YVNA - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YVNA - Uncharacterized HTH-type transcriptional regulator YvnA

UniProt:	O34692	Sequences: MDNSIHDELFQAIQQFALKRDKRVWQKVQIPSIGISSQHHDHLKKDWTLTQLHIVSCIHTSQNVNNSFLASRLHISKAAVSKAVHALLKHNIITVTKKPGNKKEIFYTLTDSGRKLAALHEQLHEKAKEQYKQLFNEFSIDDLKTVTAFFNLWIKYM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	157 (125)
Sequences:	1213 (974)
Seq/√Len:	87.1

ECOLI - SLYA MARR MPRA
BACSU - YVNA YVMB YHJH YFIV YDGG YWHA YYBA YXAD YSMB YKOM MHQR YUSO YCGE YPOP YDGJ YETL YWAE OHRR YWOH YDCH
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
120_H	124_H	3.094	1.00
53_H	120_H	3.074	1.00
138_F	152_L	2.888	1.00
58_I	93_I	2.859	1.00
51_Q	90_H	2.693	1.00
84_V	93_I	2.523	1.00
146_V	149_F	2.511	1.00
58_I	64_V	2.487	1.00
59_H	117_A	2.459	1.00
53_H	124_H	2.317	1.00
65_N	68_F	2.296	1.00
139_S	142_D	2.187	1.00
79_A	82_K	2.116	1.00
96_T	108_T	2.113	1.00
75_I	80_V	2.095	1.00
101_N	104_E	2.065	1.00
94_T	108_T	1.894	1.00
67_S	77_K	1.792	1.00
98_K	103_K	1.775	1.00
64_V	72_R	1.756	1.00
144_K	148_A	1.690	1.00
66_N	107_Y	1.640	1.00
95_V	102_K	1.639	1.00
59_H	109_L	1.614	1.00
65_N	104_E	1.577	1.00
61_S	64_V	1.556	1.00
88_L	107_Y	1.549	1.00
114_R	118_A	1.451	0.99
141_D	144_K	1.399	0.99
112_S	115_K	1.375	0.99
122_Q	126_K	1.358	0.99
142_D	148_A	1.340	0.99
84_V	88_L	1.339	0.99
137_E	152_L	1.332	0.99
81_S	101_N	1.314	0.99
65_N	106_F	1.313	0.99
111_D	114_R	1.300	0.99
126_K	129_E	1.293	0.99
66_N	84_V	1.278	0.98
91_N	112_S	1.272	0.98
58_I	105_I	1.267	0.98
98_K	101_N	1.252	0.98
138_F	149_F	1.252	0.98
63_N	108_T	1.225	0.98
125_E	129_E	1.224	0.98
54_I	83_A	1.223	0.98
28_V	31_P	1.215	0.98
55_V	59_H	1.202	0.98
52_L	116_L	1.197	0.98
142_D	145_T	1.155	0.97
91_N	94_T	1.139	0.97
148_A	152_L	1.121	0.96
117_A	121_E	1.121	0.96
51_Q	76_S	1.111	0.96
27_K	138_F	1.111	0.96
97_K	105_I	1.108	0.96
88_L	95_V	1.096	0.96
81_S	95_V	1.093	0.96
56_S	121_E	1.091	0.96
88_L	93_I	1.051	0.95
55_V	117_A	1.042	0.95
27_K	31_P	1.033	0.94
141_D	145_T	1.032	0.94
60_T	118_A	1.021	0.94
61_S	72_R	1.012	0.94
111_D	115_K	1.006	0.94
50_T	54_I	0.999	0.93
53_H	59_H	0.977	0.93
57_C	69_L	0.976	0.93
79_A	83_A	0.973	0.92
76_S	79_A	0.968	0.92
57_C	73_L	0.951	0.92
66_N	81_S	0.950	0.91
98_K	104_E	0.938	0.91
145_T	148_A	0.932	0.91
46_D	90_H	0.923	0.90
55_V	109_L	0.918	0.90
84_V	107_Y	0.917	0.90
142_D	152_L	0.898	0.89
36_S	42_H	0.891	0.89
56_S	124_H	0.889	0.89
49_L	127_A	0.887	0.88
48_T	86_A	0.875	0.88
48_T	51_Q	0.858	0.87
118_A	122_Q	0.855	0.87
66_N	95_V	0.851	0.86
84_V	121_E	0.834	0.85
129_E	136_N	0.825	0.85
37_S	41_D	0.824	0.84
92_I	112_S	0.810	0.83
56_S	117_A	0.797	0.82
56_S	60_T	0.796	0.82
