RFBF - BACSU - GREMLIN Contacts

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RFBF - Probable glucose-1-phosphate cytidylyltransferase

UniProt:	O06486	Sequences: MKAVILCGGKGTRMSEVTNDIPKPLAMIGGKPILWHIMKIYQYYGVNEFILLLGYKGEKIKEYFLDYEWKHNSLTLDSSTGEVQMLGQPETWKITFLETGVDTLTAGRILQAKDYIGDETFLLTYGDGLANINLFHLISYHQTKGAAATVTGIDKVSQFGTLTVEDGMAKTFSEKTSSDGIINGGFFVLSPKVFDYLPKDGNTMFEDEPLKNLAKDGELAVYRHYGFWTAIDTYKNLLEVNKMWNQGQQVWKVW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	254 (222)
Sequences:	22384 (13860)
Seq/√Len:	930.2

ECOLI - GALF GALU RMLA2 RMLA1 GLMU GLGC
BACSU - RFBF RMLA YTDA GTAB YNGB GLMU GLGC GLGD
HALSA - Q9HSV0 Q9HQQ4 Q9HSZ9 Q9HSZ8 Q9HS61 Q9HSW4
SULSO - Q97VX4 Q7LXE7 Q97ZD1 Q980H9 Q97XG0 Q97U06 Q7LXK9 Q7LXG3 Q980D4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_K	39_K	3.353	1.00
163_T	171_T	2.754	1.00
48_E	93_K	2.672	1.00
165_E	168_M	2.672	1.00
163_T	170_K	2.667	1.00
35_W	63_Y	2.623	1.00
103_T	107_G	2.590	1.00
196_Y	216_D	2.379	1.00
120_T	190_S	2.361	1.00
146_A	220_A	2.266	1.00
141_H	149_T	2.234	1.00
3_A	46_V	2.228	1.00
168_M	220_A	2.207	1.00
165_E	170_K	2.168	1.00
48_E	95_T	2.136	1.00
3_A	41_Y	2.110	1.00
38_M	49_F	2.048	1.00
152_G	180_G	2.032	1.00
110_L	113_K	1.998	1.00
58_E	62_E	1.951	1.00
196_Y	212_N	1.934	1.00
169_A	221_V	1.887	1.00
97_L	111_Q	1.834	1.00
212_N	216_D	1.816	1.00
41_Y	124_T	1.792	1.00
120_T	142_Q	1.789	1.00
211_K	215_K	1.779	1.00
53_L	57_G	1.776	1.00
7_C	51_L	1.768	1.00
35_W	39_K	1.760	1.00
171_T	211_K	1.759	1.00
144_K	220_A	1.749	1.00
135_F	139_S	1.730	1.00
21_I	27_M	1.730	1.00
146_A	218_E	1.727	1.00
181_I	223_R	1.714	1.00
140_Y	222_Y	1.711	1.00
15_S	19_N	1.688	1.00
208_E	211_K	1.682	1.00
50_I	115_Y	1.646	1.00
140_Y	144_K	1.645	1.00
153_I	156_V	1.632	1.00
229_T	239_E	1.631	1.00
164_V	181_I	1.626	1.00
152_G	223_R	1.625	1.00
109_I	123_L	1.616	1.00
61_K	98_E	1.615	1.00
147_A	150_V	1.608	1.00
212_N	215_K	1.601	1.00
21_I	59_K	1.569	1.00
25_L	59_K	1.562	1.00
59_K	62_E	1.558	1.00
32_P	35_W	1.549	1.00
136_H	139_S	1.545	1.00
4_V	112_A	1.515	1.00
151_T	156_V	1.497	1.00
162_L	169_A	1.449	1.00
227_F	243_M	1.447	1.00
168_M	218_E	1.438	1.00
116_I	121_F	1.429	1.00
147_A	190_S	1.422	1.00
237_L	241_N	1.413	1.00
