SCPB - ECOLI - GREMLIN Contacts

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SCPB - Methylmalonyl-CoA decarboxylase

UniProt:	P52045	Sequences: MSYQYVNVVTINKVAVIEFNYGRKLNALSKVFIDDLMQALSDLNRPEIRCIILRAPSGSKVFSAGHDIHELPSGGRDPLSYDDPLRQITRMIQKFPKPIISMVEGSVWGGAFEMIMSSDLIIAASTSTFSMTPVNLGVPYNLVGIHNLTRDAGFHIVKELIFTASPITAQRALAVGILNHVVEVEELEDFTLQMAHHISEKAPLAIAVIKEELRVLGEAHTMNSDEFERIQGMRRAVYDSEDYQEGMNAFLEKRKPNFVGH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12972
Length:	261 (246)
Sequences:	30240 (19730)
Seq/√Len:	1257.9

ECOLI - SCPB PAAG CAID PAAF MENB FADB FADJ
BACSU - FADB MENB YHAR PKSH YNGF PKSI FADN
HALSA - Q9HS32 Q9HQN4 Q9HQ61 Q9HNM6
SULSO - Q97YL2 Q97WU7 Q7LXQ1 Q97VK0 Q97VK1 Q97VU5 Q97VS6 Q980Z9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_T	166_P	3.185	1.00
123_A	178_L	2.997	1.00
180_H	190_F	2.955	1.00
125_S	183_E	2.897	1.00
101_S	118_S	2.882	1.00
16_V	192_L	2.694	1.00
190_F	193_Q	2.636	1.00
41_S	91_M	2.506	1.00
44_N	96_P	2.335	1.00
10_T	15_A	2.295	1.00
126_T	184_V	2.288	1.00
165_S	197_H	2.192	1.00
171_R	174_A	2.187	1.00
16_V	54_R	2.155	1.00
37_M	91_M	2.096	1.00
7_N	20_N	2.074	1.00
25_L	60_K	2.052	1.00
13_K	49_R	2.040	1.00
25_L	61_V	2.005	1.00
135_N	201_K	1.992	1.00
102_M	191_T	1.990	1.00
168_T	171_R	1.985	1.00
156_I	175_V	1.982	1.00
159_E	165_S	1.976	1.00
161_I	209_I	1.969	1.00
248_N	252_E	1.967	1.00
18_E	54_R	1.958	1.00
8_V	15_A	1.937	1.00
102_M	188_E	1.931	1.00
220_H	223_N	1.928	1.00
192_L	196_H	1.818	1.00
154_F	158_K	1.799	1.00
15_A	48_I	1.789	1.00
108_W	130_S	1.788	1.00
186_E	189_D	1.775	1.00
125_S	170_Q	1.765	1.00
31_V	35_D	1.733	1.00
15_A	43_L	1.721	1.00
158_K	214_R	1.703	1.00
182_V	190_F	1.692	1.00
18_E	58_G	1.687	1.00
122_I	182_V	1.684	1.00
171_R	175_V	1.622	1.00
159_E	179_N	1.609	1.00
20_N	58_G	1.584	1.00
245_E	254_R	1.567	1.00
186_E	190_F	1.561	1.00
123_A	129_F	1.559	1.00
51_I	95_F	1.551	1.00
122_I	194_M	1.541	1.00
125_S	184_V	1.534	1.00
34_D	84_P	1.532	1.00
170_Q	174_A	1.527	1.00
37_M	41_S	1.517	1.00
11_I	192_L	1.517	1.00
90_R	94_K	1.513	1.00
103_V	115_I	1.511	1.00
43_L	51_I	1.511	1.00
159_E	180_H	1.509	1.00
44_N	91_M	1.494	1.00
158_K	162_F	1.482	1.00
17_I	39_A	1.469	1.00
124_A	184_V	1.416	1.00
104_E	124_A	1.393	1.00
173_L	181_V	1.374	1.00
121_I	155_H	1.373	1.00
208_V	236_A	1.367	1.00
121_I	151_D	1.365	1.00
61_V	106_S	1.364	1.00
115_I	121_I	1.362	1.00
112_F	131_M	1.351	1.00
12_N	196_H	1.350	1.00
