YDES - BACSU - GREMLIN Contacts

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YDES - Uncharacterized HTH-type transcriptional regulator YdeS

UniProt:	P96676	Sequences: MQSKRGRPRDEGTHKAILSAAYDLLLEKGFDAVTVDKIAERAKVSKATIYKWWSNKAAVIMDSFLSTATDRLPVPDTGSSVQDIVTHATNLARFLTSREGTVIKELIGAGQLDEKLAEEYRTRFFQPRRLQAKGLLEKGIQKGELRENLDIEVSIDLIYGPIFYRLLITGDEVNDSYVRDLVMNAFKGVQATSATESM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	198 (179)
Sequences:	39995 (31958)
Seq/√Len:	2388.6

ECOLI - ENVR ACRR UIDR COMR RUTR NEMR SLMA YBIH FABR BDCR YJDC BETI RCDA
BACSU - YDES YFIR FADR PKSA YVDT BSCR YHGD YVKB YEZE YDGC YTTP YXAF LMRA YVAF YOBS 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
36_D	46_K	3.964	1.00
28_K	37_K	3.935	1.00
23_D	41_R	3.817	1.00
54_S	58_A	2.817	1.00
55_N	58_A	2.298	1.00
25_L	33_V	2.281	1.00
39_A	49_I	2.176	1.00
133_K	152_E	2.164	1.00
14_H	62_D	2.116	1.00
83_D	138_K	2.084	1.00
24_L	37_K	2.071	1.00
15_K	66_S	2.046	1.00
13_T	16_A	2.034	1.00
24_L	33_V	2.028	1.00
27_E	41_R	2.023	1.00
24_L	41_R	2.004	1.00
133_K	137_E	1.966	1.00
79_S	82_Q	1.910	1.00
137_E	141_Q	1.905	1.00
45_S	48_T	1.872	1.00
16_A	20_A	1.850	1.00
24_L	28_K	1.825	1.00
36_D	40_E	1.787	1.00
20_A	41_R	1.739	1.00
15_K	19_S	1.694	1.00
14_H	52_W	1.674	1.00
137_E	151_I	1.599	1.00
137_E	140_I	1.596	1.00
20_A	23_D	1.571	1.00
35_V	46_K	1.556	1.00
34_T	37_K	1.531	1.00
35_V	50_Y	1.518	1.00
62_D	65_L	1.516	1.00
23_D	27_E	1.486	1.00
22_Y	66_S	1.476	1.00
89_T	179_R	1.465	1.00
18_L	62_D	1.465	1.00
21_A	25_L	1.456	1.00
22_Y	67_T	1.438	1.00
138_K	142_K	1.422	1.00
153_V	180_D	1.403	1.00
29_G	33_V	1.393	1.00
37_K	41_R	1.385	1.00
139_G	145_L	1.358	1.00
33_V	38_I	1.337	1.00
66_S	70_D	1.336	1.00
37_K	40_E	1.332	1.00
81_V	85_V	1.331	1.00
29_G	32_A	1.306	1.00
184_N	188_G	1.299	1.00
140_I	147_E	1.292	1.00
35_V	49_I	1.289	1.00
19_S	66_S	1.285	1.00
85_V	179_R	1.278	1.00
61_M	65_L	1.275	1.00
157_L	161_P	1.269	1.00
113_D	116_L	1.246	1.00
45_S	51_K	1.245	1.00
22_Y	63_S	1.240	1.00
48_T	51_K	1.230	1.00
12_G	16_A	1.219	1.00
28_K	32_A	1.217	1.00
85_V	89_T	1.210	1.00
139_G	144_E	1.206	1.00
163_F	166_L	1.186	1.00
21_A	59_V	1.181	1.00
53_W	62_D	1.178	1.00
82_Q	86_T	1.177	1.00
25_L	30_F	1.176	1.00
13_T	52_W	1.163	1.00
46_K	50_Y	1.159	1.00
20_A	24_L	1.158	1.00
38_I	59_V	1.153	1.00
100_G	105_E	1.131	1.00
135_L	139_G	1.118	1.00
61_M	119_E	1.117	1.00
58_A	62_D	1.115	1.00
