YMCA - BACSU - GREMLIN Contacts

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YMCA - Uncharacterized protein YmcA

UniProt:	O31779	Sequences: MTLYSKKDIVQQARNLAKMISETEEVDFFKRAEAQINENDKVSTIVNQIKALQKQAVNLKHYEKHEALKQVEAKIDALQEELEEIPVIQEFRDSQMEVNDLLQLVAHTISNQVTNEIITSTGGDLLKGETGSKVKHSNNSCSL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	143 (119)
Sequences:	267 (181)
Seq/√Len:	16.5

BACSU - YMCA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_E	69_K	3.472	0.99
31_R	35_Q	3.238	0.99
76_D	79_Q	2.832	0.98
39_N	87_V	2.787	0.98
45_I	85_I	2.749	0.97
12_Q	15_N	2.642	0.97
18_K	22_E	2.477	0.95
49_I	61_H	2.427	0.94
29_F	122_G	2.356	0.93
85_I	90_E	2.220	0.91
64_K	67_A	2.138	0.89
27_D	31_R	2.085	0.88
76_D	80_E	2.078	0.88
79_Q	83_E	2.068	0.88
45_I	81_E	1.984	0.85
52_L	74_K	1.783	0.79
104_L	108_T	1.773	0.78
42_V	87_V	1.761	0.78
36_I	88_I	1.656	0.73
59_L	81_E	1.540	0.67
40_D	44_T	1.527	0.67
26_V	112_Q	1.520	0.66
58_N	67_A	1.514	0.66
56_A	68_L	1.506	0.66
23_T	32_A	1.491	0.65
46_V	49_I	1.490	0.65
8_D	11_Q	1.442	0.62
88_I	102_L	1.422	0.61
73_A	105_V	1.403	0.60
33_E	46_V	1.395	0.59
93_D	97_E	1.375	0.58
29_F	117_I	1.374	0.58
80_E	84_E	1.361	0.57
26_V	98_V	1.344	0.56
28_F	32_A	1.341	0.56
60_K	108_T	1.323	0.55
55_Q	63_E	1.317	0.55
60_K	68_L	1.309	0.54
34_A	80_E	1.305	0.54
30_K	121_T	1.292	0.53
73_A	77_A	1.238	0.50
57_V	81_E	1.235	0.50
116_E	119_T	1.234	0.50
18_K	116_E	1.228	0.50
5_S	21_S	1.196	0.48
83_E	92_R	1.193	0.48
68_L	72_E	1.176	0.47
21_S	30_K	1.175	0.47
8_D	100_D	1.169	0.46
7_K	11_Q	1.149	0.45
95_Q	99_N	1.124	0.44
39_N	109_I	1.104	0.42
20_I	111_N	1.075	0.41
48_Q	59_L	1.074	0.41
51_A	59_L	1.073	0.41
26_V	55_Q	1.061	0.40
91_F	95_Q	1.054	0.40
36_I	93_D	1.053	0.39
49_I	76_D	1.048	0.39
58_N	64_K	1.045	0.39
77_A	107_H	1.034	0.38
10_V	107_H	1.032	0.38
38_E	44_T	1.030	0.38
49_I	78_L	1.020	0.38
105_V	109_I	1.016	0.37
70_Q	77_A	1.011	0.37
13_A	72_E	0.980	0.35
58_N	62_Y	0.977	0.35
20_I	101_L	0.968	0.35
5_S	64_K	0.966	0.35
70_Q	112_Q	0.961	0.34
50_K	57_V	0.948	0.34
18_K	44_T	0.941	0.33
36_I	60_K	0.929	0.33
24_E	82_L	0.901	0.31
66_E	73_A	0.896	0.31
44_T	48_Q	0.885	0.31
70_Q	74_K	0.880	0.30
7_K	48_Q	0.843	0.28
44_T	117_I	0.829	0.28
31_R	90_E	0.828	0.28
48_Q	80_E	0.820	0.27
33_E	87_V	0.813	0.27
34_A	40_D	0.804	0.27
33_E	36_I	0.792	0.26
92_R	98_V	0.791	0.26
67_A	71_V	0.789	0.26
62_Y	67_A	0.788	0.26
25_E	98_V	0.787	0.26
6_K	111_N	0.786	0.26
77_A	101_L	0.777	0.25
