YKUU - BACSU - GREMLIN Contacts

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YKUU - Thioredoxin-like protein YkuU

UniProt:	O34564	Sequences: MAERMVGKQAPRFEMEAVLASKEFGKVSLEENMKNDKWTVLFFYPMDFTFVCPTEITAMSDRYDEFEDLDAEVIGVSTDTIHTHLAWINTDRKENGLGQLKYPLAADTNHEVSREYGVLIEEEGVALRGLFIINPEGELQYQTVFHNNIGRDVDETLRVLQALQTGGLCPANWKPGQKTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	180 (146)
Sequences:	9528 (5328)
Seq/√Len:	441.0

ECOLI - AHPC BCP TPX
BACSU - YKUU AHPC BCP TPX
HALSA - Q9HP28 Q9HQE6 Q9HN00
SULSO - TDXH Q97VL0 Q97WG5 Q97WP9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_E	26_K	2.937	1.00
38_W	135_P	2.934	1.00
47_D	84_H	2.724	1.00
37_K	72_E	2.719	1.00
69_L	161_Q	2.705	1.00
10_A	116_Y	2.413	1.00
14_E	28_S	2.399	1.00
63_Y	67_E	2.283	1.00
17_A	25_G	2.257	1.00
134_N	140_Q	2.170	1.00
120_I	127_L	2.122	1.00
60_S	101_K	2.114	1.00
16_E	26_K	2.078	1.00
9_Q	138_E	2.055	1.00
18_V	88_I	2.017	1.00
62_R	65_E	1.922	1.00
5_M	8_K	1.869	1.00
78_T	110_H	1.847	1.00
12_R	30_E	1.781	1.00
63_Y	101_K	1.738	1.00
111_E	115_E	1.715	1.00
78_T	113_S	1.701	1.00
62_R	153_V	1.661	1.00
28_S	31_E	1.651	1.00
15_M	112_V	1.646	1.00
48_F	98_G	1.616	1.00
141_Y	159_V	1.609	1.00
15_M	105_A	1.516	1.00
71_A	160_L	1.506	1.00
27_V	32_N	1.489	1.00
134_N	138_E	1.487	1.00
67_E	72_E	1.481	1.00
12_R	28_S	1.461	1.00
17_A	103_P	1.448	1.00
48_F	86_A	1.446	1.00
56_I	100_L	1.442	1.00
110_H	114_R	1.403	1.00
113_S	126_A	1.374	1.00
16_E	81_I	1.373	1.00
60_S	102_Y	1.364	1.00
78_T	126_A	1.359	1.00
65_E	68_D	1.339	1.00
85_L	89_N	1.317	1.00
64_D	68_D	1.295	1.00
39_T	74_I	1.293	1.00
54_T	150_G	1.291	1.00
18_V	23_E	1.248	1.00
143_T	159_V	1.207	1.00
40_V	132_I	1.203	1.00
75_G	104_L	1.174	1.00
17_A	27_V	1.170	1.00
62_R	154_D	1.170	1.00
32_N	39_T	1.163	1.00
114_R	119_L	1.160	1.00
57_T	61_D	1.157	1.00
110_H	119_L	1.148	1.00
17_A	23_E	1.144	1.00
154_D	158_R	1.144	1.00
38_W	71_A	1.136	1.00
64_D	67_E	1.128	1.00
23_E	85_L	1.128	1.00
133_I	139_L	1.124	1.00
90_T	98_G	1.123	1.00
155_E	158_R	1.121	1.00
43_F	76_V	1.116	1.00
82_H	86_A	1.088	1.00
42_F	56_I	1.087	1.00
48_F	90_T	1.084	1.00
39_T	72_E	1.084	1.00
17_A	105_A	1.084	1.00
4_R	139_L	1.070	1.00
32_N	74_I	1.062	1.00
118_V	131_F	1.060	1.00
65_E	157_L	1.040	1.00
118_V	129_G	1.037	1.00
6_V	141_Y	1.026	1.00
112_V	116_Y	1.023	1.00
38_W	140_Q	1.009	1.00
85_L	88_I	1.005	1.00
159_V	162_A	1.001	1.00
42_F	102_Y	0.995	1.00
57_T	60_S	0.992	1.00
72_E	103_P	0.974	1.00
29_L	39_T	0.974	1.00
40_V	130_L	0.967	1.00
80_T	83_T	0.960	1.00
140_Q	146_H	0.951	1.00
58_A	62_R	0.949	1.00
132_I	143_T	0.945	1.00
132_I	159_V	0.942	1.00
131_F	139_L	0.940	1.00
39_T	137_G	0.931	1.00
55_E	59_M	0.924	1.00
110_H	113_S	0.921	1.00
81_I	106_A	0.908	1.00
86_A	89_N	0.906	1.00
65_E	161_Q	0.904	1.00
151_R	154_D	0.900	1.00
66_F	157_L	0.897	1.00
40_V	71_A	0.897	1.00
13_F	116_Y	0.888	1.00
10_A	139_L	0.876	1.00
6_V	142_Q	0.876	1.00
76_V	112_V	0.875	1.00
48_F	83_T	0.874	1.00
36_D	135_P	0.867	1.00
10_A	133_I	0.866	1.00
158_R	161_Q	0.859	1.00
