YVDT - BACSU - GREMLIN Contacts

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YVDT - Uncharacterized HTH-type transcriptional regulator YvdT

UniProt:	O07001	Sequences: MPKQTSGKYEKILQAAIEVISEKGLDKASISDIVKKAGTAQGTFYLYFSSKNALIPAIAENLLTHTLDQIKGRLHGDEDFWTVLDILIDETFLITERHKDIIVLCYSGLAIDHSMEKWETIYQPYYSWLEKIINKAIANHEVTEGINSKWTARTIINLVENTAERFYIGFEQDENVEVYKKEIFTFLKRSLGTA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	194 (178)
Sequences:	42860 (33896)
Seq/√Len:	2540.6

ECOLI - SLMA ENVR ACRR UIDR COMR RUTR BETI BDCR NEMR FABR YJDC YBIH RCDA
BACSU - YVDT FADR BSCR YHGD YFIR YDGC YEZE YVKB PKSA YOBS YTTP LMRA YXAF YVAF YDES YCNC YUXN YERO
HALSA - Q9HRF3
SULSO - Q97VV1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_S	41_Q	4.007	1.00
23_K	32_D	3.845	1.00
18_E	36_K	3.534	1.00
49_S	53_A	2.708	1.00
20_I	28_A	2.379	1.00
50_S	53_A	2.192	1.00
34_V	44_F	2.062	1.00
19_V	32_D	2.057	1.00
130_E	149_K	2.030	1.00
9_Y	57_A	2.010	1.00
19_V	36_K	1.991	1.00
10_E	61_N	1.953	1.00
22_E	36_K	1.941	1.00
19_V	28_A	1.938	1.00
11_K	15_A	1.888	1.00
15_A	36_K	1.886	1.00
130_E	134_N	1.880	1.00
83_V	135_K	1.873	1.00
8_K	11_K	1.866	1.00
79_D	82_T	1.797	1.00
19_V	23_K	1.791	1.00
31_S	35_K	1.754	1.00
15_A	18_E	1.664	1.00
134_N	148_S	1.656	1.00
17_I	61_N	1.646	1.00
40_A	43_T	1.641	1.00
13_L	57_A	1.593	1.00
10_E	14_Q	1.589	1.00
134_N	138_A	1.580	1.00
30_I	45_Y	1.565	1.00
134_N	137_I	1.545	1.00
137_I	145_G	1.536	1.00
17_I	62_L	1.510	1.00
16_A	20_I	1.478	1.00
30_I	41_Q	1.472	1.00
18_E	22_E	1.466	1.00
57_A	60_E	1.463	1.00
28_A	33_I	1.457	1.00
29_S	32_D	1.447	1.00
32_D	35_K	1.432	1.00
150_W	182_E	1.427	1.00
32_D	36_K	1.394	1.00
85_D	181_K	1.392	1.00
154_T	158_L	1.391	1.00
135_K	139_N	1.390	1.00
136_A	142_V	1.363	1.00
9_Y	47_Y	1.356	1.00
16_A	54_L	1.347	1.00
43_T	46_L	1.345	1.00
17_I	58_I	1.340	1.00
71_K	128_W	1.327	1.00
30_I	44_F	1.326	1.00
61_N	65_H	1.320	1.00
24_G	28_A	1.315	1.00
136_A	141_E	1.300	1.00
24_G	27_K	1.299	1.00
48_F	57_A	1.297	1.00
7_G	11_K	1.296	1.00
15_A	19_V	1.278	1.00
89_D	180_K	1.273	1.00
89_D	177_E	1.241	1.00
14_Q	61_N	1.211	1.00
89_D	181_K	1.210	1.00
85_D	89_D	1.206	1.00
107_S	111_I	1.204	1.00
23_K	27_K	1.199	1.00
81_W	85_D	1.189	1.00
69_Q	90_E	1.174	1.00
41_Q	45_Y	1.172	1.00
56_P	60_E	1.171	1.00
39_T	43_T	1.151	1.00
42_G	46_L	1.133	1.00
82_T	86_I	1.124	1.00
126_Y	153_R	1.124	1.00
20_I	25_L	1.119	1.00
40_A	46_L	1.117	1.00
