00
19_A	153_I	1.904	1.00
138_G	170_T	1.880	1.00
185_E	211_V	1.861	1.00
27_N	120_D	1.847	1.00
56_A	184_L	1.843	1.00
163_T	197_Q	1.789	1.00
27_N	114_W	1.744	1.00
168_E	172_R	1.728	1.00
55_T	215_E	1.728	1.00
30_A	119_V	1.721	1.00
186_D	214_V	1.716	1.00
52_N	55_T	1.695	1.00
185_E	213_D	1.693	1.00
190_Q	197_Q	1.689	1.00
18_S	157_V	1.684	1.00
59_A	218_C	1.646	1.00
131_L	147_I	1.562	1.00
22_V	159_T	1.546	1.00
187_A	214_V	1.523	1.00
158_F	170_T	1.492	1.00
156_L	174_G	1.488	1.00
70_F	138_G	1.460	1.00
129_I	147_I	1.416	1.00
66_L	151_R	1.414	1.00
163_T	188_T	1.408	1.00
68_I	147_I	1.381	1.00
167_V	183_V	1.380	1.00
54_Q	58_T	1.378	1.00
22_V	57_V	1.377	1.00
45_T	48_P	1.372	1.00
60_A	157_V	1.356	1.00
61_R	128_D	1.353	1.00
52_N	187_A	1.345	1.00
163_T	201_L	1.339	1.00
168_E	203_N	1.339	1.00
149_R	179_Y	1.330	1.00
23_V	166_C	1.328	1.00
168_E	200_A	1.316	1.00
183_V	188_T	1.282	1.00
21_I	158_F	1.281	1.00
194_K	198_K	1.257	1.00
49_V	53_I	1.255	1.00
146_S	150_S	1.233	1.00
20_L	60_A	1.231	1.00
147_I	151_R	1.230	1.00
22_V	25_M	1.224	1.00
22_V	53_I	1.223	1.00
157_V	184_L	1.209	1.00
71_Q	118_L	1.202	1.00
198_K	202_F	1.200	1.00
185_E	201_L	1.191	1.00
164_N	190_Q	1.186	1.00
140_F	177_L	1.181	1.00
73_G	116_Y	1.140	1.00
54_Q	121_E	1.136	1.00
215_E	219_D	1.129	1.00
171_L	204_I	1.113	1.00
171_L	183_V	1.110	1.00
192_G	195_F	1.106	1.00
59_A	62_A	1.104	1.00
135_R	178_E	1.100	1.00
173_D	177_L	1.086	1.00
71_Q	130_V	1.072	1.00
118_L	130_V	1.068	1.00
184_L	212_S	1.056	1.00
114_W	117_Q	1.050	1.00
24_D	133_K	1.041	1.00
27_N	117_Q	1.038	1.00
138_G	144_L	1.031	1.00
57_V	61_R	1.030	1.00
21_I	144_L	1.025	1.00
73_G	132_P	1.022	1.00
77_Q	80_E	1.009	1.00
169_S	172_R	1.008	1.00
19_A	68_I	1.007	1.00
56_A	217_F	0.994	1.00
156_L	181_G	0.989	1.00
58_T	62_A	0.986	1.00
56_A	187_A	0.982	1.00
19_A	148_L	0.968	1.00
163_T	190_Q	0.960	1.00
157_V	182_V	0.955	1.00
157_V	217_F	0.955	1.00
54_Q	124_P	0.954	1.00
188_T	197_Q	0.950	1.00
23_V	158_F	0.950	1.00
125_Q	128_D	0.947	1.00
182_V	212_S	0.945	1.00
201_L	211_V	0.938	1.00
31_T	47_R	0.929	1.00
57_V	69_W	0.914	1.00
143_P	146_S	0.910	1.00
117_Q	123_V	0.909	1.00
73_G	111_K	0.909	1.00
56_A	214_V	0.894	1.00
212_S	216_T	0.883	1.00
212_S	217_F	0.878	1.00
139_F	174_G	0.874	1.00
175_F	209_G	0.872	1.00
17_Q	155_H	0.858	1.00
69_W	124_P	0.850	1.00
113_S	116_Y	0.845	1.00
68_I	151_R	0.842	1.00
69_W	118_L	0.840	1.00
53_I	187_A	0.839	1.00
199_A	202_F	0.837	1.00
55_T	214_V	0.835	1.00
216_T	219_D	0.832	1.00
25_M	161_I	0.829	1.00
110_A	113_S	0.821	1.00
51_A	121_E	0.818	1.00
56_A	159_T	0.817	1.00
69_W	128_D	0.814	1.00
173_D	176_F	0.813	1.00
180_F	210_W	0.802	1.00
158_F	167_V	0.793	1.00
182_V	210_W	0.789	1.00
154_R	180_F	0.787	1.00
55_T	218_C	0.786	1.00
58_T	125_Q	0.783	1.00
20_L	56_A	0.783	1.00
69_W	127_G	0.782	1.00
202_F	205_E	0.782	1.00
214_V	218_C	0.780	1.00
48_P	51_A	0.780	1.00
171_L	209_G	0.778	1.00
184_L	187_A	0.774	1.00
20_L	57_V	0.767	1.00
194_K	202_F	0.765	1.00
51_A	54_Q	0.758	1.00
55_T	58_T	0.754	1.00
52_N	186_D	0.752	1.00
159_T	187_A	0.752	1.00
124_P	128_D	0.752	1.00
29_Y	166_C	0.738	1.00
