RCDA - ECOLI - GREMLIN Contacts

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RCDA - HTH-type transcriptional regulator RcdA

UniProt:	P75811	Sequences: MRRANDPQRREKIIQATLEAVKLYGIHAVTHRKIATLAGVPLGSMTYYFSGIDELLLEAFSSFTEIMSRQYQAFFSDVSDAPGACQAITDMIYSSQVATPDNMELMYQLYALASRKPLLKTVMQNWMQRSQQTLEQWFEPGTARALDAFIEGMTLHFVTDRKPLSREEILRMVERVAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13680
Length:	178 (163)
Sequences:	35540 (28244)
Seq/√Len:	2212.2

ECOLI - RCDA BETI NEMR YJDC BDCR ACRR FABR COMR SLMA RUTR ENVR UIDR YBIH
BACSU - PKSA YXAF LMRA BSCR YHGD FADR YCNC YVDT YTTP YEZE YFIR YVKB YUXN YOBS YDGC YERO YVAF YDES YXBF
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
32_R	42_L	4.183	1.00
24_Y	33_K	4.147	1.00
19_E	37_L	3.871	1.00
50_S	54_E	2.822	1.00
21_V	29_V	2.551	1.00
9_R	12_K	2.272	1.00
11_E	62_S	2.182	1.00
23_L	37_L	2.170	1.00
20_A	29_V	2.164	1.00
35_A	45_M	2.073	1.00
51_G	54_E	2.053	1.00
41_P	44_S	2.032	1.00
20_A	37_L	1.928	1.00
11_E	15_Q	1.852	1.00
80_D	83_G	1.833	1.00
16_A	37_L	1.827	1.00
18_L	62_S	1.799	1.00
17_T	21_V	1.798	1.00
32_R	36_T	1.790	1.00
12_K	16_A	1.769	1.00
31_H	46_T	1.753	1.00
131_Q	135_E	1.709	1.00
20_A	33_K	1.694	1.00
14_I	58_E	1.664	1.00
31_H	42_L	1.634	1.00
10_R	58_E	1.612	1.00
19_E	23_L	1.595	1.00
58_E	61_S	1.559	1.00
20_A	24_Y	1.556	1.00
18_L	59_A	1.522	1.00
15_Q	62_S	1.478	1.00
61_S	122_V	1.463	1.00
145_A	149_F	1.462	1.00
31_H	45_M	1.450	1.00
16_A	19_E	1.441	1.00
8_Q	12_K	1.421	1.00
25_G	28_A	1.396	1.00
33_K	36_T	1.394	1.00
33_K	37_L	1.380	1.00
134_L	137_W	1.372	1.00
62_S	66_I	1.345	1.00
21_V	26_I	1.335	1.00
54_E	58_E	1.334	1.00
49_F	58_E	1.332	1.00
17_T	55_L	1.324	1.00
29_V	34_I	1.322	1.00
18_L	63_F	1.312	1.00
25_G	29_V	1.308	1.00
57_L	61_S	1.307	1.00
44_S	47_Y	1.276	1.00
30_T	33_K	1.266	1.00
40_V	44_S	1.245	1.00
8_Q	11_E	1.237	1.00
61_S	65_E	1.223	1.00
42_L	46_T	1.207	1.00
127_M	131_Q	1.189	1.00
44_S	48_Y	1.188	1.00
41_P	47_Y	1.179	1.00
133_T	137_W	1.179	1.00
70_Q	91_M	1.168	1.00
14_I	59_A	1.164	1.00
34_I	55_L	1.161	1.00
46_T	51_G	1.161	1.00
16_A	38_A	1.158	1.00
134_L	138_F	1.139	1.00
19_E	101_D	1.128	1.00
26_I	56_L	1.125	1.00
83_G	87_A	1.121	1.00
24_Y	28_A	1.120	1.00
6_D	47_Y	1.116	1.00
104_E	108_Q	1.112	1.00
148_A	152_G	1.106	1.00
130_S	137_W	1.099	1.00
54_E	57_L	1.096	1.00
16_A	20_A	1.093	1.00
17_T	59_A	1.090	1.00
128_Q	132_Q	1.065	1.00
14_I	49_F	1.052	1.00
131_Q	140_P	1.037	1.00
165_S	168_E	1.032	1.00
7_P	11_E	1.023	1.00
129_R	132_Q	1.015	1.00
43_G	47_Y	1.013	1.00
9_R	48_Y	1.007	1.00
10_R	48_Y	1.006	1.00
86_Q	90_D	1.003	1.00
123_M	127_M	0.998	1.00
87_A	90_D	0.997	1.00
82_P	86_Q	0.988	1.00
84_A	136_Q	0.974	1.00
24_Y	37_L	0.961	1.00
139_E	142_T	0.961	1.00
164_L	168_E	0.956	1.00
70_Q	73_A	0.955	1.00
42_L	47_Y	0.953	1.00
83_G	86_Q	0.950	1.00
65_E	69_R	0.942	1.00
95_S	99_T	0.936	1.00
129_R	133_T	0.934	1.00
18_L	22_K	0.931	1.00
15_Q	19_E	0.927	1.00
58_E	62_S	0.922	1.00
57_L	118_L	0.918	1.00
62_S	65_E	0.917	1.00
121_T	125_N	0.915	1.00
132_Q	136_Q	0.911	1.00
63_F	66_I	0.905	1.00
6_D	9_R	0.905	1.00
133_T	136_Q	0.901	1.00
104_E	107_Y	0.897	1.00
31_H	52_I	0.889	1.00
72_Q	76_S	0.880	1.00
135_E	140_P	0.879	1.00
36_T	42_L	0.864	1.00
45_M	55_L	0.863	1.00
9_R	40_V	0.859	1.00
140_P	144_R	0.855	1.00
68_S	72_Q	0.849	1.00
74_F	91_M	0.847	1.00