118_A	121_E	0.788	0.82
93_I	112_S	0.779	0.81
82_K	103_K	0.773	0.80
51_Q	78_A	0.773	0.80
112_S	125_E	0.772	0.80
81_S	104_E	0.766	0.80
69_L	108_T	0.765	0.80
147_T	151_N	0.764	0.80
83_A	86_A	0.757	0.79
88_L	125_E	0.755	0.79
85_H	89_K	0.743	0.78
75_I	124_H	0.740	0.77
66_N	80_V	0.737	0.77
28_V	32_S	0.728	0.76
66_N	78_A	0.727	0.76
29_Q	33_I	0.726	0.76
35_I	109_L	0.724	0.76
95_V	105_I	0.723	0.76
60_T	117_A	0.718	0.75
123_L	127_A	0.699	0.73
69_L	107_Y	0.690	0.72
62_Q	108_T	0.684	0.72
45_K	60_T	0.683	0.72
82_K	102_K	0.682	0.72
103_K	128_K	0.674	0.71
95_V	107_Y	0.671	0.70
77_K	85_H	0.666	0.70
133_Q	136_N	0.662	0.69
38_Q	41_D	0.657	0.69
28_V	52_L	0.652	0.68
66_N	76_S	0.651	0.68
52_L	58_I	0.651	0.68
54_I	84_V	0.651	0.68
52_L	120_H	0.649	0.68
70_A	95_V	0.647	0.68
50_T	86_A	0.642	0.67
100_G	125_E	0.641	0.67
70_A	100_G	0.640	0.67
76_S	86_A	0.639	0.67
63_N	133_Q	0.638	0.66
59_H	69_L	0.637	0.66
95_V	128_K	0.632	0.66
38_Q	119_L	0.630	0.65
47_W	153_W	0.626	0.65
78_A	123_L	0.626	0.65
39_H	49_L	0.619	0.64
49_L	86_A	0.618	0.64
82_K	101_N	0.616	0.64
126_K	150_F	0.615	0.64
67_S	79_A	0.613	0.63
77_K	86_A	0.611	0.63
44_K	52_L	0.602	0.62
91_N	110_T	0.596	0.61
61_S	148_A	0.590	0.60
100_G	129_E	0.590	0.60
122_Q	125_E	0.588	0.60
64_V	68_F	0.587	0.60
62_Q	107_Y	0.582	0.59
69_L	121_E	0.580	0.59
37_S	74_H	0.578	0.59
136_N	141_D	0.578	0.59
65_N	101_N	0.577	0.59
50_T	66_N	0.576	0.59
91_N	115_K	0.575	0.58
136_N	144_K	0.571	0.58
81_S	85_H	0.569	0.58
43_L	115_K	0.568	0.58
33_I	144_K	0.567	0.57
47_W	92_I	0.566	0.57
83_A	119_L	0.559	0.56
47_W	116_L	0.556	0.56
59_H	114_R	0.555	0.56
137_E	148_A	0.550	0.55
50_T	73_L	0.549	0.55
125_E	148_A	0.548	0.55
70_A	147_T	0.548	0.55
118_A	151_N	0.545	0.54
148_A	151_N	0.544	0.54
94_T	111_D	0.537	0.53
82_K	107_Y	0.535	0.53
100_G	103_K	0.528	0.52
30_I	74_H	0.527	0.52
103_K	107_Y	0.526	0.52
50_T	76_S	0.525	0.52
47_W	133_Q	0.523	0.52
80_V	123_L	0.517	0.51
68_F	80_V	0.517	0.51
118_A	141_D	0.517	0.51
76_S	82_K	0.516	0.51
82_K	85_H	0.510	0.50
75_I	79_A	0.507	0.49
90_H	153_W	0.505	0.49
56_S	146_V	0.504	0.49
92_I	116_L	0.503	0.49
93_I	144_K	0.501	0.49
68_F	71_S	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
3nqoA	2	0.9172	99.8	0.477	Contact Map
4yifA	2	0.8726	99.8	0.487	Contact Map
2fbkA	2	0.9045	99.8	0.496	Contact Map
3bj6A	2	0.9045	99.8	0.497	Contact Map
1s3jA	2	0.8981	99.8	0.498	Contact Map
3bjaA	2	0.879	99.8	0.499	Contact Map
3u2rA	4	0.8344	99.8	0.5	Contact Map
1lj9A	2	0.8535	99.8	0.501	Contact Map
3cjnA	2	0.8726	99.8	0.502	Contact Map
2rdpA	2	0.879	99.8	0.504	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.

Page generated in 0.007 seconds.