58_T	123_V	0.738	1.00
27_N	31_T	0.736	1.00
47_R	121_E	0.734	1.00
195_F	199_A	0.733	1.00
55_T	59_A	0.727	1.00
202_F	206_T	0.713	0.99
25_M	49_V	0.713	0.99
68_I	144_L	0.710	0.99
50_I	119_V	0.707	0.99
57_V	67_I	0.705	0.99
28_A	34_G	0.703	0.99
30_A	50_I	0.696	0.99
111_K	132_P	0.694	0.99
124_P	130_V	0.694	0.99
25_M	122_L	0.693	0.99
112_G	117_Q	0.693	0.99
75_D	80_E	0.693	0.99
147_I	150_S	0.689	0.99
114_W	120_D	0.688	0.99
164_N	203_N	0.684	0.99
201_L	205_E	0.683	0.99
22_V	69_W	0.682	0.99
99_R	102_P	0.682	0.99
164_N	191_A	0.675	0.99
44_S	48_P	0.668	0.99
61_R	125_Q	0.662	0.99
161_I	189_H	0.662	0.99
129_I	151_R	0.660	0.99
29_Y	162_A	0.658	0.99
158_F	181_G	0.651	0.99
51_A	55_T	0.650	0.99
199_A	203_N	0.647	0.99
61_R	127_G	0.647	0.99
105_Q	108_L	0.645	0.99
20_L	159_T	0.642	0.99
54_Q	123_V	0.640	0.99
68_I	129_I	0.640	0.99
200_A	204_I	0.640	0.99
49_V	161_I	0.639	0.99
107_K	110_A	0.638	0.99
101_Q	104_L	0.638	0.99
148_L	179_Y	0.636	0.99
120_D	123_V	0.636	0.99
66_L	153_I	0.625	0.99
27_N	119_V	0.624	0.99
183_V	201_L	0.622	0.99
43_V	46_T	0.622	0.99
100_K	104_L	0.619	0.99
66_L	147_I	0.614	0.98
140_F	176_F	0.613	0.98
69_W	130_V	0.612	0.98
28_A	109_L	0.610	0.98
49_V	189_H	0.604	0.98
57_V	128_D	0.603	0.98
72_N	162_A	0.598	0.98
102_P	106_G	0.595	0.98
119_V	122_L	0.592	0.98
75_D	78_Y	0.590	0.98
164_N	195_F	0.587	0.98
75_D	111_K	0.586	0.98
30_A	161_I	0.583	0.98
185_E	205_E	0.581	0.98
137_S	177_L	0.580	0.98
183_V	204_I	0.572	0.98
131_L	143_P	0.571	0.98
21_I	156_L	0.569	0.98
18_S	65_M	0.564	0.97
50_I	122_L	0.563	0.97
99_R	103_Q	0.563	0.97
50_I	54_Q	0.558	0.97
135_R	141_N	0.555	0.97
194_K	199_A	0.554	0.97
136_Y	175_F	0.554	0.97
57_V	60_A	0.554	0.97
100_K	103_Q	0.552	0.97
103_Q	107_K	0.551	0.97
75_D	81_A	0.545	0.97
172_R	207_F	0.543	0.97
68_I	131_L	0.541	0.97
162_A	165_V	0.538	0.97
56_A	60_A	0.535	0.96
172_R	176_F	0.534	0.96
185_E	197_Q	0.533	0.96
188_T	201_L	0.533	0.96
124_P	127_G	0.533	0.96
144_L	170_T	0.532	0.96
34_G	42_D	0.531	0.96
141_N	146_S	0.531	0.96
27_N	115_D	0.528	0.96
74_W	80_E	0.527	0.96
61_R	69_W	0.526	0.96
46_T	49_V	0.526	0.96
215_E	218_C	0.524	0.96
159_T	184_L	0.523	0.96
172_R	208_F	0.522	0.96
65_M	157_V	0.521	0.96
186_D	213_D	0.519	0.96
17_Q	152_G	0.519	0.96
123_V	127_G	0.516	0.96
30_A	46_T	0.515	0.96
71_Q	116_Y	0.514	0.95
171_L	181_G	0.509	0.95
166_C	208_F	0.509	0.95
136_Y	176_F	0.509	0.95
169_S	176_F	0.506	0.95
191_A	195_F	0.506	0.95
99_R	104_L	0.504	0.95
118_L	124_P	0.504	0.95
66_L	128_D	0.504	0.95
25_M	69_W	0.504	0.95
137_S	169_S	0.503	0.95
134_P	143_P	0.501	0.95
163_T	200_A	0.500	0.95

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
3kl2A	4	0.8913	100	0.237	Contact Map
2fq1A	2	0.8957	100	0.248	Contact Map
3irvA	2	0.8652	100	0.252	Contact Map
3hb7A	3	0.8043	100	0.253	Contact Map
3hu5A	3	0.8261	100	0.257	Contact Map
1nbaA	4	0.913	100	0.262	Contact Map
4l07A	4	0.8826	100	0.271	Contact Map
1nf9A	2	0.8391	100	0.271	Contact Map
3r2jA	2	0.8217	100	0.271	Contact Map
3ot4A	4	0.8652	100	0.278	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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