RMLA - BACSU - GREMLIN Contacts

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RMLA - Glucose-1-phosphate thymidylyltransferase

UniProt:	P39629	Sequences: MKGVILAGGNGSRLMPLTKAVNKHLLPVGPYPMIYWSIMKLQEAGIKDILLISQKEHMPQFYKLLGNGEELGVTITYQVQPAASGISDGLSYAKRFTKKESFILLLGDNIFEDSLKPYTERFEQQGKGAKVLLKEVDDPERFGIAEIDEKNKRIRSIIEKPEQPPTNLCVTGIYMYDAEVFSYIEQISPSKRGELEITDVNNLYIENSQLTYDVLSGWWVDAGTHESLYLASQLVHQALRKGQDEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	246 (229)
Sequences:	22970 (14480)
Seq/√Len:	956.9

ECOLI - RMLA2 RMLA1 GALF GALU GLMU GLGC
BACSU - RMLA YTDA YNGB GTAB RFBF GLMU GLGC GLGD
HALSA - Q9HSV0 Q9HQQ4 Q9HSZ9 Q9HSZ8 Q9HS61 Q9HSW4
SULSO - Q97U06 Q97VX4 Q7LXE7 Q97ZD1 Q980H9 Q97XG0 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
94_K	185_E	3.406	1.00
31_Y	39_M	3.014	1.00
35_Y	64_L	2.672	1.00
146_E	155_R	2.620	1.00
146_E	156_S	2.613	1.00
127_K	211_T	2.521	1.00
48_D	74_T	2.479	1.00
84_S	88_D	2.449	1.00
135_E	167_N	2.352	1.00
148_D	153_R	2.347	1.00
58_M	62_Y	2.331	1.00
183_Y	207_N	2.275	1.00
135_E	214_V	2.203	1.00
48_D	76_T	2.202	1.00
133_L	212_Y	2.147	1.00
101_S	177_D	2.146	1.00
183_Y	203_L	2.123	1.00
122_F	130_K	2.091	1.00
148_D	155_R	2.037	1.00
3_G	46_I	2.027	1.00
53_S	58_M	2.002	1.00
127_K	209_Q	1.964	1.00
3_G	41_L	1.961	1.00
38_I	49_I	1.931	1.00
153_R	211_T	1.930	1.00
58_M	79_V	1.892	1.00
91_S	94_K	1.889	1.00
203_L	207_N	1.883	1.00
78_Q	92_Y	1.812	1.00
202_N	206_E	1.792	1.00
101_S	123_E	1.773	1.00
7_A	51_L	1.762	1.00
15_M	19_K	1.719	1.00
121_R	213_D	1.716	1.00
41_L	105_L	1.707	1.00
90_L	104_L	1.699	1.00
125_Q	211_T	1.699	1.00
59_P	63_K	1.689	1.00
35_Y	39_M	1.680	1.00
4_V	93_A	1.669	1.00
168_L	214_V	1.661	1.00
116_K	120_E	1.646	1.00
146_E	166_T	1.645	1.00
156_S	202_N	1.642	1.00
220_V	230_L	1.642	1.00
128_G	177_D	1.609	1.00
21_V	27_P	1.587	1.00
21_V	60_Q	1.580	1.00
147_I	168_L	1.566	1.00
203_L	206_E	1.556	1.00
50_L	96_F	1.538	1.00
150_K	153_R	1.537	1.00
154_I	210_L	1.536	1.00
76_T	96_F	1.528	1.00
32_P	35_Y	1.506	1.00
138_D	141_R	1.505	1.00
62_Y	79_V	1.503	1.00
42_Q	73_V	1.486	1.00
154_I	212_Y	1.474	1.00
50_L	78_Q	1.446	1.00
97_T	102_F	1.431	1.00
199_D	202_N	1.430	1.00
88_D	92_Y	1.393	1.00
228_L	232_S	1.390	1.00
117_P	120_E	1.387	1.00
49_I	73_V	1.385	1.00
