RUTE - ECOLI - GREMLIN Contacts

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RUTE - Probable malonic semialdehyde reductase RutE

UniProt:	P75894	Sequences: MNEAVSPGALSTLFTDARTHNGWRETPVSDETLREIYALMKWGPTSANCSPARIVFTRTAEGKERLRPALSSGNLQKTLTAPVTAIVAWDSEFYERLPLLFPHGDARSWFTSSPQLAEETAFRNSSMQAAYLIVACRALGLDTGPMSGFDRQHVDDAFFTGSTLKSNLLINIGYGDSSKLYARLPRLSFEEACGLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13855
Length:	196 (165)
Sequences:	12622 (9448)
Seq/√Len:	735.5

ECOLI - RUTE NFNB NFSA YDJA
BACSU - YODC MHQN YFKO YDGI YFHC NFRA1 NFRA2
HALSA - Q9HQZ4
SULSO - Q97VQ3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_S	32_T	3.682	1.00
35_E	139_L	3.505	1.00
30_D	58_R	2.889	1.00
26_T	174_Y	2.636	1.00
30_D	34_R	2.611	1.00
54_I	128_Q	2.518	1.00
36_I	136_C	2.267	1.00
16_D	137_R	2.252	1.00
142_D	175_G	2.169	1.00
141_L	174_Y	2.138	1.00
32_T	139_L	2.091	1.00
133_I	143_T	2.054	1.00
38_A	41_K	2.036	1.00
12_T	16_D	1.942	1.00
65_R	157_A	1.913	1.00
39_L	135_A	1.892	1.00
129_A	168_L	1.847	1.00
60_A	64_E	1.827	1.00
67_R	79_L	1.771	1.00
155_D	166_S	1.756	1.00
40_M	132_L	1.748	1.00
55_V	88_A	1.729	1.00
62_G	65_R	1.722	1.00
24_R	176_D	1.706	1.00
22_G	176_D	1.702	1.00
88_A	164_L	1.693	1.00
9_A	12_T	1.688	1.00
32_T	141_L	1.687	1.00
10_L	14_F	1.644	1.00
129_A	170_I	1.619	1.00
133_I	145_P	1.546	1.00
54_I	85_A	1.540	1.00
64_E	79_L	1.523	1.00
36_I	132_L	1.501	1.00
32_T	174_Y	1.469	1.00
10_L	13_L	1.466	1.00
11_S	35_E	1.463	1.00
27_P	58_R	1.434	1.00
69_A	153_H	1.431	1.00
8_G	12_T	1.425	1.00
136_C	172_I	1.408	1.00
60_A	63_K	1.392	1.00
187_L	191_E	1.369	1.00
123_R	126_S	1.365	1.00
69_A	157_A	1.358	1.00
11_S	15_T	1.352	1.00
127_M	130_A	1.351	1.00
141_L	172_I	1.343	1.00
15_T	42_W	1.342	1.00
137_R	142_D	1.340	1.00
153_H	156_D	1.324	1.00
36_I	172_I	1.321	1.00
133_I	170_I	1.316	1.00
66_L	154_V	1.305	1.00
32_T	35_E	1.297	1.00
61_E	64_E	1.289	1.00
85_A	132_L	1.277	1.00
36_I	141_L	1.254	1.00
64_E	68_P	1.244	1.00
53_R	164_L	1.227	1.00
62_G	157_A	1.195	1.00
125_S	167_N	1.188	1.00
61_E	65_R	1.187	1.00
136_C	143_T	1.185	1.00
11_S	39_L	1.175	1.00
59_T	62_G	1.165	1.00
145_P	168_L	1.158	1.00
23_W	171_N	1.158	1.00
46_S	120_T	1.157	1.00
34_R	190_E	1.133	1.00
28_V	141_L	1.104	1.00
39_L	139_L	1.100	1.00
120_T	147_S	1.091	1.00
84_T	169_L	1.088	1.00
15_T	38_A	1.087	1.00
8_G	138_A	1.086	1.00
43_G	131_Y	1.080	1.00
135_A	139_L	1.078	1.00
86_I	169_L	1.078	1.00
19_T	144_G	1.076	1.00
89_W	121_A	1.065	1.00
55_V	164_L	1.063	1.00
11_S	139_L	1.046	1.00
150_D	153_H	1.046	1.00
87_V	132_L	1.042	1.00
153_H	157_A	1.038	1.00
87_V	129_A	1.036	1.00
56_F	83_V	1.034	1.00
12_T	15_T	1.027	1.00
31_E	34_R	1.023	1.00
34_R	38_A	1.011	1.00
143_T	172_I	1.002	1.00
132_L	170_I	0.994	1.00
90_D	163_T	0.988	1.00
143_T	170_I	0.983	1.00
9_A	138_A	0.979	1.00
41_K	192_A	0.978	1.00
65_R	68_P	0.971	1.00
37_Y	56_F	0.965	1.00
122_F	167_N	0.956	1.00
152_Q	156_D	0.945	1.00
135_A	138_A	0.937	1.00
76_Q	79_L	0.933	1.00
126_S	145_P	0.931	1.00
130_A	134_V	0.928	1.00
91_S	165_K	0.924	1.00
37_Y	40_M	0.923	1.00
54_I	87_V	0.909	1.00
29_S	174_Y	0.906	1.00
33_L	83_V	0.901	1.00
129_A	145_P	0.894	1.00
14_F	131_Y	0.894	1.00
87_V	125_S	0.893	1.00
144_G	171_N	0.893	1.00
127_M	145_P	0.889	1.00
10_L	134_V	0.885	1.00
132_L	172_I	0.883	1.00
92_E	163_T	0.872	1.00
131_Y	134_V	0.872	1.00
146_M	171_N	0.870	1.00
8_G	13_L	0.866	1.00