145_A	148_A	0.839	1.00
99_T	102_N	0.838	1.00
124_Q	128_Q	0.835	1.00
26_I	52_I	0.831	1.00
35_A	42_L	0.829	1.00
13_I	45_M	0.827	1.00
53_D	57_L	0.825	1.00
122_V	125_N	0.824	1.00
69_R	73_A	0.819	1.00
74_F	87_A	0.815	1.00
87_A	91_M	0.815	1.00
32_R	46_T	0.813	1.00
142_T	148_A	0.813	1.00
142_T	146_L	0.806	1.00
147_D	151_E	0.803	1.00
53_D	116_K	0.799	1.00
118_L	121_T	0.799	1.00
91_M	94_S	0.790	1.00
22_K	101_D	0.782	1.00
103_M	106_M	0.782	1.00
24_Y	29_V	0.779	1.00
90_D	94_S	0.774	1.00
14_I	18_L	0.771	1.00
21_V	56_L	0.771	1.00
139_E	143_A	0.765	1.00
9_R	44_S	0.763	1.00
126_W	130_S	0.761	1.00
129_R	137_W	0.760	1.00
132_Q	135_E	0.754	1.00
12_K	15_Q	0.747	1.00
14_I	62_S	0.736	1.00
9_R	41_P	0.732	1.00
32_R	41_P	0.730	1.00
135_E	138_F	0.729	1.00
13_I	48_Y	0.726	1.00
13_I	38_A	0.719	1.00
157_F	160_D	0.716	1.00
120_K	124_Q	0.714	1.00
69_R	72_Q	0.712	1.00
122_V	126_W	0.711	1.00
84_A	137_W	0.707	1.00
128_Q	131_Q	0.706	1.00
12_K	38_A	0.704	1.00
125_N	129_R	0.701	1.00
112_L	116_K	0.699	1.00
100_P	104_E	0.698	1.00
77_D	87_A	0.697	1.00
105_L	108_Q	0.695	1.00
118_L	122_V	0.694	1.00
142_T	147_D	0.694	1.00
94_S	98_A	0.693	1.00
120_K	123_M	0.691	1.00
78_V	84_A	0.690	1.00
113_A	116_K	0.685	1.00
80_D	84_A	0.677	1.00
66_I	69_R	0.676	1.00
151_E	156_H	0.676	1.00
117_P	120_K	0.675	1.00
133_T	138_F	0.672	1.00
109_L	112_L	0.672	1.00
73_A	77_D	0.669	1.00
23_L	33_K	0.666	1.00
68_S	129_R	0.664	1.00
31_H	35_A	0.662	1.00
20_A	23_L	0.660	1.00
18_L	66_I	0.658	1.00
144_R	148_A	0.654	1.00
94_S	166_R	0.652	1.00
131_Q	144_R	0.647	1.00
148_A	151_E	0.642	1.00
45_M	50_S	0.637	1.00
141_G	145_A	0.635	1.00
22_K	104_E	0.635	1.00
103_M	108_Q	0.635	1.00
74_F	78_V	0.633	1.00
72_Q	129_R	0.632	1.00
108_Q	111_A	0.628	1.00
78_V	87_A	0.623	1.00
42_L	45_M	0.623	1.00
142_T	145_A	0.620	1.00
117_P	121_T	0.619	1.00
125_N	128_Q	0.609	1.00
57_L	122_V	0.603	1.00
26_I	29_V	0.598	1.00
149_F	152_G	0.594	1.00
53_D	118_L	0.591	1.00
35_A	41_P	0.584	1.00
81_A	84_A	0.582	1.00
94_S	97_V	0.581	1.00
15_Q	18_L	0.579	1.00
38_A	41_P	0.578	1.00
66_I	99_T	0.575	1.00
105_L	109_L	0.575	1.00
148_A	156_H	0.570	1.00
89_T	92_I	0.569	1.00
20_A	30_T	0.567	1.00
123_M	126_W	0.566	1.00
86_Q	89_T	0.562	1.00
141_G	168_E	0.558	1.00
121_T	124_Q	0.553	1.00
113_A	117_P	0.540	1.00
92_I	96_Q	0.539	1.00
74_F	77_D	0.536	1.00
6_D	48_Y	0.536	1.00
26_I	53_D	0.534	1.00
115_R	118_L	0.531	1.00
127_M	130_S	0.530	1.00
106_M	109_L	0.530	1.00
17_T	34_I	0.528	1.00
38_A	42_L	0.527	1.00
47_Y	50_S	0.525	1.00
41_P	48_Y	0.521	1.00
70_Q	74_F	0.521	1.00
27_H	112_L	0.520	1.00
81_A	137_W	0.519	1.00
126_W	137_W	0.518	1.00
34_I	38_A	0.514	1.00
135_E	139_E	0.513	1.00
130_S	138_F	0.510	1.00
127_M	137_W	0.509	1.00
124_Q	127_M	0.509	1.00
79_S	87_A	0.507	1.00
66_I	70_Q	0.506	1.00
111_A	115_R	0.503	1.00
144_R	147_D	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
2dg8A	2	0.9719	100	0.189	Contact Map
3htaA	2	1	100	0.2	Contact Map
2np5A	3	0.9551	100	0.235	Contact Map
4kwaA	2	0.9775	100	0.238	Contact Map
3v6gA	2	0.9382	100	0.238	Contact Map
3he0A	2	0.9607	99.9	0.245	Contact Map
2gfnA	2	0.9888	99.9	0.245	Contact Map
3e7qA	2	1	99.9	0.245	Contact Map
2qkoA	2	0.9045	99.9	0.246	Contact Map
3g7rA	2	1	99.9	0.247	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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