YVCI - BACSU - GREMLIN Contacts

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YVCI - Uncharacterized Nudix hydrolase YvcI

UniProt:	O06972	Sequences: MTYLQRVTNCVLQTDDKVLLLQKPRRGWWVAPGGKMESGESVRDSVIREYREETGIYIINPQLKGVFTFIIKDGDHIVSEWMMFTFVADSYTGQNVSESEEGKLQWHDVNDIQNLPMAPGDGHILDFMMKGQGLLHGTFTYTPEFELLSYRLDPQHIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	158 (123)
Sequences:	3051 (2257)
Seq/√Len:	203.5

ECOLI - MUTT NUDG NUDJ
BACSU - YVCI YJHB MUTT
HALSA - Q9HR46 Q9HS29
SULSO - Q97WE7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_R	57_Y	5.042	1.00
13_Q	17_K	3.963	1.00
22_Q	103_K	3.555	1.00
17_K	108_D	3.431	1.00
36_M	45_S	3.089	1.00
41_S	44_D	2.634	1.00
50_Y	58_I	2.602	1.00
108_D	111_D	2.495	1.00
32_P	54_T	2.411	1.00
47_I	51_R	2.354	1.00
111_D	114_N	2.301	1.00
59_I	90_S	2.227	1.00
63_L	84_F	2.105	1.00
58_I	88_A	1.973	1.00
126_D	130_K	1.953	1.00
20_L	107_H	1.890	1.00
59_I	92_T	1.826	1.00
29_W	105_Q	1.787	1.00
8_T	45_S	1.761	1.00
57_Y	92_T	1.725	1.00
63_L	66_V	1.618	1.00
20_L	115_L	1.613	1.00
10_C	13_Q	1.528	1.00
16_D	109_V	1.500	1.00
107_H	115_L	1.499	1.00
60_N	90_S	1.474	1.00
46_V	61_P	1.445	1.00
9_N	46_V	1.432	1.00
64_K	87_V	1.431	1.00
113_Q	129_M	1.359	1.00
59_I	89_D	1.354	1.00
98_E	101_E	1.341	1.00
28_W	116_P	1.314	1.00
97_S	101_E	1.306	1.00
22_Q	102_G	1.275	1.00
67_F	127_F	1.272	1.00
42_V	68_T	1.270	1.00
50_Y	88_A	1.216	1.00
36_M	42_V	1.210	1.00
65_G	127_F	1.206	1.00
19_L	104_L	1.197	1.00
12_L	50_Y	1.188	1.00
20_L	117_M	1.173	1.00
62_Q	87_V	1.170	1.00
105_Q	111_D	1.145	1.00
13_Q	109_V	1.139	1.00
44_D	47_I	1.118	1.00
47_I	58_I	1.090	1.00
14_T	17_K	1.062	1.00
42_V	86_F	1.060	1.00
60_N	89_D	1.041	1.00
13_Q	87_V	1.019	1.00
42_V	84_F	1.007	1.00
22_Q	29_W	1.007	1.00
32_P	50_Y	1.006	1.00
61_P	89_D	0.971	1.00
13_Q	16_D	0.962	0.99
68_T	80_E	0.959	0.99
66_V	82_M	0.950	0.99
47_I	60_N	0.942	0.99
43_R	47_I	0.939	0.99
90_S	93_G	0.939	0.99
21_L	101_E	0.936	0.99
56_I	90_S	0.919	0.99
10_C	46_V	0.916	0.99
55_G	99_S	0.904	0.99
62_Q	89_D	0.891	0.99
123_H	127_F	0.882	0.99
28_W	119_P	0.881	0.99
96_V	101_E	0.879	0.99
63_L	86_F	0.878	0.99
46_V	50_Y	0.871	0.99
29_W	107_H	0.869	0.99
21_L	32_P	0.865	0.99
123_H	126_D	0.864	0.99
51_R	55_G	0.864	0.99
87_V	128_M	0.863	0.99
13_Q	89_D	0.859	0.99
23_K	26_R	0.858	0.99
88_A	91_Y	0.851	0.99
12_L	56_I	0.844	0.99
27_G	102_G	0.831	0.98
16_D	108_D	0.828	0.98
113_Q	126_D	0.816	0.98
6_R	36_M	0.810	0.98
22_Q	27_G	0.802	0.98
6_R	82_M	0.800	0.98
85_T	124_I	0.798	0.98
67_F	83_M	0.783	0.98
60_N	91_Y	0.778	0.98
47_I	57_Y	0.776	0.98
46_V	88_A	0.775	0.98
