UIDR - ECOLI - GREMLIN Contacts

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UIDR - HTH-type transcriptional regulator UidR

UniProt:	P0ACT6	Sequences: MMDNMQTEAQPTRTRILNAAREIFSENGFHSASMKAICKSCAISPGTLYHHFISKEALIQAIILQDQERALARFREPIEGIHFVDYMVESIVSLTHEAFGQRALVVEIMAEGMRNPQVAAMLKNKHMTITEFVAQRMRDAQQKGEISPDINTAMTSRLLLDLTYGVLADIEAEDLAREASFAQGLRAMIGGILTAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12667
Length:	196 (180)
Sequences:	44052 (35494)
Seq/√Len:	2645.6

ECOLI - UIDR ACRR ENVR SLMA RUTR FABR COMR NEMR BETI BDCR YJDC YBIH RCDA
BACSU - YFIR YVDT FADR BSCR PKSA YHGD YVKB YDGC YEZE LMRA YTTP YDES YCNC YOBS YXAF YVAF YERO YUXN YXBF
HALSA - Q9HRF3 Q9HM72
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
27_N	36_A	3.970	1.00
35_K	45_P	3.945	1.00
22_E	40_S	3.585	1.00
53_I	57_A	2.715	1.00
24_F	32_A	2.401	1.00
54_S	57_A	2.246	1.00
134_A	153_A	2.097	1.00
38_C	48_L	2.047	1.00
23_I	40_S	2.032	1.00
23_I	32_A	1.991	1.00
12_T	15_R	1.973	1.00
19_A	40_S	1.960	1.00
26_E	40_S	1.950	1.00
23_I	36_A	1.948	1.00
13_R	61_A	1.917	1.00
14_T	65_Q	1.913	1.00
23_I	27_N	1.882	1.00
134_A	138_R	1.857	1.00
15_R	19_A	1.836	1.00
35_K	39_K	1.754	1.00
19_A	22_E	1.752	1.00
138_R	152_T	1.682	1.00
14_T	18_N	1.670	1.00
44_S	47_T	1.598	1.00
34_M	49_Y	1.598	1.00
21_R	66_D	1.583	1.00
21_R	65_Q	1.583	1.00
17_L	61_A	1.581	1.00
138_R	142_Q	1.568	1.00
20_A	24_F	1.556	1.00
34_M	45_P	1.551	1.00
13_R	51_H	1.495	1.00
92_V	182_A	1.493	1.00
138_R	141_Q	1.489	1.00
36_A	40_S	1.486	1.00
61_A	64_L	1.478	1.00
83_F	86_Y	1.450	1.00
33_S	36_A	1.446	1.00
22_E	26_E	1.445	1.00
36_A	39_K	1.441	1.00
88_V	186_R	1.418	1.00
28_G	31_S	1.408	1.00
60_Q	64_L	1.399	1.00
75_R	132_F	1.390	1.00
65_Q	69_R	1.385	1.00
82_H	85_D	1.369	1.00
141_Q	148_P	1.364	1.00
158_L	162_L	1.353	1.00
32_A	37_I	1.348	1.00
139_D	143_K	1.346	1.00
28_G	32_A	1.341	1.00
21_R	62_I	1.332	1.00
60_Q	121_M	1.331	1.00
11_P	15_R	1.321	1.00
34_M	48_L	1.315	1.00
64_L	121_M	1.303	1.00
20_A	58_L	1.274	1.00
140_A	145_E	1.273	1.00
27_N	31_S	1.263	1.00
18_N	65_Q	1.246	1.00
177_R	180_S	1.236	1.00
45_P	49_Y	1.229	1.00
19_A	23_I	1.221	1.00
47_T	50_H	1.219	1.00
52_F	61_A	1.218	1.00
107_E	111_E	1.203	1.00
86_Y	139_D	1.201	1.00
182_A	186_R	1.191	1.00
140_A	146_I	1.189	1.00
24_F	29_F	1.183	1.00
48_L	58_L	1.154	1.00
11_P	14_T	1.150	1.00
44_S	50_H	1.149	1.00
130_T	157_R	1.122	1.00
130_T	134_A	1.121	1.00
47_T	51_H	1.118	1.00
43_I	47_T	1.105	1.00
