RUTD - ECOLI - GREMLIN Contacts

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RUTD - Putative aminoacrylate hydrolase RutD

UniProt:	P75895	Sequences: MKLSLSPPPYADAPVVVLISGLGGSGSYWLPQLAVLEQEYQVVCYDQRGTGNNPDTLAEDYSIAQMAAELHQALVAAGIEHYAVVGHALGALVGMQLALDYPASVTVLISVNGWLRINAHTRRCFQVRERLLYSGGAQAWVEAQPLFLYPADWMAARAPRLEAEDALALAHFQGKNNLLRRLNALKRADFSHHADRIRCPVQIICASDDLLVPTACSSELHAALPDSQKMVMPYGGHACNVTDPETFNALLLNGLASLLHHREAAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13856
Length:	266 (245)
Sequences:	60515 (50619)
Seq/√Len:	3233.9

ECOLI - RUTD MHPC YBFF PLDB BIOH MENH YCJY YFHR
BACSU - NAP YBFK YUGF YFHM YDJP RSBQ YISY YCGS YRAK MENH YBAC YBDG YVAM PLBAC YQJL YCLE EST YQKD CAH
HALSA - Q9HPT9 Q9HHP4 Q9HRJ0 METX Q9HPY2
SULSO - PIP Q7LXY9 Q97WG0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
83_A	107_V	4.577	1.00
48_R	69_E	3.915	1.00
32_Q	248_N	3.084	1.00
71_H	97_L	3.078	1.00
243_D	246_T	2.918	1.00
207_S	233_P	2.893	1.00
83_A	106_T	2.859	1.00
230_M	250_L	2.841	1.00
202_Q	254_G	2.742	1.00
112_N	209_D	2.707	1.00
81_H	106_T	2.631	1.00
232_M	250_L	2.568	1.00
111_V	247_F	2.530	1.00
9_P	41_Q	2.496	1.00
97_L	101_Y	2.275	1.00
71_H	104_S	2.216	1.00
71_H	75_V	2.214	1.00
71_H	101_Y	2.211	1.00
207_S	231_V	2.138	1.00
74_L	82_Y	2.134	1.00
221_H	227_S	2.092	1.00
75_V	104_S	2.088	1.00
91_A	113_G	2.072	1.00
84_V	94_G	2.061	1.00
35_V	248_N	1.910	1.00
15_V	43_V	1.904	1.00
39_E	252_L	1.904	1.00
96_Q	100_D	1.896	1.00
83_A	255_L	1.893	1.00
214_T	231_V	1.890	1.00
235_G	243_D	1.888	1.00
15_V	79_I	1.841	1.00
68_A	100_D	1.840	1.00
15_V	41_Q	1.828	1.00
98_A	108_L	1.754	1.00
83_A	109_I	1.752	1.00
202_Q	230_M	1.742	1.00
20_S	47_Q	1.716	1.00
201_V	224_L	1.695	1.00
250_L	253_N	1.640	1.00
219_E	223_A	1.639	1.00
24_G	28_Y	1.623	1.00
20_S	50_T	1.619	1.00
47_Q	93_V	1.603	1.00
94_G	108_L	1.598	1.00
40_Y	83_A	1.596	1.00
67_A	96_Q	1.585	1.00
45_Y	70_L	1.567	1.00
64_A	100_D	1.565	1.00
14_P	83_A	1.534	1.00
14_P	106_T	1.534	1.00
97_L	105_V	1.528	1.00
19_I	47_Q	1.527	1.00
101_Y	104_S	1.524	1.00
70_L	97_L	1.493	1.00
19_I	70_L	1.468	1.00
26_G	46_D	1.445	1.00
62_S	65_Q	1.438	1.00
38_Q	252_L	1.434	1.00
249_A	253_N	1.417	1.00
26_G	52_N	1.412	1.00
35_V	252_L	1.401	1.00
97_L	104_S	1.387	1.00
23_G	50_T	1.378	1.00
205_C	217_S	1.373	1.00
95_M	110_S	1.354	1.00
246_T	250_L	1.353	1.00
110_S	113_G	1.341	1.00
87_H	240_N	1.337	1.00
43_V	73_A	1.335	1.00
75_V	101_Y	1.325	1.00