28_V	174_Y	0.859	1.00
24_R	174_Y	0.859	1.00
118_E	165_K	0.842	1.00
53_R	90_D	0.841	1.00
127_M	131_Y	0.839	1.00
34_R	189_F	0.837	1.00
152_Q	155_D	0.837	1.00
22_G	177_S	0.835	1.00
14_F	134_V	0.829	1.00
58_R	83_V	0.818	1.00
45_T	52_A	0.818	1.00
27_P	60_A	0.817	1.00
33_L	172_I	0.815	1.00
123_R	147_S	0.814	1.00
10_L	138_A	0.811	1.00
86_I	166_S	0.802	1.00
88_A	160_T	0.801	1.00
64_E	67_R	0.795	1.00
26_T	29_S	0.795	1.00
161_G	164_L	0.788	1.00
160_T	164_L	0.785	1.00
11_S	138_A	0.781	1.00
85_A	172_I	0.768	1.00
35_E	39_L	0.766	1.00
76_Q	80_T	0.763	1.00
154_V	157_A	0.760	1.00
151_R	166_S	0.758	1.00
155_D	165_K	0.757	1.00
36_I	139_L	0.756	1.00
28_V	32_T	0.748	1.00
35_E	38_A	0.744	1.00
77_K	80_T	0.740	1.00
123_R	127_M	0.733	1.00
55_V	158_F	0.731	1.00
90_D	93_F	0.728	1.00
149_F	169_L	0.723	1.00
11_S	135_A	0.723	1.00
122_F	126_S	0.716	1.00
188_S	191_E	0.708	1.00
124_N	147_S	0.707	1.00
33_L	37_Y	0.707	1.00
38_A	189_F	0.703	1.00
57_T	62_G	0.698	1.00
119_E	122_F	0.697	1.00
84_T	171_N	0.689	1.00
46_S	124_N	0.688	1.00
70_L	78_T	0.669	1.00
46_S	147_S	0.668	1.00
52_A	125_S	0.665	1.00
13_L	138_A	0.663	1.00
155_D	160_T	0.662	1.00
40_M	54_I	0.660	1.00
45_T	50_S	0.654	1.00
86_I	158_F	0.653	1.00
81_A	84_T	0.651	1.00
28_V	31_E	0.650	1.00
187_L	192_A	0.646	1.00
151_R	155_D	0.640	1.00
31_E	35_E	0.639	1.00
13_L	134_V	0.634	1.00
175_G	178_S	0.633	1.00
130_A	133_I	0.626	1.00
23_W	144_G	0.625	1.00
20_H	179_K	0.623	1.00
89_W	125_S	0.622	1.00
36_I	40_M	0.621	1.00
38_A	42_W	0.620	1.00
21_N	77_K	0.617	1.00
70_L	169_L	0.615	1.00
71_S	75_L	0.612	1.00
56_F	85_A	0.610	1.00
177_S	180_L	0.606	1.00
160_T	166_S	0.604	1.00
10_L	135_A	0.602	1.00
78_T	81_A	0.598	1.00
35_E	135_A	0.595	1.00
63_K	67_R	0.594	1.00
52_A	128_Q	0.592	1.00
89_W	167_N	0.589	1.00
20_H	175_G	0.584	1.00
21_N	144_G	0.582	1.00
113_S	116_L	0.580	1.00
81_A	85_A	0.578	1.00
90_D	164_L	0.576	1.00
151_R	165_K	0.575	1.00
75_L	79_L	0.574	1.00
65_R	69_A	0.574	1.00
57_T	158_F	0.573	1.00
17_A	44_P	0.572	1.00
24_R	177_S	0.572	1.00
28_V	33_L	0.568	1.00
128_Q	192_A	0.562	1.00
62_G	158_F	0.559	1.00
28_V	82_P	0.558	1.00
134_V	138_A	0.555	1.00
185_P	188_S	0.551	1.00
68_P	157_A	0.544	1.00
129_A	133_I	0.542	1.00
20_H	142_D	0.542	1.00
87_V	170_I	0.542	1.00
40_M	128_Q	0.539	1.00
123_R	145_P	0.539	1.00
29_S	141_L	0.537	1.00
44_P	143_T	0.537	1.00
42_W	184_L	0.536	1.00
155_D	162_S	0.535	1.00
33_L	56_F	0.532	1.00
15_T	35_E	0.532	1.00
13_L	137_R	0.527	1.00
41_K	189_F	0.523	1.00
119_E	123_R	0.523	1.00
32_T	36_I	0.523	1.00
137_R	175_G	0.523	1.00
44_P	130_A	0.522	1.00
91_S	163_T	0.520	1.00
85_A	88_A	0.520	1.00
66_L	169_L	0.519	1.00
53_R	187_L	0.518	1.00
57_T	86_I	0.515	1.00
22_G	80_T	0.515	1.00
37_Y	192_A	0.511	1.00
114_P	117_A	0.510	1.00
123_R	168_L	0.508	1.00
120_T	124_N	0.506	1.00
62_G	66_L	0.504	1.00
69_A	154_V	0.503	1.00
83_V	172_I	0.500	0.99

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
4qlxA	2	0.9898	100	0.152	Contact Map
3gbhA	3	0.9847	100	0.159	Contact Map
1noxA	2	0.9541	100	0.16	Contact Map
3bemA	2	0.9745	100	0.166	Contact Map
3ge6A	2	0.9745	100	0.167	Contact Map
3of4A	3	0.9541	100	0.174	Contact Map
1icrA	2	0.9592	100	0.176	Contact Map
2b67A	2	0.9439	100	0.177	Contact Map
3gagA	4	0.949	100	0.178	Contact Map
2h0uA	2	0.8571	100	0.181	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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