156_I	159_E	1.347	1.00
90_R	222_M	1.344	1.00
8_V	43_L	1.341	1.00
40_L	95_F	1.338	1.00
119_D	210_K	1.337	1.00
160_L	167_I	1.331	1.00
54_R	188_E	1.305	1.00
103_V	107_V	1.301	1.00
11_I	16_V	1.293	1.00
44_N	95_F	1.292	1.00
16_V	188_E	1.291	1.00
37_M	87_Q	1.289	1.00
21_Y	24_K	1.289	1.00
106_S	128_T	1.285	1.00
104_E	126_T	1.279	1.00
93_Q	147_N	1.270	1.00
50_C	195_A	1.270	1.00
219_A	223_N	1.254	1.00
158_K	213_L	1.249	1.00
92_I	99_I	1.248	1.00
165_S	171_R	1.247	1.00
130_S	166_P	1.230	1.00
7_N	58_G	1.227	1.00
155_H	179_N	1.225	1.00
9_V	18_E	1.210	1.00
54_R	104_E	1.204	1.00
156_I	171_R	1.201	1.00
11_I	196_H	1.200	1.00
35_D	39_A	1.189	1.00
215_V	227_F	1.185	1.00
188_E	192_L	1.174	1.00
201_K	206_I	1.172	1.00
55_A	58_G	1.169	1.00
60_K	104_E	1.169	1.00
29_S	32_F	1.157	1.00
7_N	18_E	1.149	1.00
9_V	16_V	1.146	1.00
39_A	42_D	1.139	1.00
19_F	32_F	1.138	1.00
30_K	34_D	1.133	1.00
211_E	215_V	1.132	1.00
243_Y	247_M	1.130	1.00
204_L	242_D	1.126	1.00
30_K	70_E	1.122	1.00
124_A	187_L	1.118	1.00
54_R	102_M	1.099	1.00
113_E	144_G	1.096	1.00
167_I	175_V	1.079	1.00
94_K	222_M	1.069	1.00
188_E	191_T	1.068	1.00
99_I	118_S	1.061	1.00
51_I	99_I	1.053	1.00
169_A	181_V	1.053	1.00
35_D	38_Q	1.050	1.00
170_Q	173_L	1.041	1.00
152_A	156_I	1.041	1.00
219_A	227_F	1.037	1.00
154_F	217_G	1.036	1.00
51_I	97_K	1.029	1.00
10_T	47_E	1.029	1.00
134_V	164_A	1.029	1.00
48_I	97_K	1.018	1.00
19_F	63_S	1.017	1.00
24_K	69_H	1.007	1.00
187_L	191_T	1.007	1.00
183_E	186_E	0.996	1.00
151_D	155_H	0.993	1.00
244_Q	248_N	0.989	1.00
153_G	156_I	0.986	1.00
14_V	50_C	0.983	1.00
52_I	191_T	0.981	1.00
120_L	194_M	0.980	1.00
102_M	187_L	0.978	1.00
85_L	142_L	0.973	1.00
96_P	207_A	0.970	1.00
208_V	211_E	0.970	1.00
211_E	233_M	0.967	1.00
195_A	199_S	0.963	1.00
112_F	129_F	0.962	1.00
189_D	193_Q	0.958	1.00
38_Q	42_D	0.937	1.00
208_V	233_M	0.937	1.00
63_S	111_A	0.936	1.00
128_T	168_T	0.928	1.00
203_P	207_A	0.919	1.00
227_F	232_G	0.910	1.00
108_W	166_P	0.883	1.00
55_A	59_S	0.881	1.00
37_M	84_P	0.879	1.00
173_L	180_H	0.878	1.00
191_T	195_A	0.876	1.00
139_P	237_V	0.871	1.00
79_L	83_D	0.870	1.00
21_Y	67_D	0.866	1.00
25_L	64_A	0.866	1.00
124_A	185_E	0.863	1.00
173_L	178_L	0.863	1.00
10_T	48_I	0.860	1.00
134_V	209_I	0.857	1.00
33_I	88_I	0.854	1.00
103_V	129_F	0.854	1.00
16_V	52_I	0.853	1.00
160_L	175_V	0.851	1.00
190_F	194_M	0.849	1.00
223_N	226_E	0.846	1.00
125_S	181_V	0.844	1.00
40_L	92_I	0.844	1.00