214_T	218_S	1.319	1.00
96_Q	99_L	1.315	1.00
109_I	251_L	1.301	1.00
19_I	94_G	1.300	1.00
35_V	38_Q	1.284	1.00
18_L	85_V	1.267	1.00
193_H	196_R	1.266	1.00
33_L	44_C	1.264	1.00
73_A	77_A	1.254	1.00
18_L	42_V	1.245	1.00
88_A	237_H	1.237	1.00
224_L	227_S	1.234	1.00
246_T	249_A	1.222	1.00
85_V	111_V	1.219	1.00
218_S	222_A	1.219	1.00
109_I	202_Q	1.213	1.00
39_E	256_A	1.212	1.00
221_H	229_K	1.205	1.00
10_Y	13_A	1.168	1.00
16_V	40_Y	1.166	1.00
17_V	74_L	1.159	1.00
79_I	82_Y	1.155	1.00
82_Y	105_V	1.153	1.00
99_L	193_H	1.146	1.00
23_G	88_A	1.140	1.00
232_M	235_G	1.134	1.00
26_G	44_C	1.123	1.00
9_P	13_A	1.119	1.00
183_N	186_K	1.118	1.00
205_C	229_K	1.113	1.00
45_Y	73_A	1.105	1.00
247_F	251_L	1.099	1.00
205_C	231_V	1.096	1.00
46_D	51_G	1.096	1.00
252_L	256_A	1.094	1.00
181_R	184_A	1.092	1.00
185_L	188_A	1.077	1.00
35_V	245_E	1.074	1.00
21_G	88_A	1.061	1.00
19_I	84_V	1.052	1.00
219_E	222_A	1.050	1.00
236_G	242_T	1.049	1.00
204_I	232_M	1.049	1.00
207_S	234_Y	1.046	1.00
195_D	223_A	1.033	1.00
28_Y	240_N	1.032	1.00
40_Y	255_L	1.027	1.00
228_Q	250_L	1.027	1.00
87_H	238_A	1.026	1.00
85_V	251_L	1.023	1.00
74_L	97_L	1.022	1.00
67_A	93_V	1.019	1.00
162_E	165_D	1.014	1.00
205_C	214_T	1.005	1.00
71_H	100_D	0.999	1.00
71_H	74_L	0.997	1.00
111_V	240_N	0.997	1.00
202_Q	228_Q	0.995	1.00
245_E	249_A	0.994	1.00
64_A	96_Q	0.979	1.00
183_N	187_R	0.970	1.00
218_S	229_K	0.964	1.00
232_M	246_T	0.962	1.00
218_S	231_V	0.956	1.00
86_G	94_G	0.954	1.00
82_Y	104_S	0.954	1.00
141_V	145_P	0.953	1.00
47_Q	89_L	0.952	1.00
43_V	77_A	0.947	1.00
14_P	81_H	0.941	1.00
107_V	200_P	0.935	1.00
37_E	42_V	0.935	1.00
162_E	166_A	0.935	1.00
218_S	221_H	0.928	1.00
182_L	185_L	0.927	1.00
230_M	253_N	0.926	1.00
17_V	82_Y	0.926	1.00
74_L	79_I	0.925	1.00
136_G	139_A	0.920	1.00
40_Y	256_A	0.918	1.00
30_L	44_C	0.917	1.00
11_A	41_Q	0.904	1.00
235_G	239_C	0.893	1.00
14_P	40_Y	0.891	1.00
111_V	239_C	0.890	1.00
72_Q	75_V	0.886	1.00
60_D	65_Q	0.884	1.00
67_A	100_D	0.870	1.00
179_L	183_N	0.869	1.00
126_Q	130_R	0.865	1.00
235_G	242_T	0.857	1.00
142_E	145_P	0.853	1.00
68_A	71_H	0.851	1.00
128_R	132_L	0.851	1.00
15_V	40_Y	0.851	1.00
72_Q	76_A	0.847	1.00
107_V	254_G	0.847	1.00
96_Q	193_H	0.844	1.00
180_R	184_A	0.844	1.00
204_I	250_L	0.841	1.00
46_D	52_N	0.841	1.00
65_Q	68_A	0.839	1.00
203_I	227_S	0.837	1.00
16_V	85_V	0.833	1.00
176_N	180_R	0.832	1.00
33_L	42_V	0.831	1.00
34_A	37_E	0.826	1.00