183_M	187_K	1.112	1.00
129_R	156_D	1.104	1.00
77_T	83_D	1.101	1.00
44_V	48_T	1.100	1.00
129_R	133_K	1.096	1.00
150_D	153_V	1.095	1.00
30_F	60_I	1.083	1.00
18_L	63_S	1.081	1.00
85_V	183_M	1.054	1.00
19_S	23_D	1.053	1.00
12_G	15_K	1.051	1.00
57_A	113_D	1.045	1.00
175_D	179_R	1.044	1.00
86_T	89_T	1.035	1.00
133_K	151_I	1.030	1.00
57_A	61_M	1.029	1.00
58_A	61_M	1.023	1.00
20_A	42_A	1.010	1.00
65_L	119_E	0.997	1.00
131_Q	134_G	0.985	1.00
78_G	86_T	0.978	1.00
49_I	59_V	0.978	1.00
126_Q	130_L	0.975	1.00
79_S	144_E	0.973	1.00
22_Y	26_L	0.972	1.00
65_L	69_T	0.968	1.00
146_R	149_L	0.968	1.00
80_S	142_K	0.966	1.00
11_E	15_K	0.958	1.00
48_T	52_W	0.956	1.00
178_V	181_L	0.954	1.00
129_R	152_E	0.947	1.00
83_D	135_L	0.947	1.00
130_L	134_G	0.945	1.00
31_D	109_A	0.943	1.00
134_G	137_E	0.933	1.00
140_I	143_G	0.932	1.00
10_D	51_K	0.931	1.00
47_A	51_K	0.927	1.00
134_G	138_K	0.923	1.00
28_K	41_R	0.923	1.00
82_Q	85_V	0.921	1.00
152_E	156_D	0.918	1.00
105_E	109_A	0.907	1.00
176_S	180_D	0.904	1.00
13_T	44_V	0.889	1.00
179_R	183_M	0.889	1.00
89_T	175_D	0.886	1.00
67_T	70_D	0.881	1.00
18_L	53_W	0.881	1.00
123_R	127_P	0.880	1.00
108_G	112_L	0.877	1.00
46_K	51_K	0.876	1.00
72_L	127_P	0.868	1.00
140_I	151_I	0.866	1.00
66_S	69_T	0.858	1.00
140_I	148_N	0.855	1.00
93_R	175_D	0.853	1.00
180_D	183_M	0.847	1.00
140_I	149_L	0.847	1.00
62_D	66_S	0.845	1.00
177_Y	181_L	0.842	1.00
30_F	56_K	0.842	1.00
89_T	93_R	0.840	1.00
10_D	13_T	0.838	1.00
39_A	46_K	0.835	1.00
40_E	46_K	0.833	1.00
101_T	104_K	0.825	1.00
24_L	27_E	0.819	1.00
119_E	123_R	0.816	1.00
50_Y	55_N	0.816	1.00
21_A	63_S	0.816	1.00
138_K	141_Q	0.816	1.00
101_T	105_E	0.816	1.00
69_T	73_P	0.798	1.00
78_G	82_Q	0.793	1.00
90_N	93_R	0.793	1.00
57_A	115_K	0.791	1.00
80_S	139_G	0.783	1.00
136_L	151_I	0.783	1.00
28_K	33_V	0.779	1.00
9_R	12_G	0.777	1.00
153_V	156_D	0.770	1.00
140_I	145_L	0.764	1.00
31_D	112_L	0.760	1.00
8_P	12_G	0.756	1.00
86_T	90_N	0.755	1.00
177_Y	180_D	0.745	1.00
16_A	19_S	0.741	1.00
16_A	42_A	0.736	1.00
9_R	13_T	0.731	1.00
181_L	185_A	0.726	1.00
100_G	103_I	0.720	1.00
79_S	83_D	0.712	1.00
113_D	117_A	0.704	1.00
149_L	154_S	0.703	1.00
109_A	113_D	0.698	1.00
178_V	182_V	0.696	1.00
65_L	123_R	0.696	1.00
23_D	101_T	0.695	1.00
165_R	168_I	0.694	1.00
153_V	157_L	0.689	1.00
17_I	42_A	0.689	1.00
80_S	144_E	0.684	1.00
115_K	118_E	0.680	1.00
94_F	99_E	0.680	1.00
13_T	48_T	0.679	1.00