52_N	56_P	1.106	1.00
137_I	146_I	1.104	1.00
132_I	136_A	1.091	1.00
8_K	47_Y	1.083	1.00
53_A	57_A	1.078	1.00
126_Y	130_E	1.077	1.00
13_L	58_I	1.058	1.00
15_A	37_A	1.054	1.00
83_V	132_I	1.053	1.00
175_N	178_V	1.052	1.00
147_N	150_W	1.048	1.00
45_Y	50_S	1.040	1.00
86_I	89_D	1.039	1.00
53_A	56_P	1.036	1.00
25_L	55_I	1.034	1.00
14_Q	18_E	1.034	1.00
78_E	86_I	1.028	1.00
7_G	10_E	1.015	1.00
85_D	184_F	1.013	1.00
33_I	54_L	1.012	1.00
17_I	21_S	1.009	1.00
128_W	131_K	1.006	1.00
137_I	148_S	1.002	1.00
130_E	148_S	0.990	1.00
157_N	161_N	0.990	1.00
67_L	124_P	0.989	1.00
102_I	105_C	0.987	1.00
13_L	48_F	0.986	1.00
79_D	141_E	0.984	1.00
112_D	115_M	0.979	1.00
150_W	178_V	0.977	1.00
69_Q	72_G	0.975	1.00
143_T	146_I	0.973	1.00
73_R	90_E	0.970	1.00
43_T	47_Y	0.963	1.00
123_Q	127_S	0.956	1.00
44_F	54_L	0.955	1.00
23_K	36_K	0.946	1.00
103_V	107_S	0.942	1.00
57_A	61_N	0.937	1.00
172_Q	175_N	0.931	1.00
8_K	39_T	0.925	1.00
181_K	185_T	0.925	1.00
166_F	169_G	0.920	1.00
131_K	134_N	0.919	1.00
131_K	135_K	0.918	1.00
62_L	65_H	0.912	1.00
90_E	93_L	0.910	1.00
16_A	58_I	0.903	1.00
6_S	10_E	0.900	1.00
77_D	83_V	0.900	1.00
103_V	106_Y	0.897	1.00
82_T	85_D	0.895	1.00
60_E	64_T	0.891	1.00
178_V	182_E	0.887	1.00
120_T	124_P	0.886	1.00
80_F	139_N	0.885	1.00
34_V	41_Q	0.885	1.00
89_D	93_L	0.874	1.00
86_I	90_E	0.874	1.00
94_I	98_H	0.869	1.00
182_E	185_T	0.863	1.00
177_E	181_K	0.859	1.00
126_Y	149_K	0.859	1.00
52_N	114_S	0.858	1.00
127_S	131_K	0.856	1.00
61_N	64_T	0.848	1.00
85_D	185_T	0.847	1.00
108_G	111_I	0.843	1.00
80_F	136_A	0.842	1.00
146_I	151_T	0.821	1.00
71_K	75_H	0.817	1.00
73_R	86_I	0.809	1.00
41_Q	46_L	0.808	1.00
18_E	100_D	0.806	1.00
19_V	22_E	0.802	1.00
35_K	41_Q	0.801	1.00
137_I	140_H	0.790	1.00
130_E	152_A	0.783	1.00
135_K	138_A	0.781	1.00
64_T	68_D	0.778	1.00
78_E	82_T	0.778	1.00
132_I	135_K	0.775	1.00
68_D	72_G	0.772	1.00
149_K	153_R	0.770	1.00
12_I	44_F	0.768	1.00
11_K	14_Q	0.766	1.00
11_K	37_A	0.764	1.00
165_R	168_I	0.760	1.00
180_K	184_F	0.758	1.00
88_I	155_I	0.755	1.00
13_L	61_N	0.741	1.00
67_L	71_K	0.740	1.00
124_P	128_W	0.736	1.00
52_N	112_D	0.728	1.00
25_L	51_K	0.728	1.00
101_I	104_L	0.723	1.00
119_E	123_Q	0.716	1.00
104_L	108_G	0.712	1.00
65_H	68_D	0.712	1.00
177_E	180_K	0.710	1.00
89_D	184_F	0.707	1.00
104_L	107_S	0.707	1.00
77_D	82_T	0.705	1.00
113_H	116_E	0.702	1.00
26_D	111_I	0.692	1.00
23_K	28_A	0.684	1.00