130_R	134_S	0.826	1.00
16_V	42_V	0.819	1.00
181_R	185_L	0.818	1.00
108_L	201_V	0.813	1.00
27_S	30_L	0.812	1.00
230_M	246_T	0.811	1.00
129_E	133_Y	0.804	1.00
217_S	229_K	0.802	1.00
19_I	45_Y	0.802	1.00
26_G	45_Y	0.800	1.00
66_M	89_L	0.799	1.00
98_A	105_V	0.798	1.00
198_R	225_P	0.796	1.00
13_A	41_Q	0.793	1.00
78_G	81_H	0.793	1.00
216_C	219_E	0.783	1.00
159_P	163_A	0.782	1.00
15_V	82_Y	0.782	1.00
180_R	183_N	0.781	1.00
178_L	182_L	0.777	1.00
158_A	162_E	0.775	1.00
122_R	126_Q	0.768	1.00
31_P	34_A	0.760	1.00
22_L	89_L	0.757	1.00
86_G	91_A	0.751	1.00
17_V	70_L	0.750	1.00
14_P	107_V	0.749	1.00
109_I	255_L	0.746	1.00
206_A	239_C	0.742	1.00
47_Q	66_M	0.741	1.00
190_F	193_H	0.739	1.00
173_Q	176_N	0.739	1.00
174_G	177_N	0.734	1.00
184_A	188_A	0.730	1.00
16_V	255_L	0.729	1.00
172_F	175_K	0.724	1.00
215_A	218_S	0.724	1.00
68_A	72_Q	0.722	1.00
109_I	254_G	0.719	1.00
137_A	141_V	0.719	1.00
232_M	243_D	0.717	1.00
165_D	168_A	0.717	1.00
248_N	252_L	0.716	1.00
143_A	147_F	0.715	1.00
67_A	97_L	0.714	1.00
92_L	114_W	0.711	1.00
112_N	239_C	0.711	1.00
112_N	205_C	0.709	1.00
20_S	45_Y	0.709	1.00
23_G	89_L	0.705	1.00
163_A	167_L	0.704	1.00
84_V	97_L	0.702	1.00
127_V	130_R	0.700	1.00
207_S	214_T	0.698	1.00
234_Y	243_D	0.697	1.00
87_H	112_N	0.694	1.00
40_Y	252_L	0.692	1.00
138_Q	142_E	0.690	1.00
84_V	105_V	0.690	1.00
204_I	247_F	0.689	1.00
107_V	255_L	0.688	1.00
182_L	186_K	0.688	1.00
98_A	199_C	0.684	1.00
9_P	12_D	0.683	1.00
192_H	195_D	0.682	1.00
171_H	175_K	0.672	1.00
123_R	126_Q	0.671	1.00
43_V	79_I	0.667	1.00
99_L	196_R	0.666	1.00
41_Q	79_I	0.666	1.00
33_L	37_E	0.661	1.00
171_H	174_G	0.658	1.00
85_V	109_I	0.654	1.00
139_A	143_A	0.652	1.00
151_A	154_M	0.649	1.00
123_R	127_V	0.648	1.00
95_M	115_L	0.645	1.00
112_N	206_A	0.645	1.00
208_D	234_Y	0.643	1.00
16_V	83_A	0.643	1.00
82_Y	106_T	0.642	1.00
18_L	29_W	0.639	1.00
105_V	199_C	0.638	1.00
48_R	66_M	0.638	1.00
64_A	68_A	0.638	1.00
121_T	128_R	0.637	1.00
159_P	162_E	0.637	1.00
47_Q	50_T	0.636	1.00
138_Q	141_V	0.633	1.00
164_E	168_A	0.632	1.00
87_H	111_V	0.632	1.00
126_Q	129_E	0.632	1.00
124_C	128_R	0.631	1.00
32_Q	35_V	0.631	1.00
249_A	252_L	0.631	1.00
131_L	135_G	0.630	1.00
244_P	248_N	0.623	1.00
117_I	121_T	0.622	1.00
177_N	180_R	0.622	1.00
82_Y	97_L	0.621	1.00
141_V	144_Q	0.620	1.00
109_I	204_I	0.619	1.00
128_R	131_L	0.618	1.00
30_L	34_A	0.617	1.00
140_W	144_Q	0.616	1.00
86_G	90_G	0.610	1.00
125_F	128_R	0.608	1.00
