YVAV - BACSU - GREMLIN Contacts

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YVAV - Putative HTH-type transcriptional regulator YvaV

UniProt:	C0SPB8	Sequences: MEKDPLTIIEQAEDHFIERIAENMHAFGMPSTVGRVLGIIYMNRKPMTLTELSEATGMSKTRMSQVVREMLDANIAEKVFEKGVRKDLYEVEQDYYQTFITLFSATWSKVVSKNKMMHKKLNRELLSVLDEELTPEAEEKVNELLKELKEWLDYYNWLSRLIEFFESEDIFKYVPKP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	177 (154)
Sequences:	673 (467)
Seq/√Len:	37.6

BACSU - YVAV OPCR GBSR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_T	58_M	4.158	1.00
48_T	88_L	3.899	1.00
84_V	88_L	3.854	1.00
34_G	37_L	3.265	1.00
136_E	139_E	2.560	1.00
139_E	142_N	2.462	1.00
45_K	81_E	2.448	1.00
49_L	60_K	2.347	1.00
36_V	52_L	2.285	0.99
45_K	51_E	2.235	0.99
59_S	65_Q	2.124	0.99
81_E	88_L	2.115	0.99
58_M	87_D	2.098	0.99
20_I	37_L	2.096	0.99
52_L	63_M	1.994	0.99
49_L	63_M	1.884	0.98
20_I	34_G	1.877	0.98
138_E	142_N	1.873	0.98
111_V	160_R	1.859	0.98
46_P	87_D	1.856	0.98
99_F	155_Y	1.849	0.98
72_D	141_V	1.848	0.98
12_A	117_M	1.830	0.98
39_I	47_M	1.774	0.97
156_N	160_R	1.748	0.97
30_P	111_V	1.731	0.97
82_K	99_F	1.580	0.94
116_M	119_K	1.541	0.93
31_S	35_R	1.518	0.93
59_S	82_K	1.507	0.93
127_S	135_P	1.450	0.91
29_M	86_K	1.442	0.91
135_P	139_E	1.422	0.90
79_V	90_E	1.401	0.90
126_L	138_E	1.392	0.89
110_V	113_K	1.355	0.88
95_Y	99_F	1.353	0.88
21_A	31_S	1.344	0.87
79_V	88_L	1.318	0.86
155_Y	159_S	1.299	0.86
62_R	65_Q	1.296	0.85
68_R	77_E	1.295	0.85
50_T	86_K	1.292	0.85
56_T	70_M	1.271	0.84
94_D	108_S	1.268	0.84
97_Q	101_T	1.261	0.84
12_A	83_G	1.241	0.83
11_Q	124_E	1.230	0.82
102_L	148_L	1.181	0.80
139_E	143_E	1.180	0.80
49_L	64_S	1.164	0.79
23_N	96_Y	1.159	0.78
58_M	61_T	1.158	0.78
15_H	120_K	1.154	0.78
74_N	112_S	1.151	0.78
45_K	48_T	1.150	0.78
129_L	135_P	1.138	0.77
32_T	99_F	1.130	0.76
61_T	65_Q	1.118	0.76
13_E	55_A	1.118	0.76
103_F	148_L	1.117	0.76
89_Y	151_W	1.115	0.76
10_E	135_P	1.109	0.75
75_I	98_T	1.090	0.74
50_T	53_S	1.079	0.73
8_I	130_D	1.067	0.72
35_R	84_V	1.058	0.72
19_R	22_E	1.052	0.71
13_E	140_K	1.051	0.71
105_A	108_S	1.028	0.69
135_P	142_N	1.025	0.69
86_K	147_E	1.018	0.69
30_P	35_R	1.016	0.68
34_G	38_G	1.010	0.68
8_I	76_A	1.009	0.68
21_A	35_R	1.009	0.68
49_L	114_N	1.008	0.68
119_K	149_K	1.001	0.67
40_I	81_E	0.993	0.67
68_R	78_K	0.992	0.67
8_I	134_T	0.974	0.65
58_M	99_F	0.962	0.64
29_M	33_V	0.958	0.64
115_K	119_K	0.956	0.64
49_L	96_Y	0.955	0.64
71_L	89_Y	0.954	0.63
25_H	141_V	0.941	0.62
40_I	43_N	0.937	0.62
30_P	56_T	0.937	0.62
9_I	45_K	0.934	0.62
102_L	106_T	0.930	0.61
38_G	103_F	0.930	0.61
54_E	156_N	0.915	0.60
74_N	155_Y	0.910	0.60
126_L	156_N	0.910	0.60
35_R	87_D	0.907	0.60
54_E	139_E	0.904	0.59
36_V	66_V	0.899	0.59
76_A	138_E	0.896	0.59
20_I	27_F	0.892	0.58
139_E	153_D	0.888	0.58
23_N	49_L	0.887	0.58
39_I	56_T	0.884	0.58
123_R	130_D	0.881	0.57
134_T	137_A	0.879	0.57
10_E	45_K	0.869	0.56
56_T	66_V	0.869	0.56
32_T	42_M	0.856	0.55
56_T	81_E	0.851	0.55
126_L	149_K	0.851	0.55
58_M	63_M	0.850	0.55
40_I	76_A	0.843	0.54
50_T	155_Y	0.841	0.54
122_N	136_E	0.837	0.53
119_K	123_R	0.836	0.53
16_F	42_M	0.833	0.53