69_H	251_L	0.844	1.00
161_I	213_L	0.839	1.00
193_Q	197_H	0.837	1.00
10_T	42_D	0.833	1.00
104_E	187_L	0.821	1.00
44_N	97_K	0.820	1.00
17_I	51_I	0.814	1.00
197_H	201_K	0.814	1.00
159_E	163_T	0.808	1.00
180_H	194_M	0.804	1.00
233_M	236_A	0.801	1.00
53_L	118_S	0.800	1.00
146_H	224_S	0.794	1.00
30_K	84_P	0.786	1.00
122_I	180_H	0.785	1.00
135_N	166_P	0.784	1.00
154_F	214_R	0.781	1.00
208_V	237_V	0.781	1.00
8_V	39_A	0.777	1.00
34_D	38_Q	0.768	1.00
89_T	117_S	0.766	1.00
152_A	160_L	0.765	1.00
192_L	195_A	0.763	1.00
104_E	184_V	0.759	1.00
194_M	197_H	0.759	1.00
193_Q	196_H	0.759	1.00
41_S	45_R	0.757	1.00
75_G	78_P	0.756	1.00
46_P	97_K	0.752	1.00
215_V	219_A	0.752	1.00
72_P	248_N	0.750	1.00
37_M	88_I	0.748	1.00
221_T	225_D	0.748	1.00
153_G	157_V	0.745	1.00
116_M	177_I	0.745	1.00
172_A	177_I	0.745	1.00
103_V	121_I	0.745	1.00
227_F	233_M	0.743	1.00
241_E	244_Q	0.742	1.00
120_L	179_N	0.735	1.00
200_E	255_K	0.735	1.00
148_L	152_A	0.735	1.00
145_I	228_E	0.732	1.00
6_V	39_A	0.730	1.00
198_I	206_I	0.729	1.00
169_A	178_L	0.728	1.00
189_D	192_L	0.728	1.00
28_L	32_F	0.724	1.00
202_A	242_D	0.722	1.00
25_L	106_S	0.715	1.00
95_F	99_I	0.713	1.00
129_F	178_L	0.711	1.00
21_Y	29_S	0.707	1.00
212_E	233_M	0.705	1.00
41_S	87_Q	0.705	1.00
79_L	232_G	0.704	1.00
146_H	149_T	0.701	1.00
83_D	87_Q	0.696	1.00
96_P	211_E	0.694	1.00
61_V	104_E	0.694	1.00
196_H	200_E	0.693	1.00
29_S	70_E	0.691	1.00
8_V	42_D	0.687	1.00
156_I	173_L	0.686	1.00
43_L	48_I	0.685	1.00
204_L	240_S	0.683	1.00
52_I	102_M	0.682	1.00
212_E	227_F	0.681	1.00
139_P	212_E	0.678	1.00
163_T	194_M	0.673	1.00
49_R	203_P	0.669	1.00
41_S	44_N	0.666	1.00
83_D	229_R	0.665	1.00
247_M	251_L	0.665	1.00
100_I	195_A	0.662	1.00
87_Q	90_R	0.659	1.00
39_A	43_L	0.658	1.00
103_V	127_S	0.658	1.00
49_R	199_S	0.652	1.00
31_V	34_D	0.650	1.00
53_L	99_I	0.649	1.00
123_A	127_S	0.647	1.00
79_L	235_R	0.646	1.00
106_S	166_P	0.645	1.00
32_F	35_D	0.645	1.00
14_V	52_I	0.640	1.00
87_Q	91_M	0.639	1.00
80_S	84_P	0.637	1.00
170_Q	181_V	0.632	1.00
21_Y	27_A	0.630	1.00
182_V	187_L	0.626	1.00
245_E	249_A	0.625	1.00
108_W	132_T	0.625	1.00
122_I	187_L	0.621	1.00
113_E	133_P	0.621	1.00
50_C	199_S	0.621	1.00
241_E	245_E	0.621	1.00
167_I	172_A	0.619	1.00
226_E	232_G	0.619	1.00
14_V	192_L	0.617	1.00
52_I	192_L	0.617	1.00
159_E	171_R	0.615	1.00
248_N	251_L	0.614	1.00
50_C	100_I	0.613	1.00
226_E	229_R	0.613	1.00
154_F	213_L	0.612	1.00
131_M	144_G	0.609	1.00
