YOBS - BACSU - GREMLIN Contacts

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YOBS - Uncharacterized HTH-type transcriptional regulator YobS

UniProt:	O34892	Sequences: MSPRIGLTQKMIVDAAAEIADQEGVNGVSLAALSKKMNVRPPSLYNHINGLQAIRAELAVRGLTKLFDQMADSVTERKGDSAMLSLAHAYVDFAIENPGYYEAALLKVHDKRTEIVSDQIVCLVTKLLIENGYASEKTAIHATRGLRSLLHGFTVLIAKEAFEREEDILESLSFSIRTFLSGLLINNKNIM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	191 (175)
Sequences:	34010 (27312)
Seq/√Len:	2064.6

ECOLI - RUTR FABR SLMA ACRR UIDR BETI ENVR BDCR COMR YBIH NEMR YJDC RCDA
BACSU - YOBS BSCR YVDT YDGC YFIR FADR YHGD YVKB YEZE PKSA YTTP LMRA YCNC YVAF YXAF YDES 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
23_E	32_A	4.239	1.00
31_A	41_P	4.015	1.00
18_E	36_K	3.684	1.00
49_N	53_A	3.018	1.00
20_A	28_V	2.549	1.00
15_A	36_K	2.341	1.00
50_G	53_A	2.298	1.00
19_I	36_K	2.182	1.00
8_T	11_M	2.161	1.00
22_Q	36_K	2.140	1.00
15_A	18_E	2.117	1.00
10_K	61_R	1.993	1.00
19_I	32_A	1.991	1.00
34_S	44_L	1.986	1.00
19_I	28_V	1.970	1.00
40_R	43_S	1.920	1.00
19_I	23_E	1.894	1.00
10_K	14_D	1.843	1.00
11_M	15_A	1.813	1.00
17_A	61_R	1.807	1.00
48_I	57_E	1.805	1.00
78_K	81_S	1.802	1.00
9_Q	57_E	1.793	1.00
30_L	41_P	1.772	1.00
18_E	22_Q	1.746	1.00
84_L	173_S	1.744	1.00
13_V	57_E	1.742	1.00
31_A	35_K	1.701	1.00
125_T	129_I	1.665	1.00
32_A	36_K	1.651	1.00
32_A	35_K	1.637	1.00
30_L	45_Y	1.554	1.00
88_H	169_L	1.548	1.00
7_L	11_M	1.510	1.00
16_A	20_A	1.506	1.00
24_G	27_G	1.500	1.00
88_H	173_S	1.483	1.00
17_A	58_L	1.470	1.00
123_L	127_L	1.459	1.00
57_E	60_V	1.440	1.00
61_R	65_K	1.432	1.00
23_E	27_G	1.417	1.00
17_A	62_G	1.396	1.00
14_D	61_R	1.363	1.00
28_V	33_L	1.350	1.00
145_G	149_L	1.348	1.00
39_V	43_S	1.336	1.00
16_A	54_I	1.334	1.00
16_A	58_L	1.316	1.00
30_L	44_L	1.306	1.00
84_L	88_H	1.305	1.00
138_T	142_A	1.289	1.00
20_A	25_V	1.282	1.00
121_V	125_T	1.277	1.00
24_G	28_V	1.268	1.00
69_Q	89_A	1.248	1.00
9_Q	47_H	1.242	1.00
43_S	46_N	1.237	1.00
45_Y	50_G	1.222	1.00
13_V	48_I	1.219	1.00
29_S	32_A	1.214	1.00
21_D	99_G	1.209	1.00
40_R	46_N	1.209	1.00
80_D	84_L	1.202	1.00
15_A	37_M	1.199	1.00
15_A	19_I	1.184	1.00
84_L	177_R	1.182	1.00
167_D	170_E	1.174	1.00
53_A	57_E	1.170	1.00
43_S	47_H	1.168	1.00
82_A	130_E	1.165	1.00
135_S	138_T	1.153	1.00
134_A	137_K	1.145	1.00
128_L	131_N	1.143	1.00
56_A	60_V	1.136	1.00
41_P	45_Y	1.133	1.00