12_T	51_H	1.087	1.00
141_Q	150_I	1.086	1.00
46_G	50_H	1.085	1.00
56_E	60_Q	1.079	1.00
151_N	154_M	1.075	1.00
132_F	135_Q	1.074	1.00
136_R	140_A	1.074	1.00
21_R	25_S	1.068	1.00
57_A	61_A	1.062	1.00
92_V	186_R	1.053	1.00
17_L	62_I	1.051	1.00
147_S	150_I	1.050	1.00
56_E	115_N	1.048	1.00
88_V	92_V	1.048	1.00
57_A	60_Q	1.043	1.00
9_A	50_H	1.043	1.00
18_N	22_E	1.040	1.00
107_E	110_A	1.038	1.00
89_E	92_V	1.035	1.00
17_L	52_F	1.032	1.00
183_Q	186_R	1.018	1.00
37_I	58_L	1.015	1.00
121_M	124_N	1.009	1.00
29_F	59_I	1.008	1.00
110_A	114_R	1.002	1.00
134_A	152_T	1.001	1.00
19_A	41_C	0.993	1.00
64_L	68_E	0.992	1.00
38_C	45_P	0.990	1.00
27_N	40_S	0.986	1.00
93_S	96_H	0.954	1.00
71_L	128_T	0.950	1.00
83_F	87_M	0.944	1.00
85_D	89_E	0.935	1.00
20_A	62_I	0.934	1.00
12_T	43_I	0.931	1.00
75_R	79_E	0.923	1.00
73_R	76_E	0.915	1.00
49_Y	54_S	0.914	1.00
141_Q	152_T	0.913	1.00
56_E	117_Q	0.899	1.00
135_Q	139_D	0.898	1.00
106_V	110_A	0.893	1.00
161_D	165_G	0.891	1.00
82_H	86_Y	0.886	1.00
45_P	50_H	0.885	1.00
10_Q	14_T	0.884	1.00
65_Q	68_E	0.877	1.00
61_A	65_Q	0.875	1.00
102_R	107_E	0.873	1.00
72_A	76_E	0.866	1.00
66_D	69_R	0.865	1.00
71_L	75_R	0.861	1.00
30_H	111_E	0.859	1.00
39_K	45_P	0.852	1.00
8_E	11_P	0.849	1.00
120_A	124_N	0.846	1.00
23_I	26_E	0.838	1.00
141_Q	144_G	0.838	1.00
85_D	88_V	0.837	1.00
64_L	125_K	0.831	1.00
141_Q	146_I	0.829	1.00
131_E	135_Q	0.824	1.00
121_M	125_K	0.823	1.00
124_N	128_T	0.819	1.00
94_L	98_A	0.819	1.00
135_Q	138_R	0.819	1.00
127_M	131_E	0.815	1.00
154_M	184_G	0.813	1.00
153_A	157_R	0.813	1.00
134_A	156_S	0.808	1.00
136_R	139_D	0.807	1.00
130_T	153_A	0.806	1.00
15_R	41_C	0.804	1.00
180_S	184_G	0.800	1.00
103_A	106_V	0.797	1.00
83_F	143_K	0.796	1.00
169_D	172_A	0.791	1.00
73_R	93_S	0.790	1.00
139_D	142_Q	0.782	1.00
87_M	92_V	0.780	1.00
106_V	109_M	0.779	1.00
68_E	72_A	0.779	1.00
84_V	88_V	0.777	1.00
88_V	91_I	0.776	1.00
103_A	111_E	0.775	1.00
154_M	180_S	0.774	1.00
15_R	18_N	0.771	1.00
150_I	155_T	0.770	1.00
128_T	132_F	0.764	1.00
152_T	156_S	0.759	1.00
178_E	182_A	0.758	1.00
91_I	94_L	0.754	1.00
82_H	145_E	0.752	1.00
179_A	182_A	0.752	1.00
161_D	164_Y	0.748	1.00
84_V	87_M	0.747	1.00
92_V	96_H	0.742	1.00
71_L	132_F	0.741	1.00
27_N	32_A	0.738	1.00
34_M	55_K	0.738	1.00
69_R	72_A	0.734	1.00
16_I	48_L	0.733	1.00
34_M	38_C	0.723	1.00
9_A	12_T	0.722	1.00
8_E	12_T	0.719	1.00
72_A	75_R	0.718	1.00
97_E	101_Q	0.716	1.00