107_G	111_Q	1.393	1.00
192_K	195_D	1.376	1.00
57_G	61_K	1.366	1.00
42_Q	92_W	1.359	1.00
57_G	98_E	1.353	1.00
50_I	97_L	1.345	1.00
125_Y	185_G	1.340	1.00
120_T	188_V	1.340	1.00
233_T	236_N	1.336	1.00
160_G	174_E	1.329	1.00
95_T	115_Y	1.305	1.00
120_T	191_P	1.297	1.00
139_S	143_T	1.290	1.00
119_E	191_P	1.283	1.00
10_K	102_D	1.259	1.00
53_L	61_K	1.247	1.00
14_M	26_A	1.246	1.00
173_S	178_S	1.234	1.00
65_L	96_F	1.232	1.00
121_F	191_P	1.231	1.00
238_L	242_K	1.222	1.00
49_F	92_W	1.213	1.00
164_V	221_V	1.191	1.00
53_L	98_E	1.164	1.00
207_D	211_K	1.158	1.00
8_G	52_L	1.157	1.00
131_N	227_F	1.151	1.00
50_I	112_A	1.144	1.00
25_L	63_Y	1.136	1.00
231_I	240_V	1.132	1.00
163_T	173_S	1.130	1.00
137_L	188_V	1.129	1.00
147_A	218_E	1.126	1.00
152_G	156_V	1.120	1.00
35_W	67_Y	1.112	1.00
133_N	136_H	1.112	1.00
229_T	243_M	1.111	1.00
169_A	219_L	1.106	1.00
122_L	188_V	1.106	1.00
107_G	110_L	1.103	1.00
209_P	212_N	1.088	1.00
34_L	64_F	1.087	1.00
236_N	239_E	1.075	1.00
189_L	210_L	1.067	1.00
46_V	122_L	1.063	1.00
123_L	189_L	1.050	1.00
56_K	59_K	1.045	1.00
152_G	155_K	1.045	1.00
146_A	149_T	1.030	1.00
136_H	140_Y	1.029	1.00
53_L	96_F	1.021	1.00
196_Y	209_P	1.020	1.00
146_A	150_V	1.014	1.00
34_L	51_L	1.013	1.00
31_K	36_H	1.007	1.00
183_N	187_F	0.998	1.00
53_L	60_I	0.997	1.00
155_K	158_Q	0.995	1.00
239_E	242_K	0.994	1.00
220_A	223_R	0.991	1.00
54_G	57_G	0.980	1.00
157_S	175_K	0.968	1.00
33_I	231_I	0.958	1.00
50_I	95_T	0.958	1.00
67_Y	90_E	0.950	1.00
140_Y	220_A	0.945	1.00
161_T	182_I	0.943	1.00
33_I	37_I	0.941	1.00
113_K	194_F	0.941	1.00
167_G	223_R	0.940	1.00
4_V	121_F	0.940	1.00
158_Q	236_N	0.940	1.00
5_I	126_G	0.939	1.00
34_L	60_I	0.938	1.00
145_G	149_T	0.936	1.00
235_K	239_E	0.934	1.00
140_Y	143_T	0.932	1.00
27_M	32_P	0.928	1.00
31_K	35_W	0.924	1.00
58_E	61_K	0.923	1.00
242_K	245_N	0.922	1.00
229_T	240_V	0.922	1.00
14_M	18_T	0.916	1.00
61_K	96_F	0.911	1.00
138_I	141_H	0.901	1.00
105_T	125_Y	0.899	1.00
198_P	201_G	0.896	1.00
148_A	189_L	0.895	1.00
24_P	126_G	0.894	1.00
141_H	190_S	0.882	1.00
118_D	191_P	0.882	1.00
128_G	228_W	0.879	1.00
145_G	190_S	0.878	1.00
32_P	63_Y	0.873	1.00
239_E	243_M	0.871	1.00
62_E	65_L	0.864	1.00
39_K	42_Q	0.864	1.00
