RMLA2 - ECOLI - GREMLIN Contacts

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RMLA2 - Glucose-1-phosphate thymidylyltransferase 2

UniProt:	P61887	Sequences: MKGIILAGGSGTRLHPITRGVSKQLLPIYDKPMIYYPLSVLMLAGIREILIITTPEDKGYFQRLLGDGSEFGIQLEYAEQPSPDGLAQAFIIGETFLNGEPSCLVLGDNIFFGQGFSPKLRHVAARTEGATVFGYQVMDPERFGVVEFDDNFRAISLEEKPKQPKSNWAVTGLYFYDSKVVEYAKQVKPSERGELEITSINQMYLEAGNLTVELLGRGFAWLDTGTHDSLIEASTFVQTVEKRQGFKIACLEEIAWRNGWLDDEGVKRAASSLAKTGYGQYLLELLRARPRQY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11454
Length:	293 (239)
Sequences:	22261 (13880)
Seq/√Len:	897.8

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

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_E	185_K	3.666	1.00
31_K	39_S	3.121	1.00
147_E	155_I	2.941	1.00
147_E	156_S	2.778	1.00
35_Y	64_L	2.733	1.00
136_Q	167_N	2.652	1.00
128_E	211_T	2.531	1.00
48_E	74_Q	2.487	1.00
183_Y	207_A	2.487	1.00
84_D	88_Q	2.432	1.00
149_D	153_R	2.429	1.00
48_E	76_E	2.319	1.00
101_P	177_D	2.271	1.00
183_Y	203_M	2.261	1.00
136_Q	214_L	2.237	1.00
134_G	212_V	2.204	1.00
149_D	155_I	2.185	1.00
3_G	46_I	2.144	1.00
123_V	131_T	2.072	1.00
58_K	62_Q	2.069	1.00
38_L	49_I	2.049	1.00
3_G	41_L	2.039	1.00
91_I	94_E	1.952	1.00
153_R	211_T	1.948	1.00
202_Q	206_E	1.943	1.00
203_M	207_A	1.938	1.00
168_W	214_L	1.915	1.00
53_T	58_K	1.878	1.00
147_E	166_S	1.847	1.00
122_H	213_E	1.835	1.00
7_A	51_I	1.809	1.00
222_L	232_E	1.803	1.00
156_S	202_Q	1.788	1.00
78_A	92_I	1.759	1.00
59_G	63_R	1.757	1.00
58_K	79_E	1.750	1.00
41_L	105_V	1.733	1.00
90_F	104_L	1.727	1.00
160_K	164_P	1.714	1.00
203_M	206_E	1.713	1.00
154_A	212_V	1.700	1.00
126_R	211_T	1.677	1.00
35_Y	39_S	1.668	1.00
129_G	177_D	1.668	1.00
139_D	142_R	1.661	1.00
21_V	27_P	1.647	1.00
117_S	121_R	1.644	1.00
15_H	19_R	1.642	1.00
101_P	124_A	1.641	1.00
148_F	168_W	1.630	1.00
21_V	60_Y	1.614	1.00
50_L	96_F	1.574	1.00
4_I	93_G	1.566	1.00
62_Q	79_E	1.554	1.00
128_E	209_N	1.512	1.00
32_P	35_Y	1.488	1.00
60_Y	63_R	1.473	1.00
199_S	202_Q	1.466	1.00
122_H	126_R	1.456	1.00
76_E	96_F	1.454	1.00
118_P	121_R	1.452	1.00
25_L	60_Y	1.422	1.00
50_L	78_A	1.409	1.00
88_Q	92_I	1.409	1.00
146_V	154_A	1.402	1.00
230_L	234_S	1.379	1.00
215_L	218_G	1.338	1.00
134_G	146_V	1.320	1.00
179_K	182_E	1.317	1.00
97_L	102_S	1.317	1.00
130_A	176_Y	1.306	1.00
115_G	118_P	1.304	1.00
