YTZA - BACSU - GREMLIN Contacts

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YTZA - UPF0716 protein YtzA

UniProt:	O32064	Sequences: MRFLFLLFIVFPAIEIGIFLFLGNLIGILPTVLFMILTGIIGAAAAKKQGTEVYYKVQRDLQYGKMPGEAIADGLCIFIGGLLLMLPGFLSDLAGACLLIPFTRGWCKPILFKWLRGMSKNKRIIIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	127 (115)
Sequences:	1272 (911)
Seq/√Len:	84.9

ECOLI - FXSA
BACSU - YTZA
HALSA - Q9HNX1

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_I	90_L	3.150	1.00
60_D	65_K	3.147	1.00
28_I	32_V	3.029	1.00
38_T	95_G	2.828	1.00
73_D	108_K	2.827	1.00
22_L	89_F	2.811	1.00
80_G	98_L	2.809	1.00
58_Q	62_Q	2.601	1.00
100_I	103_T	2.576	1.00
17_G	28_I	2.439	1.00
82_L	86_L	2.347	1.00
18_I	90_L	2.279	1.00
37_L	41_I	2.275	1.00
97_C	107_C	2.182	1.00
26_I	30_P	2.094	1.00
11_F	91_S	2.084	1.00
43_A	85_M	1.973	1.00
55_Y	58_Q	1.967	1.00
35_M	38_T	1.953	1.00
19_F	89_F	1.779	1.00
56_K	70_A	1.714	1.00
29_L	33_L	1.614	1.00
59_R	63_Y	1.558	1.00
53_V	77_I	1.539	1.00
57_V	75_L	1.517	1.00
102_F	106_W	1.488	0.99
86_L	96_A	1.472	0.99
46_A	81_G	1.415	0.99
79_I	82_L	1.355	0.99
103_T	106_W	1.350	0.99
76_C	98_L	1.272	0.98
9_I	12_P	1.258	0.98
13_A	17_G	1.215	0.98
27_G	31_T	1.208	0.98
76_C	107_C	1.198	0.97
100_I	106_W	1.190	0.97
16_I	19_F	1.188	0.97
52_E	56_K	1.186	0.97
10_V	13_A	1.178	0.97
55_Y	59_R	1.165	0.97
49_Q	52_E	1.164	0.97
18_I	22_L	1.128	0.96
22_L	34_F	1.123	0.96
33_L	37_L	1.099	0.96
59_R	62_Q	1.090	0.95
38_T	96_A	1.084	0.95
20_L	23_G	1.078	0.95
114_W	117_G	1.078	0.95
19_F	90_L	1.060	0.95
19_F	35_M	1.058	0.95
114_W	118_M	1.053	0.95
73_D	104_R	1.053	0.95
105_G	108_K	1.038	0.94
46_A	77_I	1.015	0.93
103_T	108_K	1.001	0.93
80_G	95_G	0.996	0.93
93_L	97_C	0.988	0.92
113_K	116_R	0.971	0.92
4_L	43_A	0.969	0.92
64_G	67_P	0.933	0.90
15_E	49_Q	0.930	0.90
69_E	112_F	0.929	0.90
49_Q	99_L	0.926	0.90
73_D	76_C	0.923	0.90
21_F	24_N	0.917	0.89
80_G	99_L	0.899	0.88
43_A	86_L	0.898	0.88
23_G	27_G	0.897	0.88
10_V	43_A	0.884	0.88
69_E	109_P	0.883	0.88
44_A	48_K	0.874	0.87
57_V	76_C	0.870	0.87
57_V	61_L	0.869	0.87
53_V	56_K	0.868	0.87
11_F	90_L	0.861	0.86
16_I	23_G	0.854	0.86
89_F	92_D	0.847	0.85
106_W	110_I	0.843	0.85
81_G	85_M	0.837	0.85
57_V	74_G	0.817	0.83
76_C	111_L	0.789	0.81
14_I	17_G	0.780	0.80
76_C	108_K	0.770	0.79
80_G	103_T	0.767	0.79
11_F	86_L	0.764	0.79
23_G	104_R	0.755	0.78
69_E	72_A	0.743	0.77