117_G	191_P	0.863	1.00
44_Y	135_F	0.863	1.00
238_L	241_N	0.860	1.00
97_L	112_A	0.856	1.00
241_N	245_N	0.850	1.00
122_L	138_I	0.846	1.00
43_Y	132_I	0.843	1.00
201_G	205_F	0.836	1.00
32_P	36_H	0.830	1.00
141_H	188_V	0.825	1.00
61_K	65_L	0.824	1.00
6_L	125_Y	0.812	1.00
158_Q	175_K	0.809	1.00
52_L	108_R	0.803	1.00
110_L	197_L	0.799	1.00
210_L	219_L	0.797	1.00
157_S	177_S	0.796	1.00
139_S	142_Q	0.793	1.00
46_V	138_I	0.784	1.00
137_L	222_Y	0.780	1.00
18_T	26_A	0.779	1.00
26_A	237_L	0.772	1.00
136_H	222_Y	0.769	1.00
29_G	241_N	0.768	1.00
68_E	90_E	0.762	1.00
36_H	244_W	0.759	1.00
145_G	150_V	0.758	1.00
151_T	155_K	0.757	1.00
40_I	44_Y	0.757	1.00
42_Q	49_F	0.753	1.00
124_T	134_L	0.752	1.00
97_L	115_Y	0.751	1.00
135_F	138_I	0.749	1.00
109_I	193_V	0.747	1.00
162_L	221_V	0.746	1.00
4_V	52_L	0.744	1.00
39_K	90_E	0.743	1.00
118_D	192_K	0.738	1.00
22_P	59_K	0.731	1.00
145_G	148_A	0.731	1.00
65_L	68_E	0.730	1.00
172_F	183_N	0.727	1.00
54_G	102_D	0.727	1.00
38_M	64_F	0.725	1.00
67_Y	96_F	0.724	1.00
53_L	58_E	0.719	1.00
4_V	50_I	0.719	1.00
29_G	36_H	0.717	1.00
17_V	21_I	0.713	1.00
192_K	196_Y	0.711	1.00
27_M	30_G	0.710	1.00
104_L	207_D	0.704	1.00
138_I	142_Q	0.703	1.00
42_Q	47_N	0.703	1.00
206_E	209_P	0.702	1.00
129_L	240_V	0.701	1.00
203_T	206_E	0.698	1.00
28_I	241_N	0.690	1.00
144_K	149_T	0.688	1.00
199_K	202_N	0.679	1.00
36_H	39_K	0.679	1.00
99_T	108_R	0.678	1.00
130_A	133_N	0.678	1.00
146_A	168_M	0.677	1.00
51_L	64_F	0.676	1.00
134_L	137_L	0.674	1.00
30_G	36_H	0.672	1.00
125_Y	128_G	0.672	1.00
47_N	93_K	0.669	1.00
40_I	132_I	0.667	1.00
153_I	180_G	0.665	1.00
102_D	107_G	0.664	1.00
170_K	173_S	0.661	1.00
230_A	236_N	0.660	1.00
42_Q	91_T	0.656	1.00
211_K	214_A	0.653	1.00
173_S	176_T	0.653	1.00
38_M	94_I	0.650	1.00
17_V	20_D	0.649	1.00
129_L	132_I	0.649	1.00
42_Q	67_Y	0.649	1.00
52_L	112_A	0.647	1.00
117_G	120_T	0.647	1.00
35_W	64_F	0.646	1.00
193_V	197_L	0.643	1.00
105_T	183_N	0.641	1.00
11_G	23_K	0.640	1.00
116_I	194_F	0.639	1.00
124_T	186_F	0.638	1.00
36_H	40_I	0.635	1.00
38_M	51_L	0.633	1.00
137_L	149_T	0.630	1.00
134_L	141_H	0.629	1.00
41_Y	122_L	0.627	1.00
99_T	107_G	0.625	1.00
181_I	221_V	0.625	1.00
6_L	105_T	0.619	1.00
192_K	218_E	0.616	1.00