60_Q	63_K	1.374	1.00
68_G	71_L	1.349	1.00
188_S	191_K	1.340	1.00
121_R	125_Q	1.326	1.00
145_A	154_I	1.323	1.00
120_E	124_Q	1.316	1.00
133_L	145_A	1.316	1.00
25_L	60_Q	1.315	1.00
153_R	209_Q	1.299	1.00
229_Y	233_Q	1.297	1.00
160_K	164_P	1.274	1.00
129_A	176_Y	1.265	1.00
100_E	178_A	1.252	1.00
91_S	185_E	1.244	1.00
218_W	234_L	1.240	1.00
102_F	178_A	1.223	1.00
186_Q	203_L	1.219	1.00
146_E	158_I	1.214	1.00
57_H	60_Q	1.213	1.00
224_T	227_S	1.190	1.00
101_S	178_A	1.183	1.00
179_E	182_S	1.181	1.00
53_S	62_Y	1.181	1.00
147_I	212_Y	1.178	1.00
66_G	77_Y	1.165	1.00
128_G	209_Q	1.164	1.00
106_L	172_G	1.160	1.00
222_A	231_A	1.152	1.00
158_I	165_P	1.143	1.00
53_S	79_V	1.137	1.00
183_Y	200_V	1.135	1.00
118_Y	132_L	1.135	1.00
88_D	91_S	1.129	1.00
50_L	93_A	1.126	1.00
10_N	83_A	1.123	1.00
117_P	121_R	1.115	1.00
133_L	168_L	1.114	1.00
148_D	151_N	1.114	1.00
98_K	101_S	1.114	1.00
114_S	117_P	1.107	1.00
34_I	65_L	1.105	1.00
220_V	234_L	1.103	1.00
176_Y	201_N	1.102	1.00
103_I	175_M	1.092	1.00
118_Y	175_M	1.090	1.00
227_S	230_L	1.072	1.00
186_Q	207_N	1.067	1.00
187_I	191_K	1.062	1.00
25_L	64_L	1.057	1.00
101_S	175_M	1.057	1.00
53_S	61_F	1.054	1.00
14_L	26_L	1.047	1.00
53_S	77_Y	1.034	1.00
50_L	76_T	1.031	1.00
182_S	185_E	1.018	1.00
33_M	222_A	1.013	1.00
233_Q	236_H	1.009	1.00
104_L	176_Y	1.009	1.00
62_Y	77_Y	1.008	1.00
46_I	103_I	1.004	1.00
112_E	218_W	0.998	1.00
210_L	215_L	0.980	1.00
34_I	51_L	0.977	1.00
85_G	198_T	0.976	1.00
91_S	184_I	0.974	1.00
8_G	52_I	0.974	1.00
31_Y	36_W	0.972	1.00
121_R	211_T	0.968	1.00
143_G	159_E	0.964	1.00
32_P	64_L	0.961	1.00
4_V	102_F	0.959	1.00
34_I	61_F	0.952	1.00
170_V	174_Y	0.949	1.00
182_S	186_Q	0.947	1.00
140_E	160_K	0.933	1.00
226_E	230_L	0.930	1.00
5_I	107_G	0.923	1.00
229_Y	232_S	0.921	1.00
73_V	76_T	0.920	1.00
35_Y	68_G	0.918	1.00
31_Y	35_Y	0.913	1.00
54_Q	57_H	0.904	1.00
198_T	202_N	0.903	1.00
105_L	115_L	0.899	1.00
24_H	107_G	0.899	1.00
121_R	124_Q	0.893	1.00
59_P	62_Y	0.892	1.00
39_M	42_Q	0.888	1.00
183_Y	186_Q	0.884	1.00
103_I	119_T	0.878	1.00
122_F	175_M	0.878	1.00
38_I	65_L	0.874	1.00
141_R	227_S	0.874	1.00
130_K	134_K	0.860	1.00
73_V	77_Y	0.857	1.00
39_M	71_L	0.855	1.00
230_L	233_Q	0.853	1.00
14_L	18_T	0.853	1.00
94_K	181_F	0.852	1.00
44_A	116_K	0.852	1.00