137_M	152_T	0.715	1.00
102_R	105_V	0.710	1.00
16_I	41_C	0.702	1.00
184_G	188_M	0.699	1.00
116_P	120_A	0.693	1.00
17_L	21_R	0.692	1.00
22_E	103_A	0.690	1.00
77_P	80_G	0.689	1.00
29_F	55_K	0.686	1.00
86_Y	136_R	0.686	1.00
154_M	158_L	0.684	1.00
119_A	123_K	0.682	1.00
111_E	114_R	0.679	1.00
178_E	181_F	0.679	1.00
128_T	131_E	0.677	1.00
89_E	93_S	0.673	1.00
154_M	183_Q	0.672	1.00
93_S	97_E	0.668	1.00
131_E	134_A	0.665	1.00
35_K	49_Y	0.659	1.00
116_P	119_A	0.658	1.00
76_E	80_G	0.657	1.00
182_A	185_L	0.652	1.00
17_L	65_Q	0.649	1.00
180_S	183_Q	0.647	1.00
184_G	187_A	0.646	1.00
25_S	103_A	0.643	1.00
96_H	182_A	0.640	1.00
18_N	21_R	0.639	1.00
30_H	114_R	0.638	1.00
77_P	93_S	0.634	1.00
26_E	36_A	0.634	1.00
41_C	44_S	0.631	1.00
154_M	157_R	0.629	1.00
96_H	178_E	0.626	1.00
29_F	32_A	0.623	1.00
103_A	107_E	0.616	1.00
158_L	161_D	0.613	1.00
24_F	59_I	0.612	1.00
105_V	108_I	0.609	1.00
101_Q	104_L	0.609	1.00
181_F	185_L	0.603	1.00
38_C	43_I	0.599	1.00
151_N	155_T	0.595	1.00
12_T	47_T	0.595	1.00
94_L	97_E	0.593	1.00
137_M	159_L	0.593	1.00
137_M	141_Q	0.586	1.00
87_M	139_D	0.586	1.00
123_K	126_H	0.571	1.00
183_Q	187_A	0.570	1.00
81_I	85_D	0.565	1.00
78_I	132_F	0.565	1.00
81_I	89_E	0.564	1.00
154_M	187_A	0.558	1.00
29_F	56_E	0.556	1.00
16_I	51_H	0.555	1.00
77_P	89_E	0.555	1.00
126_H	130_T	0.552	1.00
60_Q	117_Q	0.551	1.00
179_A	183_Q	0.550	1.00
81_I	86_Y	0.548	1.00
164_Y	168_A	0.547	1.00
86_Y	89_E	0.545	1.00
170_I	173_E	0.541	1.00
10_Q	13_R	0.539	1.00
124_N	127_M	0.536	1.00
83_F	88_V	0.536	1.00
155_T	158_L	0.535	1.00
90_S	94_L	0.534	1.00
35_K	44_S	0.533	1.00
165_G	168_A	0.532	1.00
125_K	128_T	0.532	1.00
45_P	48_L	0.530	1.00
64_L	124_N	0.527	1.00
117_Q	120_A	0.526	1.00
111_E	115_N	0.526	1.00
9_A	51_H	0.525	1.00
92_V	183_Q	0.525	1.00
148_P	151_N	0.523	1.00
41_C	45_P	0.515	1.00
16_I	43_I	0.515	1.00
123_K	127_M	0.514	1.00
68_E	125_K	0.502	1.00
120_A	123_K	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
2xdnA	2	0.9796	100	0.203	Contact Map
4udsA	2	0.9337	100	0.204	Contact Map
3g1oA	2	0.9592	100	0.212	Contact Map
4cgrA	2	0.9592	100	0.214	Contact Map
3crjA	2	0.949	100	0.217	Contact Map
2raeA	2	0.9694	100	0.223	Contact Map
2ibdA	2	0.9643	100	0.224	Contact Map
3dcfA	2	0.9235	100	0.225	Contact Map
4jykA	2	0.9745	100	0.226	Contact Map
3npiA	2	0.9592	100	0.226	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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