165_D	169_L	0.606	1.00
17_V	84_V	0.598	1.00
110_S	203_I	0.595	1.00
127_V	131_L	0.595	1.00
88_A	238_A	0.594	1.00
189_D	193_H	0.594	1.00
17_V	45_Y	0.591	1.00
12_D	41_Q	0.590	1.00
125_F	132_L	0.590	1.00
18_L	44_C	0.589	1.00
145_P	149_Y	0.589	1.00
160_R	163_A	0.588	1.00
66_M	93_V	0.587	1.00
142_E	146_L	0.585	1.00
63_I	96_Q	0.576	1.00
163_A	166_A	0.574	1.00
95_M	113_G	0.573	1.00
164_E	167_L	0.571	1.00
73_A	76_A	0.570	1.00
145_P	148_L	0.567	1.00
209_D	237_H	0.565	1.00
184_A	187_R	0.560	1.00
121_T	125_F	0.559	1.00
80_E	104_S	0.558	1.00
203_I	229_K	0.558	1.00
161_L	165_D	0.558	1.00
173_Q	177_N	0.557	1.00
13_A	40_Y	0.554	1.00
91_A	110_S	0.553	1.00
46_D	53_N	0.553	1.00
178_L	181_R	0.551	1.00
29_W	33_L	0.550	1.00
168_A	171_H	0.549	1.00
148_L	154_M	0.548	1.00
125_F	129_E	0.548	1.00
74_L	104_S	0.548	1.00
217_S	221_H	0.545	1.00
13_A	39_E	0.544	1.00
251_L	255_L	0.543	1.00
67_A	71_H	0.543	1.00
120_H	123_R	0.542	1.00
139_A	142_E	0.542	1.00
204_I	230_M	0.540	1.00
32_Q	247_F	0.539	1.00
36_L	251_L	0.539	1.00
107_V	202_Q	0.536	1.00
203_I	221_H	0.536	1.00
143_A	148_L	0.535	1.00
24_G	238_A	0.534	1.00
130_R	133_Y	0.534	1.00
47_Q	70_L	0.532	1.00
22_L	88_A	0.530	1.00
98_A	197_I	0.529	1.00
125_F	131_L	0.528	1.00
203_I	217_S	0.528	1.00
253_N	256_A	0.527	1.00
117_I	120_H	0.526	1.00
208_D	235_G	0.525	1.00
138_Q	144_Q	0.524	1.00
160_R	164_E	0.522	1.00
178_L	185_L	0.522	1.00
100_D	193_H	0.522	1.00
10_Y	41_Q	0.522	1.00
24_G	241_V	0.521	1.00
197_I	201_V	0.519	1.00
239_C	247_F	0.519	1.00
220_L	224_L	0.519	1.00
179_L	184_A	0.518	1.00
19_I	93_V	0.517	1.00
179_L	182_L	0.517	1.00
157_R	160_R	0.516	1.00
175_K	179_L	0.516	1.00
119_A	122_R	0.515	1.00
111_V	204_I	0.512	1.00
144_Q	147_F	0.508	1.00
120_H	125_F	0.506	1.00
203_I	224_L	0.506	1.00
68_A	101_Y	0.502	1.00
63_I	93_V	0.502	1.00
197_I	224_L	0.502	1.00
49_G	61_Y	0.502	1.00
172_F	176_N	0.500	1.00
28_Y	87_H	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
3v48A	2	1	100	0.151	Contact Map
3om8A	4	0.9474	100	0.159	Contact Map
2pujA	4	0.9549	100	0.163	Contact Map
2wueA	4	0.9549	100	0.166	Contact Map
4inzA	1	0.9436	100	0.166	Contact Map
3oosA	1	0.9436	100	0.171	Contact Map
1ehyA	1	0.9023	100	0.171	Contact Map
2xuaA	2	0.9436	100	0.173	Contact Map
3bf7A	1	0.9323	100	0.174	Contact Map
4psuA	1	0.9511	100	0.174	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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