10_C	50_Y	0.769	0.97
107_H	111_D	0.768	0.97
47_I	59_I	0.766	0.97
119_P	122_G	0.760	0.97
97_S	100_E	0.755	0.97
66_V	84_F	0.750	0.97
16_D	110_N	0.750	0.97
61_P	88_A	0.747	0.97
56_I	96_V	0.746	0.97
21_L	104_L	0.741	0.97
30_V	120_G	0.735	0.97
21_L	30_V	0.731	0.97
21_L	102_G	0.722	0.96
72_K	78_V	0.710	0.96
109_V	129_M	0.710	0.96
28_W	118_A	0.704	0.96
70_I	80_E	0.703	0.96
42_V	82_M	0.703	0.96
6_R	13_Q	0.698	0.96
6_R	84_F	0.697	0.96
8_T	121_D	0.694	0.95
55_G	97_S	0.691	0.95
121_D	124_I	0.686	0.95
71_I	74_G	0.683	0.95
58_I	61_P	0.682	0.95
40_E	44_D	0.681	0.95
29_W	115_L	0.673	0.95
14_T	94_Q	0.667	0.94
20_L	105_Q	0.660	0.94
11_V	31_A	0.659	0.94
24_P	98_E	0.654	0.94
112_I	125_L	0.654	0.94
47_I	50_Y	0.640	0.93
30_V	33_G	0.636	0.93
7_V	81_W	0.636	0.93
12_L	16_D	0.632	0.93
36_M	84_F	0.627	0.92
8_T	31_A	0.617	0.92
69_F	83_M	0.617	0.92
22_Q	105_Q	0.616	0.92
81_W	121_D	0.613	0.91
127_F	130_K	0.607	0.91
14_T	89_D	0.604	0.91
83_M	120_G	0.602	0.91
85_T	118_A	0.601	0.91
30_V	121_D	0.600	0.91
12_L	87_V	0.594	0.90
62_Q	131_G	0.593	0.90
32_P	102_G	0.588	0.90
127_F	131_G	0.584	0.89
47_I	62_Q	0.583	0.89
98_E	102_G	0.583	0.89
26_R	81_W	0.583	0.89
118_A	121_D	0.581	0.89
120_G	124_I	0.579	0.89
99_S	102_G	0.576	0.89
116_P	122_G	0.576	0.89
92_T	110_N	0.574	0.89
31_A	85_T	0.571	0.88
35_K	121_D	0.569	0.88
13_Q	108_D	0.567	0.88
40_E	48_R	0.566	0.88
71_I	79_S	0.563	0.88
69_F	85_T	0.563	0.88
7_V	45_S	0.555	0.87
9_N	85_T	0.553	0.87
35_K	84_F	0.552	0.87
118_A	124_I	0.552	0.87
47_I	61_P	0.552	0.87
85_T	128_M	0.551	0.87
122_G	126_D	0.550	0.86
23_K	101_E	0.550	0.86
70_I	79_S	0.549	0.86
20_L	29_W	0.545	0.86
12_L	109_V	0.535	0.85
31_A	125_L	0.535	0.85
127_F	132_Q	0.532	0.85
30_V	81_W	0.530	0.84
114_N	130_K	0.529	0.84
6_R	11_V	0.528	0.84
117_M	120_G	0.528	0.84
22_Q	28_W	0.526	0.84
30_V	83_M	0.523	0.84
68_T	82_M	0.522	0.83
113_Q	122_G	0.516	0.83
31_A	83_M	0.516	0.83
29_W	116_P	0.505	0.81
6_R	9_N	0.505	0.81
14_T	90_S	0.505	0.81
41_S	68_T	0.502	0.81
30_V	35_K	0.502	0.81
59_I	62_Q	0.500	0.81

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
3fk9A	2	0.9684	100	0.306	Contact Map
3q93A	1	0.9557	100	0.353	Contact Map
4c9xA	2	0.9557	99.9	0.385	Contact Map
2azwA	1	0.8228	99.9	0.427	Contact Map
3q1pA	2	0.8797	99.9	0.43	Contact Map
4dywA	2	0.7722	99.9	0.431	Contact Map
3gwyA	2	0.7975	99.9	0.432	Contact Map
1mutA	1	0.7911	99.9	0.432	Contact Map
3i7uA	4	0.8481	99.9	0.432	Contact Map
3exqA	2	0.9557	99.9	0.432	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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