26_I	29_L	0.743	0.77
47_K	51_T	0.741	0.77
25_L	29_L	0.735	0.76
99_L	103_T	0.731	0.76
38_T	92_D	0.729	0.75
27_G	30_P	0.729	0.75
38_T	85_M	0.722	0.75
9_I	39_G	0.718	0.74
8_F	21_F	0.714	0.74
74_G	95_G	0.713	0.74
17_G	23_G	0.712	0.74
84_L	95_G	0.696	0.72
7_L	74_G	0.693	0.72
16_I	78_F	0.691	0.72
57_V	72_A	0.684	0.71
60_D	70_A	0.675	0.70
45_A	54_Y	0.671	0.69
21_F	25_L	0.664	0.69
46_A	80_G	0.663	0.68
15_E	98_L	0.661	0.68
22_L	39_G	0.658	0.68
61_L	66_M	0.657	0.68
6_L	11_F	0.656	0.68
39_G	104_R	0.654	0.67
36_I	40_I	0.653	0.67
51_T	68_G	0.650	0.67
74_G	78_F	0.646	0.66
8_F	81_G	0.645	0.66
35_M	95_G	0.643	0.66
16_I	89_F	0.642	0.66
72_A	114_W	0.630	0.64
107_C	110_I	0.629	0.64
25_L	30_P	0.625	0.64
13_A	16_I	0.624	0.64
30_P	33_L	0.620	0.63
6_L	110_I	0.619	0.63
52_E	57_V	0.618	0.63
46_A	98_L	0.617	0.63
63_Y	94_A	0.615	0.63
77_I	104_R	0.612	0.62
99_L	105_G	0.611	0.62
5_F	8_F	0.609	0.62
90_L	110_I	0.608	0.62
7_L	12_P	0.595	0.60
69_E	73_D	0.591	0.60
45_A	49_Q	0.584	0.59
46_A	78_F	0.584	0.59
14_I	18_I	0.582	0.58
31_T	36_I	0.582	0.58
54_Y	75_L	0.579	0.58
32_V	35_M	0.577	0.58
37_L	93_L	0.576	0.58
60_D	77_I	0.573	0.57
98_L	103_T	0.572	0.57
7_L	75_L	0.571	0.57
7_L	36_I	0.570	0.57
45_A	56_K	0.569	0.57
102_F	105_G	0.567	0.56
32_V	84_L	0.562	0.56
85_M	91_S	0.562	0.56
59_R	109_P	0.560	0.56
29_L	36_I	0.558	0.55
36_I	83_L	0.558	0.55
23_G	26_I	0.552	0.54
12_P	91_S	0.551	0.54
48_K	113_K	0.548	0.54
13_A	36_I	0.547	0.54
66_M	79_I	0.547	0.54
34_F	91_S	0.547	0.54
32_V	116_R	0.546	0.54
81_G	92_D	0.543	0.53
17_G	21_F	0.542	0.53
15_E	20_L	0.539	0.53
18_I	40_I	0.538	0.53
90_L	93_L	0.537	0.52
86_L	92_D	0.536	0.52
29_L	113_K	0.536	0.52
23_G	28_I	0.534	0.52
64_G	70_A	0.524	0.51
72_A	75_L	0.510	0.49
21_F	28_I	0.507	0.48
72_A	76_C	0.507	0.48
18_I	93_L	0.506	0.48
8_F	16_I	0.502	0.48
4_L	106_W	0.500	0.48

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
4mt1A	3	0.8583	19.3	0.923	Contact Map
4dx5A	3	0.9213	14.8	0.927	Contact Map
2ipqX	1	0.5669	10.3	0.932	Contact Map
3w9iA	3	0.8504	9.8	0.933	Contact Map
3rkoA	1	0.4331	5.8	0.94	Contact Map
4k0jA	3	0.8031	5.4	0.94	Contact Map
3aqpA	1	0.9843	4.6	0.942	Contact Map
2xq2A	2	0.4016	2.8	0.948	Contact Map
2m20A	2	0.4331	2.1	0.951	Contact Map
3ne5A	3	0.8425	1.9	0.953	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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