108_G	112_D	0.681	1.00
133_I	155_I	0.672	1.00
31_S	45_Y	0.668	1.00
182_E	186_F	0.668	1.00
136_A	140_H	0.667	1.00
26_D	108_G	0.666	1.00
12_I	37_A	0.658	1.00
127_S	130_E	0.657	1.00
133_I	148_S	0.655	1.00
76_G	86_I	0.650	1.00
14_Q	17_I	0.650	1.00
180_K	183_I	0.646	1.00
137_I	142_V	0.645	1.00
93_L	177_E	0.644	1.00
124_P	127_S	0.642	1.00
85_D	88_I	0.642	1.00
67_L	128_W	0.638	1.00
148_S	152_A	0.633	1.00
73_R	76_G	0.633	1.00
96_E	176_V	0.631	1.00
79_D	83_V	0.630	1.00
8_K	40_A	0.629	1.00
119_E	122_Y	0.627	1.00
37_A	40_A	0.626	1.00
77_D	86_I	0.625	1.00
179_Y	183_I	0.619	1.00
30_I	34_V	0.619	1.00
150_W	154_T	0.617	1.00
157_N	160_E	0.617	1.00
102_I	106_Y	0.615	1.00
154_T	157_N	0.615	1.00
122_Y	126_Y	0.614	1.00
25_L	52_N	0.610	1.00
8_K	43_T	0.609	1.00
176_V	180_K	0.608	1.00
22_E	32_D	0.607	1.00
13_L	17_I	0.606	1.00
93_L	176_V	0.604	1.00
133_I	137_I	0.604	1.00
137_I	143_T	0.603	1.00
72_G	90_E	0.602	1.00
165_R	169_G	0.598	1.00
80_F	141_E	0.594	1.00
150_W	153_R	0.593	1.00
91_T	95_T	0.589	1.00
107_S	110_A	0.583	1.00
114_S	117_K	0.583	1.00
68_D	71_K	0.580	1.00
12_I	47_Y	0.578	1.00
121_I	125_Y	0.570	1.00
60_E	121_I	0.570	1.00
64_T	121_I	0.569	1.00
34_V	39_T	0.568	1.00
20_I	55_I	0.566	1.00
174_E	177_E	0.564	1.00
158_L	183_I	0.560	1.00
133_I	151_T	0.557	1.00
174_E	178_V	0.557	1.00
134_N	149_K	0.547	1.00
94_I	97_R	0.544	1.00
6_S	9_Y	0.544	1.00
83_V	136_A	0.538	1.00
93_L	180_K	0.536	1.00
178_V	181_K	0.533	1.00
112_D	116_E	0.531	1.00
179_Y	182_E	0.529	1.00
160_E	164_E	0.529	1.00
41_Q	44_F	0.529	1.00
93_L	97_R	0.525	1.00
142_V	147_N	0.521	1.00
39_T	47_Y	0.521	1.00
8_K	12_I	0.521	1.00
72_G	76_G	0.521	1.00
121_I	124_P	0.519	1.00
56_P	114_S	0.517	1.00
145_G	148_S	0.513	1.00
65_H	69_Q	0.512	1.00
19_V	29_S	0.510	1.00
151_T	154_T	0.509	1.00
30_I	51_K	0.505	1.00
161_N	164_E	0.503	1.00
122_Y	125_Y	0.502	1.00
69_Q	94_I	0.501	1.00
81_W	141_E	0.500	1.00

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
2f07A	2	1	100	0.19	Contact Map
2iaiA	2	0.9639	100	0.201	Contact Map
2ibdA	2	0.9742	100	0.204	Contact Map
3npiA	2	0.9794	100	0.207	Contact Map
3g1oA	2	0.9794	100	0.21	Contact Map
4udsA	2	0.9433	100	0.213	Contact Map
3ppbA	2	0.9639	100	0.219	Contact Map
2xdnA	2	0.9948	100	0.222	Contact Map
3nrgA	2	1	100	0.222	Contact Map
3q0wA	2	0.9794	100	0.222	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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