157_L	161_Q	0.857	1.00
59_M	73_V	0.848	1.00
111_E	114_R	0.845	1.00
70_D	135_P	0.841	1.00
122_E	125_V	0.838	1.00
148_N	151_R	0.838	1.00
59_M	156_T	0.838	1.00
27_V	74_I	0.837	1.00
12_R	29_L	0.836	1.00
54_T	57_T	0.834	1.00
41_L	116_Y	0.827	1.00
65_E	69_L	0.820	1.00
39_T	133_I	0.815	1.00
58_A	61_D	0.813	1.00
60_S	63_Y	0.811	1.00
16_E	108_T	0.797	1.00
158_R	162_A	0.795	1.00
74_I	105_A	0.793	1.00
113_S	119_L	0.792	1.00
13_F	112_V	0.788	1.00
80_T	108_T	0.780	1.00
44_Y	47_D	0.778	1.00
57_T	98_G	0.776	1.00
10_A	29_L	0.772	1.00
35_N	137_G	0.763	1.00
141_Y	155_E	0.759	1.00
143_T	156_T	0.754	1.00
18_V	85_L	0.728	1.00
18_V	81_I	0.727	1.00
6_V	139_L	0.723	1.00
64_D	101_K	0.720	1.00
10_A	112_V	0.717	1.00
151_R	155_E	0.711	1.00
127_L	145_F	0.706	1.00
18_V	103_P	0.706	1.00
46_M	125_V	0.705	1.00
142_Q	145_F	0.703	1.00
41_L	133_I	0.700	1.00
56_I	75_G	0.699	1.00
132_I	141_Y	0.686	1.00
69_L	160_L	0.686	1.00
130_L	156_T	0.682	1.00
32_N	72_E	0.678	1.00
40_V	156_T	0.675	1.00
38_W	160_L	0.669	1.00
42_F	75_G	0.664	1.00
46_M	79_D	0.663	1.00
23_E	88_I	0.663	1.00
69_L	157_L	0.661	1.00
140_Q	163_L	0.657	1.00
44_Y	75_G	0.656	1.00
62_R	66_F	0.655	1.00
127_L	146_H	0.646	0.99
45_P	49_T	0.635	0.99
41_L	76_V	0.633	0.99
139_L	142_Q	0.631	0.99
63_Y	73_V	0.630	0.99
30_E	35_N	0.630	0.99
47_D	83_T	0.623	0.99
29_L	32_N	0.617	0.99
59_M	153_V	0.615	0.99
9_Q	35_N	0.614	0.99
42_F	55_E	0.613	0.99
38_W	70_D	0.612	0.99
37_K	70_D	0.605	0.99
120_I	123_E	0.597	0.99
49_T	128_R	0.595	0.99
58_A	153_V	0.591	0.99
11_P	115_E	0.588	0.99
82_H	85_L	0.586	0.99
43_F	116_Y	0.585	0.99
56_I	102_Y	0.582	0.99
143_T	155_E	0.578	0.99
129_G	145_F	0.576	0.99
51_V	149_I	0.576	0.99
129_G	142_Q	0.571	0.99
58_A	154_D	0.568	0.99
81_I	85_L	0.566	0.99
37_K	67_E	0.565	0.99
46_M	80_T	0.565	0.99
12_R	35_N	0.563	0.99
24_F	81_I	0.563	0.99
73_V	102_Y	0.562	0.99
74_I	103_P	0.557	0.98
50_F	53_P	0.555	0.98
78_T	119_L	0.555	0.98
43_F	118_V	0.551	0.98
5_M	142_Q	0.540	0.98
133_I	137_G	0.540	0.98
112_V	115_E	0.536	0.98
54_T	149_I	0.535	0.98
149_I	162_A	0.530	0.98
127_L	147_N	0.529	0.98
63_Y	72_E	0.526	0.98
125_V	147_N	0.519	0.98
40_V	160_L	0.518	0.98
123_E	127_L	0.518	0.98
8_K	142_Q	0.513	0.97
44_Y	87_W	0.512	0.97
24_F	85_L	0.510	0.97
121_E	124_G	0.509	0.97
120_I	125_V	0.506	0.97
130_L	152_D	0.505	0.97
66_F	73_V	0.504	0.97
10_A	39_T	0.503	0.97
105_A	112_V	0.503	0.97
71_A	156_T	0.503	0.97
66_F	71_A	0.502	0.97
35_N	136_E	0.501	0.97
149_I	163_L	0.500	0.97
42_F	84_H	0.500	0.97

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
2v2gA	2	0.9556	100	0.301	Contact Map
1prxA	2	0.9667	100	0.303	Contact Map
3a2vA	5	0.9667	100	0.308	Contact Map
1xccA	2	0.9667	100	0.311	Contact Map
3w6gA	6	0.9444	100	0.313	Contact Map
3tjjA	3	0.9056	100	0.395	Contact Map
2c0dA	2	0.95	100	0.416	Contact Map
3zl5A	3	0.8833	100	0.416	Contact Map
4rqxA	3	0.9	100	0.418	Contact Map
2pn8A	4	0.9667	100	0.422	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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