4_Y	19_M	0.776	0.25
12_Q	71_V	0.773	0.25
77_A	81_E	0.773	0.25
72_E	81_E	0.767	0.25
37_N	106_A	0.746	0.24
90_E	95_Q	0.741	0.24
23_T	98_V	0.741	0.24
31_R	73_A	0.737	0.24
7_K	119_T	0.730	0.23
49_I	56_A	0.726	0.23
114_T	122_G	0.722	0.23
97_E	100_D	0.719	0.23
59_L	65_H	0.716	0.23
12_Q	106_A	0.715	0.23
103_Q	109_I	0.703	0.22
11_Q	116_E	0.694	0.22
38_E	84_E	0.691	0.22
29_F	118_I	0.689	0.22
6_K	122_G	0.688	0.22
33_E	82_L	0.686	0.22
13_A	32_A	0.680	0.21
37_N	76_D	0.677	0.21
62_Y	97_E	0.676	0.21
108_T	116_E	0.673	0.21
20_I	97_E	0.670	0.21
29_F	105_V	0.666	0.21
109_I	113_V	0.665	0.21
54_K	57_V	0.663	0.21
54_K	99_N	0.662	0.21
25_E	32_A	0.660	0.21
13_A	33_E	0.653	0.20
39_N	121_T	0.642	0.20
24_E	36_I	0.638	0.20
48_Q	113_V	0.635	0.20
19_M	23_T	0.625	0.19
63_E	93_D	0.618	0.19
75_I	102_L	0.615	0.19
26_V	74_K	0.612	0.19
30_K	117_I	0.611	0.19
80_E	96_M	0.610	0.19
6_K	22_E	0.609	0.19
43_S	79_Q	0.603	0.18
34_A	121_T	0.599	0.18
21_S	92_R	0.592	0.18
50_K	54_K	0.591	0.18
100_D	111_N	0.591	0.18
37_N	90_E	0.588	0.18
43_S	66_E	0.587	0.18
28_F	69_K	0.586	0.18
85_I	95_Q	0.583	0.18
54_K	75_I	0.582	0.18
31_R	101_L	0.579	0.18
65_H	82_L	0.577	0.18
22_E	42_V	0.575	0.17
89_Q	94_S	0.573	0.17
16_L	90_E	0.569	0.17
96_M	100_D	0.567	0.17
24_E	107_H	0.567	0.17
26_V	48_Q	0.566	0.17
26_V	101_L	0.564	0.17
61_H	97_E	0.556	0.17
30_K	56_A	0.554	0.17
36_I	46_V	0.554	0.17
88_I	93_D	0.553	0.17
62_Y	100_D	0.548	0.17
68_L	108_T	0.547	0.17
32_A	109_I	0.547	0.17
35_Q	113_V	0.540	0.16
16_L	115_N	0.537	0.16
43_S	73_A	0.537	0.16
15_N	20_I	0.532	0.16
4_Y	35_Q	0.526	0.16
42_V	81_E	0.523	0.16
59_L	120_S	0.521	0.16
25_E	46_V	0.520	0.16
36_I	97_E	0.519	0.16
40_D	66_E	0.518	0.16
32_A	101_L	0.518	0.16
100_D	107_H	0.513	0.15
61_H	87_V	0.512	0.15
97_E	108_T	0.511	0.15
72_E	95_Q	0.509	0.15
52_L	55_Q	0.509	0.15
44_T	59_L	0.508	0.15
40_D	48_Q	0.507	0.15
66_E	76_D	0.506	0.15
19_M	105_V	0.500	0.15

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
2pihA	2	0.8601	100	0.423	Contact Map
2oeeA	2	0.6503	99.8	0.607	Contact Map
2oeqA	4	0.8252	99.8	0.62	Contact Map
2iazA	4	0.7832	99.7	0.629	Contact Map
4f01A	2	0.7063	16	0.943	Contact Map
4jneA	2	0.7063	12.7	0.946	Contact Map
3ghgA	2	0.5804	11.1	0.947	Contact Map
4po2A	4	0.7343	7.8	0.951	Contact Map
1j1vA	1	0.3846	7.8	0.951	Contact Map
3epzA	1	0.3846	6.9	0.952	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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