33_L	54_I	1.124	1.00
169_L	173_S	1.118	1.00
60_V	64_T	1.116	1.00
126_K	130_E	1.103	1.00
8_T	47_H	1.102	1.00
7_L	10_K	1.102	1.00
81_S	85_S	1.082	1.00
62_G	65_K	1.077	1.00
121_V	140_I	1.057	1.00
13_V	61_R	1.053	1.00
23_E	36_K	1.033	1.00
34_S	41_P	1.033	1.00
138_T	141_H	1.028	1.00
12_I	44_L	1.018	1.00
42_P	46_N	1.015	1.00
117_S	121_V	1.012	1.00
69_Q	72_D	1.012	1.00
17_A	21_D	1.011	1.00
102_E	106_L	1.006	1.00
172_L	175_S	1.002	1.00
85_S	88_H	0.995	1.00
13_V	58_L	0.974	1.00
93_F	97_N	0.972	1.00
173_S	177_R	0.966	1.00
170_E	174_F	0.963	1.00
41_P	46_N	0.961	1.00
5_I	46_N	0.959	1.00
174_F	178_T	0.959	1.00
89_A	92_D	0.953	1.00
53_A	56_A	0.943	1.00
174_F	177_R	0.942	1.00
141_H	174_F	0.935	1.00
52_Q	56_A	0.934	1.00
57_E	61_R	0.926	1.00
149_L	175_S	0.926	1.00
148_S	152_G	0.925	1.00
25_V	55_R	0.919	1.00
35_K	41_P	0.910	1.00
123_L	126_K	0.908	1.00
14_D	18_E	0.897	1.00
125_T	128_L	0.891	1.00
125_T	139_A	0.890	1.00
18_E	99_G	0.885	1.00
145_G	148_S	0.884	1.00
97_N	100_Y	0.883	1.00
11_M	14_D	0.877	1.00
85_S	89_A	0.867	1.00
8_T	39_V	0.864	1.00
81_S	84_L	0.853	1.00
6_G	10_K	0.853	1.00
151_H	155_V	0.847	1.00
116_V	119_Q	0.830	1.00
175_S	179_F	0.827	1.00
124_V	131_N	0.818	1.00
122_C	125_T	0.817	1.00
127_L	131_N	0.811	1.00
126_K	129_I	0.811	1.00
128_L	136_E	0.809	1.00
157_I	160_E	0.798	1.00
115_I	119_Q	0.780	1.00
92_D	96_E	0.780	1.00
71_A	75_T	0.779	1.00
61_R	64_T	0.776	1.00
73_S	89_A	0.773	1.00
172_L	176_I	0.772	1.00
68_D	72_D	0.772	1.00
73_S	85_S	0.770	1.00
92_D	169_L	0.769	1.00
60_V	116_V	0.767	1.00
141_H	170_E	0.764	1.00
122_C	126_K	0.764	1.00
5_I	8_T	0.759	1.00
11_M	37_M	0.758	1.00
13_V	17_A	0.758	1.00
88_H	172_L	0.754	1.00
67_F	71_A	0.753	1.00
64_T	68_D	0.750	1.00
109_H	112_R	0.745	1.00
168_I	171_S	0.744	1.00
127_L	130_E	0.742	1.00
51_L	55_R	0.740	1.00
169_L	172_L	0.725	1.00
30_L	51_L	0.721	1.00
141_H	145_G	0.720	1.00
44_L	54_I	0.719	1.00
8_T	43_S	0.716	1.00
118_D	122_C	0.715	1.00
23_E	28_V	0.713	1.00
19_I	22_Q	0.706	1.00
12_I	37_M	0.705	1.00
110_D	114_E	0.699	1.00
41_P	44_L	0.696	1.00
168_I	172_L	0.694	1.00
120_I	127_L	0.692	1.00
22_Q	32_A	0.692	1.00
88_H	92_D	0.691	1.00
128_L	133_Y	0.690	1.00
112_R	116_V	0.690	1.00
166_E	169_L	0.680	1.00
136_E	139_A	0.680	1.00
21_D	97_N	0.677	1.00
112_R	115_I	0.676	1.00
141_H	144_R	0.676	1.00
73_S	77_R	0.674	1.00
102_E	105_L	0.674	1.00