171_T	215_K	0.616	1.00
101_V	107_G	0.614	1.00
5_I	124_T	0.612	1.00
151_T	154_D	0.608	1.00
47_N	91_T	0.605	1.00
204_M	207_D	0.603	1.00
210_L	214_A	0.603	1.00
64_F	94_I	0.603	1.00
95_T	98_E	0.603	1.00
5_I	37_I	0.598	1.00
17_V	26_A	0.598	1.00
158_Q	233_T	0.594	1.00
192_K	216_D	0.594	1.00
238_L	245_N	0.594	1.00
193_V	213_L	0.593	1.00
151_T	182_I	0.593	1.00
29_G	244_W	0.590	1.00
138_I	188_V	0.590	1.00
142_Q	145_G	0.587	1.00
113_K	121_F	0.586	1.00
134_L	138_I	0.586	1.00
38_M	92_W	0.585	1.00
207_D	210_L	0.582	1.00
192_K	217_G	0.582	1.00
210_L	213_L	0.582	1.00
103_T	204_M	0.580	1.00
10_K	15_S	0.577	1.00
191_P	194_F	0.572	1.00
51_L	94_I	0.570	1.00
17_V	234_Y	0.568	1.00
37_I	40_I	0.567	1.00
39_K	67_Y	0.566	1.00
40_I	186_F	0.566	1.00
41_Y	46_V	0.564	1.00
132_I	135_F	0.562	1.00
63_Y	66_D	0.561	1.00
152_G	181_I	0.561	1.00
137_L	141_H	0.560	1.00
13_R	23_K	0.559	1.00
198_P	203_T	0.559	1.00
8_G	102_D	0.557	1.00
24_P	60_I	0.552	1.00
234_Y	238_L	0.552	1.00
43_Y	135_F	0.548	1.00
51_L	96_F	0.548	1.00
199_K	203_T	0.544	1.00
9_G	13_R	0.542	1.00
235_K	238_L	0.540	1.00
208_E	212_N	0.539	1.00
20_D	56_K	0.534	1.00
112_A	115_Y	0.532	1.00
52_L	99_T	0.532	1.00
22_P	56_K	0.529	1.00
26_A	241_N	0.522	1.00
213_L	217_G	0.522	1.00
144_K	218_E	0.520	1.00
96_F	99_T	0.520	1.00
92_W	96_F	0.518	1.00
209_P	214_A	0.517	1.00
229_T	236_N	0.517	1.00
100_G	111_Q	0.516	1.00
163_T	180_G	0.516	1.00
38_M	42_Q	0.513	1.00
159_F	174_E	0.512	1.00
221_V	224_H	0.511	1.00
172_F	207_D	0.509	1.00
7_C	34_L	0.508	1.00
209_P	213_L	0.508	1.00
37_I	124_T	0.507	1.00
113_K	195_D	0.506	1.00
234_Y	237_L	0.505	1.00
23_K	127_D	0.505	1.00
40_I	43_Y	0.505	1.00
59_K	63_Y	0.502	1.00
6_L	123_L	0.501	1.00
10_K	19_N	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
1tzfA	4	0.9646	100	0.298	Contact Map
3jukA	3	0.9488	100	0.32	Contact Map
2ux8A	4	0.9921	100	0.327	Contact Map
2e3dA	3	0.9921	100	0.329	Contact Map
2pa4A	3	1	100	0.346	Contact Map
3brkX	2	0.9055	100	0.354	Contact Map
4y7uA	1	0.8819	100	0.355	Contact Map
1iimA	3	0.9213	100	0.357	Contact Map
4ho4A	3	0.9213	100	0.358	Contact Map
1lvwA	3	0.9213	100	0.359	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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