YTAB - BACSU - GREMLIN Contacts

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YTAB - Uncharacterized membrane protein YtaB

UniProt:	O34694	Sequences: MKKIVGALAVFVITYALFSAAGYLFPVDQEWYNSLKKPDWTPSGTAIGIIWAILFALISLSAAIVYAAFSFKGAKSFWFTLLINYVLNQAFSYFQFTQKNLLAASLDCLLVAITAIVLLIIAKKYSRAASYLLLPYFLWSAFATFLSFTINSMNL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	155 (147)
Sequences:	1745 (1371)
Seq/√Len:	113.0

BACSU - YTAB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
112_A	141_A	4.324	1.00
94_F	107_D	3.719	1.00
115_A	140_S	3.659	1.00
64_I	126_S	3.549	1.00
40_W	145_F	3.293	1.00
45_T	49_I	3.089	1.00
102_L	151_N	2.864	1.00
105_S	148_F	2.559	1.00
15_Y	56_A	2.421	1.00
118_L	133_L	2.316	1.00
80_T	121_I	2.204	1.00
149_T	152_S	2.101	1.00
105_S	147_S	2.022	1.00
61_S	133_L	2.012	1.00
87_L	114_T	1.968	1.00
119_L	130_S	1.897	1.00
17_L	89_Q	1.891	1.00
148_F	152_S	1.837	1.00
31_W	101_L	1.814	1.00
112_A	140_S	1.794	1.00
108_C	144_T	1.750	1.00
69_F	74_A	1.716	1.00
149_T	153_M	1.684	1.00
123_K	130_S	1.660	1.00
7_A	63_A	1.619	1.00
118_L	122_A	1.582	1.00
37_K	41_T	1.518	1.00
14_T	81_L	1.510	1.00
31_W	99_K	1.491	1.00
94_F	104_A	1.461	1.00
112_A	144_T	1.460	1.00
62_A	78_W	1.429	1.00
80_T	117_V	1.426	1.00
131_Y	134_L	1.391	1.00
36_K	153_M	1.320	1.00
55_F	88_N	1.288	0.99
119_L	133_L	1.282	0.99
119_L	137_F	1.271	0.99
10_V	62_A	1.270	0.99
32_Y	41_T	1.238	0.99
40_W	149_T	1.238	0.99
108_C	147_S	1.236	0.99
39_D	149_T	1.215	0.99
65_V	122_A	1.203	0.99
52_A	56_A	1.197	0.99
87_L	107_D	1.194	0.99
68_A	126_S	1.179	0.99
33_N	44_G	1.174	0.99
15_Y	18_F	1.170	0.99
14_T	59_S	1.154	0.99
31_W	41_T	1.152	0.99
77_F	125_Y	1.150	0.99
145_F	149_T	1.136	0.99
62_A	81_L	1.120	0.98
61_S	129_A	1.115	0.98
11_F	59_S	1.093	0.98
117_V	121_I	1.086	0.98
111_V	136_Y	1.074	0.98
116_I	137_F	1.069	0.98
58_I	62_A	1.067	0.98
11_F	15_Y	1.067	0.98
39_D	145_F	1.059	0.98
101_L	151_N	1.049	0.98
101_L	150_I	1.046	0.98
123_K	131_Y	1.037	0.97
61_S	118_L	1.031	0.97
14_T	62_A	1.026	0.97
123_K	127_R	1.011	0.97
45_T	48_G	1.008	0.97
65_V	125_Y	1.001	0.97
138_L	142_F	0.993	0.97
76_S	121_I	0.986	0.97
105_S	144_T	0.986	0.97
86_V	90_A	0.972	0.96
10_V	81_L	0.958	0.96
90_A	107_D	0.957	0.96
100_N	103_A	0.955	0.96
104_A	107_D	0.954	0.96
81_L	122_A	0.953	0.96
91_F	147_S	0.947	0.96
112_A	115_A	0.933	0.95
10_V	66_Y	0.932	0.95
18_F	59_S	0.925	0.95
64_I	67_A	0.917	0.95
37_K	150_I	0.915	0.95
93_Y	98_Q	0.906	0.94
31_W	37_K	0.906	0.94
17_L	21_A	0.897	0.94
111_V	115_A	0.886	0.94
88_N	136_Y	0.878	0.93
50_I	54_L	0.876	0.93
134_L	138_L	0.871	0.93
63_A	67_A	0.870	0.93
100_N	104_A	0.868	0.93
38_P	149_T	0.862	0.93
91_F	95_Q	0.861	0.93
28_D	44_G	0.860	0.93
21_A	24_L	0.855	0.93
65_V	77_F	0.852	0.92
87_L	110_L	0.850	0.92
40_W	142_F	0.832	0.92
25_F	92_S	0.828	0.91
19_S	23_Y	0.821	0.91
84_N	118_L	0.820	0.91
78_W	82_L	0.818	0.91
79_F	83_I	0.814	0.91
128_A	131_Y	0.807	0.90
71_F	74_A	0.805	0.90
85_Y	89_Q	0.803	0.90
122_A	130_S	0.798	0.90