91_I	185_K	1.292	1.00
121_R	125_A	1.287	1.00
153_R	209_N	1.282	1.00
226_T	229_S	1.282	1.00
147_E	158_E	1.271	1.00
102_S	178_S	1.271	1.00
49_I	73_I	1.265	1.00
119_K	133_F	1.262	1.00
66_G	77_Y	1.258	1.00
88_Q	91_I	1.248	1.00
176_Y	201_N	1.248	1.00
186_Q	203_M	1.241	1.00
224_T	233_A	1.236	1.00
101_P	178_S	1.235	1.00
183_Y	200_I	1.234	1.00
186_Q	207_A	1.213	1.00
112_F	240_V	1.211	1.00
118_P	122_H	1.192	1.00
183_Y	186_Q	1.186	1.00
129_G	209_N	1.182	1.00
158_E	165_K	1.180	1.00
103_C	175_F	1.175	1.00
189_P	195_L	1.164	1.00
231_I	235_T	1.158	1.00
182_E	186_Q	1.157	1.00
62_Q	77_Y	1.135	1.00
134_G	168_W	1.132	1.00
222_L	236_F	1.128	1.00
119_K	175_F	1.122	1.00
50_L	93_G	1.121	1.00
100_E	178_S	1.119	1.00
10_S	83_P	1.110	1.00
31_K	36_Y	1.103	1.00
34_I	65_L	1.094	1.00
53_T	62_Q	1.091	1.00
106_L	172_G	1.087	1.00
25_L	64_L	1.087	1.00
46_I	103_C	1.084	1.00
182_E	185_K	1.082	1.00
33_M	224_T	1.072	1.00
229_S	232_E	1.066	1.00
68_G	71_F	1.066	1.00
14_L	26_L	1.058	1.00
219_F	236_F	1.054	1.00
53_T	61_F	1.050	1.00
191_E	194_E	1.043	1.00
35_Y	68_G	1.038	1.00
101_P	175_F	1.036	1.00
42_M	73_I	1.036	1.00
50_L	76_E	1.035	1.00
141_E	160_K	1.031	1.00
53_T	79_E	1.030	1.00
148_F	152_F	1.023	1.00
8_G	52_I	1.016	1.00
39_S	42_M	1.016	1.00
104_L	176_Y	1.005	1.00
56_E	60_Y	0.989	1.00
228_D	232_E	0.983	1.00
32_P	64_L	0.977	1.00
189_P	194_E	0.974	1.00
34_I	51_I	0.972	1.00
59_G	62_Q	0.957	1.00
152_F	214_L	0.950	1.00
235_T	238_Q	0.949	1.00
53_T	77_Y	0.946	1.00
103_C	120_L	0.938	1.00
231_I	234_S	0.930	1.00
144_G	159_E	0.927	1.00
34_I	61_F	0.925	1.00
121_R	124_A	0.923	1.00
91_I	184_A	0.921	1.00
94_E	181_V	0.916	1.00
38_L	65_L	0.914	1.00
148_F	212_V	0.908	1.00
200_I	203_M	0.899	1.00
27_P	32_P	0.896	1.00
24_Q	107_G	0.891	1.00
222_L	233_A	0.884	1.00
54_T	57_D	0.881	1.00
44_A	117_S	0.877	1.00
14_L	18_T	0.877	1.00
29_Y	234_S	0.872	1.00
156_S	163_Q	0.865	1.00
170_V	174_Y	0.861	1.00
145_V	169_A	0.847	1.00
33_M	37_P	0.842	1.00
127_T	177_D	0.841	1.00
232_E	235_T	0.839	1.00
123_V	177_D	0.839	1.00
201_N	210_L	0.838	1.00
4_I	102_S	0.838	1.00
22_S	60_Y	0.837	1.00
142_R	229_S	0.831	1.00
40_V	44_A	0.829	1.00
6_L	106_L	0.825	1.00
236_F	239_T	0.825	1.00
190_S	193_G	0.822	1.00
109_N	221_W	0.822	1.00
232_E	236_F	0.818	1.00
122_H	211_T	0.817	1.00
123_V	175_F	0.816	1.00
164_P	167_N	0.811	1.00
