YGZB - BACSU - GREMLIN Contacts

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YGZB - UPF0295 protein YgzB

UniProt:	Q7WY74	Sequences: MAKYSSKINKIRTFALSLVFVGFIIMYIGIFFKESVLLSSLFMILGLLSIGLSTVVYFWIGMLSTKAVRVICPGCDKETKVLGVVDMCMHCREPLTLDKGLEGKEFDESYNKKKMSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	117 (111)
Sequences:	160 (83)
Seq/√Len:	7.8

BACSU - YGZB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_I	49_S	4.526	0.99
29_G	58_F	2.859	0.84
10_K	13_T	2.399	0.71
24_I	42_F	2.266	0.67
24_I	40_S	2.228	0.66
87_M	93_E	2.135	0.62
5_S	10_K	2.022	0.58
14_F	56_V	1.974	0.56
17_S	21_V	1.938	0.54
21_V	49_S	1.921	0.54
78_E	90_H	1.871	0.52
67_A	113_K	1.817	0.49
51_G	63_L	1.811	0.49
55_V	74_G	1.808	0.49
44_I	112_K	1.769	0.47
76_D	99_K	1.745	0.46
87_M	107_D	1.594	0.40
35_S	38_L	1.569	0.39
62_M	66_K	1.567	0.39
48_L	70_V	1.559	0.39
19_V	50_I	1.514	0.37
3_K	58_F	1.491	0.36
47_L	70_V	1.459	0.35
25_I	66_K	1.453	0.35
104_K	110_Y	1.443	0.35
24_I	35_S	1.439	0.35
58_F	65_T	1.417	0.34
108_E	112_K	1.411	0.34
28_I	56_V	1.399	0.33
24_I	28_I	1.360	0.32
71_I	76_D	1.338	0.31
81_V	99_K	1.330	0.31
23_F	50_I	1.324	0.30
10_K	74_G	1.324	0.30
26_M	95_L	1.311	0.30
55_V	65_T	1.297	0.30
8_I	96_T	1.296	0.29
96_T	101_L	1.285	0.29
15_A	20_F	1.284	0.29
23_F	56_V	1.252	0.28
14_F	23_F	1.234	0.27
67_A	77_K	1.224	0.27
41_L	44_I	1.217	0.27
76_D	90_H	1.202	0.26
74_G	93_E	1.190	0.26
69_R	78_E	1.174	0.26
81_V	108_E	1.169	0.25
8_I	101_L	1.165	0.25
13_T	17_S	1.153	0.25
25_I	51_G	1.153	0.25
15_A	27_Y	1.146	0.25
39_S	67_A	1.144	0.25
54_T	78_E	1.127	0.24
84_V	107_D	1.114	0.24
52_L	90_H	1.099	0.23
17_S	93_E	1.090	0.23
49_S	93_E	1.090	0.23
21_V	37_L	1.053	0.22
48_L	51_G	1.053	0.22
33_K	77_K	1.049	0.22
28_I	51_G	1.036	0.22
59_W	68_V	1.034	0.21
30_I	47_L	1.031	0.21
84_V	103_G	1.031	0.21
102_E	106_F	1.025	0.21
14_F	60_I	1.025	0.21
9_N	60_I	0.979	0.20
23_F	47_L	0.963	0.20
15_A	66_K	0.948	0.19
22_G	98_D	0.924	0.19
94_P	103_G	0.923	0.19
6_S	63_L	0.911	0.18
21_V	45_L	0.907	0.18
40_S	44_I	0.906	0.18
47_L	54_T	0.890	0.18
17_S	81_V	0.889	0.18
11_I	32_F	0.872	0.17
63_L	81_V	0.845	0.17
4_Y	89_M	0.843	0.17
37_L	112_K	0.841	0.17
11_I	14_F	0.835	0.17
44_I	93_E	0.831	0.16
36_V	109_S	0.816	0.16
6_S	90_H	0.811	0.16
30_I	43_M	0.802	0.16
25_I	100_G	0.801	0.16