77_F	122_A	0.795	0.90
127_R	131_Y	0.788	0.89
112_A	137_F	0.787	0.89
144_T	148_F	0.781	0.89
77_F	118_L	0.772	0.88
24_L	97_T	0.771	0.88
31_W	44_G	0.770	0.88
49_I	53_I	0.769	0.88
54_L	58_I	0.768	0.88
41_T	150_I	0.768	0.88
69_F	125_Y	0.764	0.88
14_T	58_I	0.759	0.87
89_Q	93_Y	0.755	0.87
28_D	33_N	0.751	0.87
46_A	50_I	0.749	0.87
95_Q	150_I	0.748	0.87
121_I	124_K	0.746	0.86
15_Y	21_A	0.743	0.86
48_G	52_A	0.743	0.86
20_A	24_L	0.741	0.86
21_A	25_F	0.741	0.86
116_I	120_I	0.737	0.86
62_A	66_Y	0.732	0.85
25_F	28_D	0.730	0.85
21_A	89_Q	0.726	0.85
70_S	74_A	0.725	0.85
84_N	115_A	0.722	0.85
7_A	11_F	0.721	0.85
143_A	146_L	0.716	0.84
94_F	103_A	0.715	0.84
109_L	113_I	0.713	0.84
98_Q	101_L	0.704	0.83
38_P	153_M	0.704	0.83
41_T	142_F	0.703	0.83
31_W	35_L	0.701	0.83
38_P	46_A	0.696	0.82
7_A	60_L	0.689	0.82
19_S	22_G	0.687	0.82
11_F	18_F	0.686	0.81
112_A	116_I	0.680	0.81
84_N	88_N	0.679	0.81
120_I	124_K	0.675	0.80
142_F	145_F	0.674	0.80
84_N	114_T	0.673	0.80
61_S	65_V	0.667	0.80
80_T	118_L	0.662	0.79
49_I	52_A	0.661	0.79
132_L	135_P	0.661	0.79
47_I	91_F	0.659	0.79
80_T	114_T	0.655	0.78
59_S	63_A	0.651	0.78
120_I	131_Y	0.646	0.77
28_D	31_W	0.645	0.77
36_K	79_F	0.645	0.77
115_A	118_L	0.642	0.77
105_S	109_L	0.640	0.77
55_F	136_Y	0.639	0.77
68_A	74_A	0.638	0.77
137_F	140_S	0.630	0.76
66_Y	78_W	0.627	0.75
57_L	61_S	0.623	0.75
30_E	34_S	0.621	0.75
48_G	143_A	0.612	0.74
46_A	49_I	0.609	0.73
77_F	121_I	0.604	0.73
14_T	17_L	0.601	0.72
40_W	153_M	0.600	0.72
82_L	86_V	0.598	0.72
29_Q	33_N	0.598	0.72
83_I	114_T	0.596	0.72
55_F	89_Q	0.591	0.71
55_F	58_I	0.591	0.71
81_L	85_Y	0.591	0.71
84_N	87_L	0.590	0.71
59_S	62_A	0.588	0.71
107_D	114_T	0.578	0.69
58_I	118_L	0.572	0.69
21_A	93_Y	0.572	0.69
59_S	89_Q	0.570	0.68
94_F	100_N	0.570	0.68
10_V	63_A	0.568	0.68
7_A	10_V	0.566	0.68
18_F	89_Q	0.564	0.67
58_I	85_Y	0.564	0.67
18_F	21_A	0.562	0.67
107_D	110_L	0.553	0.66
108_C	140_S	0.552	0.66
102_L	106_L	0.550	0.66
55_F	93_Y	0.546	0.65
16_A	19_S	0.545	0.65
61_S	122_A	0.540	0.64
81_L	133_L	0.538	0.64
58_I	84_N	0.536	0.64
76_S	83_I	0.536	0.64
46_A	142_F	0.535	0.63
69_F	75_K	0.530	0.63
54_L	88_N	0.530	0.63
84_N	111_V	0.526	0.62
9_A	13_I	0.523	0.62
13_I	17_L	0.522	0.62
10_V	14_T	0.522	0.62
122_A	129_A	0.522	0.62
142_F	146_L	0.514	0.60
76_S	79_F	0.513	0.60
57_L	60_L	0.507	0.59
22_G	26_P	0.506	0.59
89_Q	92_S	0.505	0.59
39_D	152_S	0.501	0.58
41_T	49_I	0.500	0.58
83_I	86_V	0.500	0.58

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
4ryoA	1	0.9677	100	0.12	Contact Map
4uc1A	3	0.9742	100	0.158	Contact Map
2mgyA	1	1	100	0.179	Contact Map
1yewC	1	0.5742	46.5	0.922	Contact Map
4phzK	1	0.7484	22.2	0.934	Contact Map
4ev6A	3	0.4129	6	0.949	Contact Map
4i0uA	4	0.4	4.7	0.951	Contact Map
3b5dA	2	0.6516	3.9	0.953	Contact Map
3dh4A	3	0.4323	2.7	0.957	Contact Map
4cadC	1	0.7419	1.6	0.962	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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