17_I	49_I	0.677	1.00
133_K	155_I	0.662	1.00
36_D	50_Y	0.655	1.00
72_L	131_Q	0.655	1.00
70_D	73_P	0.654	1.00
118_E	121_R	0.651	1.00
127_P	131_Q	0.650	1.00
114_E	117_A	0.649	1.00
130_L	133_K	0.646	1.00
182_V	186_F	0.645	1.00
175_D	178_V	0.644	1.00
135_L	138_K	0.642	1.00
93_R	97_S	0.641	1.00
30_F	57_A	0.641	1.00
127_P	130_L	0.640	1.00
18_L	22_Y	0.638	1.00
150_D	180_D	0.637	1.00
81_V	186_F	0.636	1.00
109_A	112_L	0.636	1.00
103_I	106_L	0.635	1.00
42_A	45_S	0.632	1.00
185_A	188_G	0.632	1.00
117_A	121_R	0.631	1.00
17_I	52_W	0.628	1.00
176_S	179_R	0.628	1.00
113_D	120_Y	0.628	1.00
115_K	119_E	0.620	1.00
35_V	39_A	0.616	1.00
158_I	185_A	0.613	1.00
74_V	78_G	0.613	1.00
100_G	104_K	0.612	1.00
88_A	158_I	0.612	1.00
136_L	140_I	0.612	1.00
77_T	82_Q	0.612	1.00
26_L	101_T	0.611	1.00
179_R	182_V	0.608	1.00
174_N	177_Y	0.605	1.00
25_L	60_I	0.601	1.00
11_E	14_H	0.600	1.00
8_P	11_E	0.598	1.00
117_A	120_Y	0.597	1.00
164_Y	169_T	0.596	1.00
180_D	184_N	0.593	1.00
85_V	186_F	0.592	1.00
46_K	49_I	0.590	1.00
146_R	187_K	0.587	1.00
164_Y	168_I	0.586	1.00
77_T	86_T	0.584	1.00
113_D	121_R	0.580	1.00
10_D	52_W	0.573	1.00
80_S	83_D	0.571	1.00
85_V	88_A	0.566	1.00
13_T	45_S	0.566	1.00
136_L	158_I	0.565	1.00
78_G	83_D	0.562	1.00
85_V	182_V	0.559	1.00
27_E	37_K	0.553	1.00
19_S	22_Y	0.552	1.00
36_D	45_S	0.549	1.00
90_N	94_F	0.544	1.00
81_V	183_M	0.540	1.00
89_T	178_V	0.536	1.00
106_L	109_A	0.534	1.00
88_A	91_L	0.534	1.00
93_R	96_T	0.534	1.00
104_K	108_G	0.533	1.00
13_T	17_I	0.533	1.00
137_E	152_E	0.525	1.00
166_L	169_T	0.524	1.00
139_G	143_G	0.522	1.00
140_I	146_R	0.521	1.00
10_D	14_H	0.521	1.00
30_F	33_V	0.520	1.00
163_F	168_I	0.518	1.00
169_T	173_V	0.518	1.00
157_L	160_G	0.517	1.00
156_D	160_G	0.516	1.00
89_T	182_V	0.516	1.00
145_L	150_D	0.513	1.00
91_L	95_L	0.511	1.00
94_F	97_S	0.511	1.00
39_A	42_A	0.504	1.00
65_L	124_F	0.503	1.00
14_H	53_W	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
2fq4A	2	0.9293	100	0.22	Contact Map
2zb9A	2	0.9444	100	0.232	Contact Map
2id3A	4	0.9596	100	0.244	Contact Map
3npiA	2	0.9495	100	0.263	Contact Map
2ibdA	2	0.9192	100	0.267	Contact Map
3g1oA	2	0.9192	100	0.268	Contact Map
2qwtA	1	0.8232	100	0.279	Contact Map
3nrgA	2	0.9646	100	0.28	Contact Map
3s5rA	2	0.9141	100	0.281	Contact Map
3q0wA	2	0.9141	100	0.288	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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