100_I	103_F	0.833	0.53
146_K	160_R	0.819	0.52
9_I	43_N	0.817	0.52
8_I	139_E	0.804	0.51
14_D	136_E	0.803	0.50
31_S	109_K	0.796	0.50
20_I	24_M	0.789	0.49
35_R	112_S	0.787	0.49
99_F	148_L	0.787	0.49
125_L	141_V	0.782	0.49
89_Y	93_Q	0.782	0.49
103_F	158_L	0.780	0.48
47_M	126_L	0.774	0.48
57_G	78_K	0.770	0.47
29_M	41_Y	0.766	0.47
16_F	106_T	0.765	0.47
141_V	156_N	0.759	0.47
79_V	87_D	0.758	0.46
20_I	38_G	0.758	0.46
48_T	155_Y	0.753	0.46
53_S	67_V	0.751	0.46
71_L	87_D	0.750	0.46
23_N	114_N	0.747	0.45
16_F	91_V	0.746	0.45
17_I	45_K	0.745	0.45
63_M	114_N	0.742	0.45
46_P	88_L	0.734	0.44
115_K	123_R	0.730	0.44
22_E	40_I	0.725	0.44
16_F	25_H	0.723	0.43
53_S	76_A	0.723	0.43
117_M	120_K	0.718	0.43
37_L	66_V	0.700	0.41
8_I	44_R	0.700	0.41
67_V	96_Y	0.699	0.41
20_I	33_V	0.699	0.41
124_E	127_S	0.694	0.41
62_R	114_N	0.691	0.41
19_R	114_N	0.688	0.40
23_N	95_Y	0.684	0.40
96_Y	110_V	0.677	0.39
45_K	143_E	0.677	0.39
21_A	27_F	0.672	0.39
13_E	42_M	0.671	0.39
143_E	153_D	0.669	0.39
19_R	68_R	0.664	0.38
62_R	70_M	0.660	0.38
116_M	139_E	0.654	0.37
13_E	144_L	0.653	0.37
18_E	57_G	0.651	0.37
9_I	149_K	0.646	0.37
130_D	136_E	0.640	0.36
41_Y	95_Y	0.640	0.36
13_E	43_N	0.634	0.36
47_M	51_E	0.633	0.36
42_M	144_L	0.633	0.36
60_K	113_K	0.631	0.36
58_M	66_V	0.630	0.35
26_A	63_M	0.629	0.35
111_V	122_N	0.623	0.35
92_E	157_W	0.620	0.35
89_Y	98_T	0.618	0.34
65_Q	88_L	0.618	0.34
129_L	138_E	0.617	0.34
37_L	75_I	0.614	0.34
154_Y	157_W	0.612	0.34
31_S	96_Y	0.611	0.34
51_E	55_A	0.605	0.33
122_N	164_F	0.604	0.33
92_E	101_T	0.603	0.33
38_G	91_V	0.603	0.33
122_N	153_D	0.601	0.33
72_D	81_E	0.596	0.33
154_Y	158_L	0.594	0.33
39_I	52_L	0.594	0.33
81_E	122_N	0.591	0.32
30_P	73_A	0.590	0.32
108_S	123_R	0.590	0.32
160_R	164_F	0.587	0.32
58_M	103_F	0.586	0.32
10_E	55_A	0.580	0.32
63_M	107_W	0.577	0.31
136_E	142_N	0.575	0.31
16_F	29_M	0.573	0.31
130_D	137_A	0.570	0.31
10_E	88_L	0.567	0.31
156_N	163_E	0.563	0.30
129_L	143_E	0.559	0.30
39_I	113_K	0.555	0.30
14_D	18_E	0.553	0.29
75_I	89_Y	0.549	0.29
137_A	142_N	0.548	0.29
55_A	118_H	0.544	0.29
29_M	57_G	0.541	0.29
142_N	149_K	0.539	0.28
30_P	65_Q	0.538	0.28
62_R	106_T	0.536	0.28
32_T	62_R	0.536	0.28
14_D	57_G	0.532	0.28
11_Q	116_M	0.528	0.28
23_N	110_V	0.527	0.28
116_M	127_S	0.520	0.27
71_L	76_A	0.519	0.27
33_V	69_E	0.516	0.27
21_A	109_K	0.516	0.27
30_P	33_V	0.515	0.27
112_S	128_V	0.514	0.27
97_Q	104_S	0.512	0.27
52_L	76_A	0.512	0.27
48_T	58_M	0.508	0.26
50_T	62_R	0.507	0.26
116_M	136_E	0.506	0.26
25_H	110_V	0.505	0.26
26_A	148_L	0.502	0.26
34_G	103_F	0.500	0.26

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
4nb5A	4	0.8362	99.6	0.702	Contact Map
1ku9A	2	0.8531	99.3	0.749	Contact Map
3qphA	2	0.8531	98.9	0.785	Contact Map
3deuA	2	0.7458	98.8	0.79	Contact Map
3kp7A	2	0.7571	98.8	0.791	Contact Map
4l9nA	2	0.7797	98.8	0.793	Contact Map
3g3zA	2	0.8023	98.8	0.794	Contact Map
3fm5A	4	0.7853	98.8	0.794	Contact Map
4yifA	2	0.774	98.8	0.796	Contact Map
3oopA	2	0.7514	98.7	0.796	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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