36_Y	237_V	0.808	1.00
18_T	26_L	0.808	1.00
62_Q	66_G	0.808	1.00
78_A	96_F	0.804	1.00
211_T	214_L	0.803	1.00
42_M	49_I	0.799	1.00
5_I	107_G	0.798	1.00
234_S	238_Q	0.795	1.00
51_I	75_L	0.794	1.00
192_R	195_L	0.794	1.00
81_P	84_D	0.793	1.00
155_I	158_E	0.791	1.00
43_L	117_S	0.789	1.00
130_A	210_L	0.787	1.00
65_L	75_L	0.787	1.00
152_F	155_I	0.785	1.00
63_R	66_G	0.783	1.00
31_K	35_Y	0.781	1.00
120_L	124_A	0.777	1.00
17_I	227_H	0.777	1.00
191_E	195_L	0.777	1.00
42_M	47_R	0.773	1.00
179_K	183_Y	0.773	1.00
120_L	175_F	0.772	1.00
69_S	73_I	0.765	1.00
29_Y	36_Y	0.764	1.00
39_S	71_F	0.764	1.00
38_L	75_L	0.764	1.00
47_R	74_Q	0.763	1.00
56_E	59_G	0.762	1.00
26_L	230_L	0.762	1.00
237_V	241_E	0.753	1.00
141_E	162_K	0.753	1.00
96_F	99_G	0.751	1.00
179_K	209_N	0.743	1.00
98_N	178_S	0.742	1.00
36_Y	39_S	0.741	1.00
189_P	192_R	0.739	1.00
51_I	65_L	0.737	1.00
129_G	179_K	0.734	1.00
130_A	204_Y	0.732	1.00
142_R	160_K	0.727	1.00
30_D	36_Y	0.726	1.00
131_T	135_Y	0.724	1.00
134_G	137_V	0.723	1.00
238_Q	242_K	0.720	1.00
194_E	198_T	0.720	1.00
187_V	203_M	0.720	1.00
128_E	153_R	0.718	1.00
46_I	120_L	0.716	1.00
209_N	212_V	0.712	1.00
105_V	116_F	0.711	1.00
86_L	106_L	0.711	1.00
4_I	52_I	0.707	1.00
130_A	201_N	0.699	1.00
97_L	181_V	0.698	1.00
180_V	204_Y	0.696	1.00
198_T	202_Q	0.695	1.00
183_Y	209_N	0.692	1.00
4_I	50_L	0.691	1.00
52_I	89_A	0.691	1.00
119_K	131_T	0.689	1.00
157_L	170_V	0.688	1.00
13_R	23_K	0.684	1.00
39_S	68_G	0.682	1.00
11_G	23_K	0.679	1.00
91_I	195_L	0.676	1.00
78_A	93_G	0.673	1.00
53_T	57_D	0.673	1.00
142_R	226_T	0.672	1.00
158_E	161_P	0.669	1.00
17_I	21_V	0.664	1.00
90_F	180_V	0.663	1.00
110_I	233_A	0.663	1.00
130_A	134_G	0.662	1.00
38_L	51_I	0.659	1.00
95_T	98_N	0.657	1.00
35_Y	65_L	0.651	1.00
132_V	146_V	0.650	1.00
235_T	239_T	0.648	1.00
187_V	200_I	0.646	1.00
32_P	36_Y	0.646	1.00
179_K	207_A	0.645	1.00
27_P	30_D	0.643	1.00
147_E	165_K	0.643	1.00
236_F	240_V	0.642	1.00
122_H	125_A	0.639	1.00
136_Q	168_W	0.638	1.00
119_K	213_E	0.638	1.00
188_K	194_E	0.634	1.00
111_F	171_T	0.634	1.00
186_Q	210_L	0.633	1.00
106_L	109_N	0.629	1.00
75_L	79_E	0.626	1.00
75_L	80_Q	0.626	1.00
131_T	211_T	0.625	1.00
126_R	131_T	0.625	1.00
17_I	26_L	0.625	1.00
239_T	243_R	0.622	1.00
41_L	103_C	0.622	1.00
178_S	181_V	0.618	1.00
3_G	49_I	0.616	1.00
52_I	78_A	0.614	1.00