27_P	32_P	0.850	1.00
113_D	116_K	0.848	1.00
33_M	37_S	0.842	1.00
232_S	236_H	0.836	1.00
201_N	210_L	0.831	1.00
220_V	231_A	0.827	1.00
78_Q	96_F	0.812	1.00
144_I	169_C	0.811	1.00
109_N	219_W	0.810	1.00
155_R	158_I	0.796	1.00
51_L	75_I	0.793	1.00
126_G	177_D	0.793	1.00
6_L	106_L	0.792	1.00
43_E	113_D	0.790	1.00
122_F	177_D	0.789	1.00
120_E	123_E	0.787	1.00
230_L	234_L	0.786	1.00
42_Q	49_I	0.780	1.00
211_T	214_V	0.778	1.00
18_T	26_L	0.774	1.00
86_I	106_L	0.765	1.00
78_Q	93_A	0.764	1.00
119_T	123_E	0.762	1.00
42_Q	47_K	0.755	1.00
62_Y	66_G	0.750	1.00
36_W	235_V	0.749	1.00
38_I	75_I	0.749	1.00
29_G	36_W	0.746	1.00
98_K	178_A	0.744	1.00
156_S	163_Q	0.743	1.00
130_K	211_T	0.743	1.00
196_E	200_V	0.740	1.00
47_K	74_T	0.738	1.00
29_G	232_S	0.738	1.00
99_K	178_A	0.736	1.00
129_A	210_L	0.736	1.00
26_L	228_L	0.735	1.00
32_P	36_W	0.734	1.00
46_I	119_T	0.732	1.00
3_G	49_I	0.731	1.00
51_L	65_L	0.729	1.00
22_N	60_Q	0.722	1.00
141_R	160_K	0.716	1.00
179_E	183_Y	0.714	1.00
187_I	203_L	0.706	1.00
30_P	36_W	0.703	1.00
118_Y	213_D	0.702	1.00
157_I	170_V	0.700	1.00
36_W	39_M	0.699	1.00
131_V	145_A	0.694	1.00
76_T	79_V	0.692	1.00
40_K	44_A	0.690	1.00
63_K	66_G	0.690	1.00
129_A	204_Y	0.690	1.00
200_V	203_L	0.688	1.00
128_G	179_E	0.687	1.00
90_L	180_V	0.683	1.00
17_L	21_V	0.681	1.00
119_T	175_M	0.681	1.00
131_V	136_V	0.675	1.00
133_L	136_V	0.674	1.00
94_K	182_S	0.673	1.00
4_V	52_I	0.672	1.00
40_K	113_D	0.670	1.00
110_I	231_A	0.670	1.00
17_L	225_H	0.667	1.00
158_I	161_P	0.665	1.00
38_I	73_V	0.663	1.00
42_Q	74_T	0.662	1.00
147_I	150_K	0.662	1.00
136_V	139_P	0.660	1.00
68_G	72_G	0.660	1.00
125_Q	128_G	0.660	1.00
17_L	20_A	0.658	1.00
127_K	153_R	0.657	1.00
188_S	195_L	0.656	1.00
125_Q	130_K	0.652	1.00
43_E	116_K	0.652	1.00
183_Y	204_Y	0.650	1.00
229_Y	236_H	0.646	1.00
146_E	165_P	0.644	1.00
4_V	50_L	0.642	1.00
225_H	229_Y	0.639	1.00
35_Y	65_L	0.635	1.00
97_T	181_F	0.635	1.00
29_G	235_V	0.634	1.00
117_P	213_D	0.634	1.00
149_E	153_R	0.628	1.00
192_R	196_E	0.627	1.00
115_L	122_F	0.627	1.00
179_E	209_Q	0.624	1.00
168_L	212_Y	0.624	1.00
38_I	51_L	0.624	1.00
5_I	105_L	0.623	1.00
191_K	196_E	0.623	1.00
129_A	133_L	0.609	1.00
131_V	135_E	0.609	1.00
118_Y	122_F	0.609	1.00
85_G	199_D	0.608	1.00
94_K	102_F	0.608	1.00