101_S	121_I	0.604	1.00
145_I	224_S	0.603	1.00
146_H	150_R	0.602	1.00
163_T	197_H	0.598	1.00
178_L	181_V	0.595	1.00
204_L	237_V	0.594	1.00
14_V	195_A	0.590	1.00
229_R	235_R	0.589	1.00
126_T	169_A	0.589	1.00
222_M	226_E	0.589	1.00
152_A	157_V	0.587	1.00
209_I	212_E	0.587	1.00
72_P	251_L	0.585	1.00
162_F	206_I	0.583	1.00
245_E	248_N	0.582	1.00
38_Q	41_S	0.581	1.00
134_V	206_I	0.580	1.00
138_V	243_Y	0.580	1.00
13_K	47_E	0.577	1.00
163_T	198_I	0.575	1.00
24_K	67_D	0.569	1.00
122_I	191_T	0.568	1.00
130_S	164_A	0.567	1.00
33_I	37_M	0.567	1.00
101_S	115_I	0.566	1.00
8_V	17_I	0.564	1.00
40_L	99_I	0.564	1.00
115_I	118_S	0.563	1.00
140_Y	209_I	0.561	1.00
156_I	174_A	0.556	1.00
109_G	132_T	0.554	1.00
232_G	236_A	0.553	1.00
86_R	90_R	0.551	1.00
131_M	161_I	0.550	1.00
112_F	177_I	0.549	1.00
17_I	43_L	0.548	1.00
150_R	217_G	0.548	1.00
120_L	198_I	0.544	1.00
121_I	178_L	0.544	1.00
197_H	200_E	0.544	1.00
133_P	141_N	0.543	1.00
72_P	247_M	0.540	1.00
10_T	13_K	0.540	1.00
17_I	53_L	0.537	1.00
84_P	87_Q	0.537	1.00
112_F	116_M	0.534	1.00
36_L	88_I	0.533	1.00
40_L	91_M	0.533	1.00
155_H	158_K	0.532	1.00
66_H	71_L	0.531	1.00
68_I	136_L	0.531	1.00
104_E	188_E	0.529	1.00
113_E	131_M	0.529	1.00
95_F	98_P	0.528	1.00
74_G	78_P	0.528	1.00
152_A	175_V	0.528	1.00
210_K	214_R	0.527	1.00
28_L	110_G	0.526	1.00
151_D	179_N	0.524	1.00
159_E	194_M	0.523	1.00
219_A	224_S	0.520	1.00
59_S	104_E	0.518	1.00
43_L	97_K	0.517	1.00
186_E	193_Q	0.517	1.00
134_V	201_K	0.516	1.00
150_R	220_H	0.516	1.00
133_P	140_Y	0.515	1.00
50_C	191_T	0.513	1.00
122_I	190_F	0.512	1.00
24_K	27_A	0.511	1.00
31_V	70_E	0.509	1.00
81_Y	85_L	0.509	1.00
52_I	100_I	0.509	1.00
211_E	227_F	0.508	1.00
129_F	172_A	0.507	1.00
165_S	180_H	0.506	1.00
203_P	206_I	0.506	1.00
99_I	119_D	0.503	1.00
93_Q	221_T	0.502	1.00
123_A	169_A	0.501	1.00
131_M	148_L	0.501	1.00
149_T	213_L	0.500	1.00
172_A	178_L	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
2fbmA	3	0.9387	100	0.059	Contact Map
1ef8A	5	0.9655	100	0.062	Contact Map
3hinA	5	0.9693	100	0.067	Contact Map
2pbpA	5	0.9732	100	0.072	Contact Map
3h81A	5	0.977	100	0.073	Contact Map
4lk5A	3	0.954	100	0.075	Contact Map
3kqfA	3	0.977	100	0.075	Contact Map
2gtrA	3	0.9693	100	0.078	Contact Map
2ej5A	3	0.9579	100	0.079	Contact Map
3swxA	3	0.977	100	0.079	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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