53_T	59_G	0.613	1.00
183_Y	204_Y	0.613	1.00
111_F	173_L	0.612	1.00
40_V	173_L	0.611	1.00
228_D	242_K	0.610	1.00
94_E	102_S	0.608	1.00
6_L	86_L	0.607	1.00
241_E	244_Q	0.605	1.00
25_L	61_F	0.605	1.00
83_P	88_Q	0.602	1.00
154_A	157_L	0.600	1.00
114_Q	117_S	0.598	1.00
184_A	187_V	0.597	1.00
52_I	93_G	0.596	1.00
85_G	199_S	0.594	1.00
187_V	195_L	0.594	1.00
38_L	42_M	0.581	1.00
190_S	194_E	0.581	1.00
179_K	208_G	0.581	1.00
232_E	242_K	0.580	1.00
188_K	195_L	0.579	1.00
227_H	231_I	0.577	1.00
36_Y	40_V	0.574	1.00
77_Y	80_Q	0.573	1.00
231_I	238_Q	0.573	1.00
135_Y	171_T	0.573	1.00
28_I	234_S	0.572	1.00
37_P	40_V	0.572	1.00
80_Q	83_P	0.570	1.00
187_V	199_S	0.570	1.00
5_I	105_V	0.570	1.00
39_S	43_L	0.569	1.00
228_D	243_R	0.569	1.00
171_T	221_W	0.564	1.00
5_I	37_P	0.563	1.00
137_V	140_P	0.561	1.00
132_V	136_Q	0.561	1.00
80_Q	89_A	0.560	1.00
231_I	236_F	0.560	1.00
105_V	173_L	0.560	1.00
94_E	98_N	0.559	1.00
76_E	80_Q	0.559	1.00
17_I	20_G	0.559	1.00
129_G	133_F	0.559	1.00
192_R	196_E	0.558	1.00
135_Y	169_A	0.557	1.00
37_P	105_V	0.556	1.00
195_L	198_T	0.554	1.00
74_Q	80_Q	0.552	1.00
76_E	79_E	0.552	1.00
7_A	34_I	0.551	1.00
116_F	119_K	0.551	1.00
88_Q	195_L	0.551	1.00
6_L	89_A	0.546	1.00
23_K	108_D	0.544	1.00
120_L	123_V	0.544	1.00
42_M	74_Q	0.540	1.00
182_E	207_A	0.539	1.00
82_S	88_Q	0.538	1.00
4_I	90_F	0.533	1.00
133_F	137_V	0.532	1.00
132_V	137_V	0.530	1.00
103_C	116_F	0.526	1.00
156_S	206_E	0.526	1.00
143_F	223_D	0.526	1.00
199_S	203_M	0.523	1.00
163_Q	166_S	0.522	1.00
94_E	182_E	0.518	1.00
86_L	170_V	0.517	1.00
90_F	181_V	0.516	1.00
188_K	191_E	0.516	1.00
149_D	152_F	0.513	1.00
135_Y	221_W	0.511	1.00
73_I	76_E	0.511	1.00
24_Q	61_F	0.509	1.00
41_L	46_I	0.509	1.00
183_Y	187_V	0.506	1.00
58_K	61_F	0.506	1.00
54_T	83_P	0.504	1.00
222_L	229_S	0.504	1.00
184_A	195_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
1mc3A	3	0.9898	100	0.32	Contact Map
1lvwA	3	0.9966	100	0.325	Contact Map
4ho4A	3	1	100	0.331	Contact Map
1iimA	3	0.9761	100	0.34	Contact Map
3jukA	3	0.8055	100	0.372	Contact Map
2e3dA	3	0.8601	100	0.379	Contact Map
3brkX	2	0.9454	100	0.385	Contact Map
2ux8A	4	0.8635	100	0.387	Contact Map
2ggoA	3	0.942	100	0.392	Contact Map
1yp2A	4	0.959	100	0.4	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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