135_E	168_L	0.606	1.00
119_T	122_F	0.606	1.00
52_I	89_G	0.605	1.00
129_A	201_N	0.604	1.00
6_L	86_I	0.603	1.00
99_K	179_E	0.600	1.00
116_K	119_T	0.600	1.00
91_S	195_L	0.599	1.00
65_L	75_I	0.599	1.00
141_R	224_T	0.598	1.00
178_A	181_F	0.597	1.00
83_A	88_D	0.596	1.00
40_K	43_E	0.594	1.00
13_R	23_K	0.594	1.00
52_I	93_A	0.593	1.00
180_V	204_Y	0.590	1.00
39_M	68_G	0.588	1.00
118_Y	130_K	0.587	1.00
221_D	227_S	0.586	1.00
193_G	196_E	0.586	1.00
151_N	214_V	0.585	1.00
156_S	206_E	0.585	1.00
17_L	26_L	0.582	1.00
53_S	57_H	0.581	1.00
111_F	171_T	0.580	1.00
11_G	23_K	0.576	1.00
41_L	103_I	0.575	1.00
106_L	109_N	0.574	1.00
151_N	155_R	0.574	1.00
22_N	57_H	0.573	1.00
199_D	203_L	0.572	1.00
54_Q	83_A	0.570	1.00
82_A	88_D	0.569	1.00
179_E	207_N	0.568	1.00
37_S	40_K	0.566	1.00
179_E	208_S	0.564	1.00
226_E	229_Y	0.562	1.00
27_P	30_P	0.560	1.00
5_I	37_S	0.560	1.00
53_S	59_P	0.558	1.00
182_S	207_N	0.556	1.00
25_L	61_F	0.554	1.00
40_K	173_I	0.554	1.00
128_G	132_L	0.552	1.00
151_N	211_T	0.552	1.00
85_G	194_E	0.552	1.00
80_Q	89_G	0.549	1.00
105_L	173_I	0.542	1.00
103_I	115_L	0.538	1.00
52_I	78_Q	0.535	1.00
80_Q	83_A	0.533	1.00
36_W	40_K	0.531	1.00
133_L	214_V	0.530	1.00
93_A	96_F	0.530	1.00
10_N	15_M	0.530	1.00
55_K	58_M	0.530	1.00
145_A	212_Y	0.530	1.00
90_L	181_F	0.527	1.00
9_G	13_R	0.527	1.00
194_E	198_T	0.527	1.00
86_I	170_V	0.526	1.00
37_S	105_L	0.526	1.00
196_E	199_D	0.523	1.00
39_M	43_E	0.518	1.00
122_F	213_D	0.515	1.00
134_K	169_C	0.514	1.00
187_I	200_V	0.513	1.00
51_L	77_Y	0.511	1.00
28_V	232_S	0.511	1.00
188_S	192_R	0.510	1.00
42_Q	72_G	0.507	1.00
58_M	61_F	0.506	1.00
190_S	193_G	0.505	1.00
7_A	34_I	0.503	1.00
41_L	46_I	0.503	1.00
130_K	133_L	0.503	1.00
115_L	118_Y	0.502	1.00
204_Y	208_S	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
3jukA	3	0.9634	100	0.259	Contact Map
2e3dA	3	0.9878	100	0.265	Contact Map
1iimA	3	0.9959	100	0.267	Contact Map
1lvwA	3	0.9959	100	0.267	Contact Map
4ho4A	3	0.9959	100	0.269	Contact Map
1mc3A	3	0.9959	100	0.274	Contact Map
2ux8A	4	0.9919	100	0.277	Contact Map
4ecmA	3	0.9878	100	0.289	Contact Map
2pa4A	3	0.9919	100	0.297	Contact Map
3brkX	2	0.9512	100	0.312	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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