24_I	32_F	0.797	0.16
87_M	92_R	0.795	0.16
38_L	112_K	0.794	0.16
28_I	81_V	0.793	0.16
29_G	39_S	0.793	0.16
6_S	69_R	0.784	0.15
5_S	108_E	0.780	0.15
24_I	37_L	0.760	0.15
54_T	105_E	0.754	0.15
41_L	78_E	0.753	0.15
76_D	100_G	0.751	0.15
21_V	30_I	0.749	0.15
41_L	81_V	0.730	0.14
37_L	41_L	0.724	0.14
96_T	103_G	0.723	0.14
27_Y	94_P	0.718	0.14
76_D	92_R	0.718	0.14
21_V	56_V	0.709	0.14
23_F	87_M	0.709	0.14
68_V	97_L	0.704	0.14
47_L	78_E	0.697	0.14
42_F	45_L	0.694	0.14
34_E	43_M	0.688	0.13
45_L	82_L	0.685	0.13
36_V	112_K	0.684	0.13
13_T	52_L	0.680	0.13
8_I	11_I	0.677	0.13
59_W	99_K	0.677	0.13
4_Y	108_E	0.676	0.13
35_S	40_S	0.674	0.13
103_G	111_N	0.666	0.13
103_G	106_F	0.661	0.13
17_S	56_V	0.659	0.13
28_I	37_L	0.653	0.13
5_S	60_I	0.651	0.13
85_V	93_E	0.647	0.13
5_S	9_N	0.645	0.13
106_F	111_N	0.637	0.13
37_L	52_L	0.630	0.12
34_E	38_L	0.618	0.12
82_L	96_T	0.617	0.12
48_L	69_R	0.606	0.12
30_I	78_E	0.606	0.12
42_F	47_L	0.605	0.12
37_L	100_G	0.605	0.12
48_L	56_V	0.605	0.12
6_S	30_I	0.598	0.12
67_A	95_L	0.597	0.12
30_I	56_V	0.594	0.12
50_I	66_K	0.594	0.12
23_F	76_D	0.592	0.12
21_V	25_I	0.591	0.12
50_I	77_K	0.575	0.11
28_I	45_L	0.573	0.11
81_V	112_K	0.569	0.11
5_S	49_S	0.566	0.11
78_E	109_S	0.565	0.11
85_V	96_T	0.556	0.11
38_L	52_L	0.554	0.11
45_L	92_R	0.553	0.11
62_M	113_K	0.553	0.11
29_G	38_L	0.551	0.11
6_S	99_K	0.551	0.11
30_I	41_L	0.545	0.11
11_I	60_I	0.541	0.11
68_V	105_E	0.539	0.11
44_I	76_D	0.537	0.11
19_V	47_L	0.534	0.11
94_P	106_F	0.534	0.11
31_F	93_E	0.530	0.11
56_V	71_I	0.526	0.11
32_F	68_V	0.523	0.11
22_G	67_A	0.522	0.11
31_F	70_V	0.518	0.11
43_M	107_D	0.516	0.11
5_S	89_M	0.515	0.11
36_V	40_S	0.512	0.10
109_S	113_K	0.509	0.10
31_F	35_S	0.504	0.10
69_R	97_L	0.500	0.10

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
4bbrM	1	0.4103	81.1	0.924	Contact Map
4qiwP	1	0.3248	79.9	0.925	Contact Map
3k1fM	1	0.4103	76.7	0.927	Contact Map
3wwlA	1	0.3504	74.8	0.929	Contact Map
3o9xA	2	0.4188	64.8	0.933	Contact Map
2apoB	1	0.4017	55.1	0.937	Contact Map
1pftA	1	0.3761	48.1	0.94	Contact Map
4aybP	1	0.3333	47.6	0.94	Contact Map
4e2xA	1	0.4103	44.6	0.941	Contact Map
3ga8A	1	0.4017	37.4	0.944	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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