68_D	71_A	0.673	1.00
114_E	118_D	0.672	1.00
110_D	113_T	0.671	1.00
135_S	139_A	0.669	1.00
111_K	114_E	0.666	1.00
137_K	142_A	0.666	1.00
67_F	119_Q	0.658	1.00
78_K	82_A	0.655	1.00
131_N	134_A	0.652	1.00
82_A	126_K	0.651	1.00
140_I	144_R	0.650	1.00
77_R	85_S	0.645	1.00
64_T	116_V	0.639	1.00
25_V	51_L	0.629	1.00
39_V	42_P	0.625	1.00
125_T	140_I	0.624	1.00
171_S	175_S	0.619	1.00
71_A	123_L	0.619	1.00
87_A	146_L	0.618	1.00
76_E	85_S	0.618	1.00
157_I	161_A	0.615	1.00
46_N	49_N	0.612	1.00
120_I	124_V	0.610	1.00
101_Y	104_A	0.608	1.00
78_K	132_G	0.608	1.00
62_G	100_Y	0.607	1.00
39_V	47_H	0.607	1.00
60_V	112_R	0.603	1.00
127_L	132_G	0.601	1.00
90_Y	94_A	0.599	1.00
30_L	34_S	0.598	1.00
65_K	68_D	0.597	1.00
69_Q	93_F	0.597	1.00
91_V	172_L	0.593	1.00
8_T	40_R	0.589	1.00
40_R	44_L	0.584	1.00
103_A	106_L	0.584	1.00
74_V	126_K	0.583	1.00
167_D	171_S	0.581	1.00
165_E	168_I	0.580	1.00
156_L	159_K	0.580	1.00
99_G	102_E	0.576	1.00
115_I	118_D	0.575	1.00
73_S	76_E	0.573	1.00
165_E	169_L	0.572	1.00
149_L	152_G	0.572	1.00
160_E	163_E	0.570	1.00
172_L	178_T	0.570	1.00
153_F	157_I	0.568	1.00
66_L	93_F	0.567	1.00
139_A	143_T	0.564	1.00
90_Y	151_H	0.559	1.00
94_A	101_Y	0.554	1.00
33_L	37_M	0.552	1.00
170_E	173_S	0.551	1.00
121_V	128_L	0.548	1.00
151_H	156_L	0.547	1.00
87_A	150_L	0.544	1.00
152_G	155_V	0.542	1.00
37_M	40_R	0.538	1.00
91_V	157_I	0.534	1.00
133_Y	136_E	0.533	1.00
146_L	179_F	0.531	1.00
56_A	112_R	0.529	1.00
12_I	47_H	0.529	1.00
17_A	65_K	0.528	1.00
128_L	132_G	0.527	1.00
147_R	151_H	0.525	1.00
116_V	120_I	0.523	1.00
74_V	123_L	0.518	1.00
45_Y	53_A	0.517	1.00
84_L	87_A	0.514	1.00
129_I	139_A	0.513	1.00
91_V	95_I	0.510	1.00
127_L	133_Y	0.510	1.00
148_S	156_L	0.509	1.00
71_A	119_Q	0.505	1.00
171_S	174_F	0.505	1.00
25_V	52_Q	0.502	1.00
82_A	127_L	0.500	1.00
34_S	39_V	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
1zk8A	2	0.9319	100	0.235	Contact Map
4jykA	2	0.9686	100	0.273	Contact Map
2iaiA	2	0.9372	100	0.274	Contact Map
2f07A	2	0.9686	100	0.275	Contact Map
3on2A	1	0.9476	100	0.28	Contact Map
3bjbA	4	0.9476	100	0.283	Contact Map
4udsA	2	0.9162	100	0.289	Contact Map
3npiA	2	0.9791	100	0.292	Contact Map
3nrgA	2	0.9738	100	0.292	Contact Map
2dg7A	2	0.9529	100	0.293	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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