ACRR - ECOLI - GREMLIN Contacts

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ACRR - HTH-type transcriptional regulator AcrR

UniProt:	P0ACS9	Sequences: MARKTKQEAQETRQHILDVALRLFSQQGVSSTSLGEIAKAAGVTRGAIYWHFKDKSDLFSEIWELSESNIGELELEYQAKFPGDPLSVLREILIHVLESTVTEERRRLLMEIIFHKCEFVGEMAVVQQAQRNLCLESYDRIEQTLKHCIEAKMLPADLMTRRAAIIMRGYISGLMENWLFAPQSFDLKKEARDYVAILLEMYLLCPTLRNPATNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12116
Length:	215 (189)
Sequences:	44375 (35287)
Seq/√Len:	2566.7

ECOLI - ACRR ENVR SLMA UIDR RUTR COMR FABR NEMR BETI BDCR YJDC YBIH RCDA
BACSU - FADR YFIR YHGD PKSA YVDT BSCR YDGC YTTP YVKB YEZE LMRA YVAF YXAF YDES 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
35_G	45_R	4.020	1.00
27_Q	36_E	3.961	1.00
22_R	40_A	3.470	1.00
53_K	57_D	2.684	1.00
24_F	32_T	2.441	1.00
54_D	57_D	2.217	1.00
38_A	48_I	2.116	1.00
142_E	161_R	2.113	1.00
23_L	40_A	2.030	1.00
13_R	61_E	1.978	1.00
142_E	146_K	1.960	1.00
26_Q	40_A	1.957	1.00
23_L	32_T	1.950	1.00
23_L	36_E	1.931	1.00
14_Q	65_L	1.926	1.00
19_V	40_A	1.922	1.00
12_T	15_H	1.896	1.00
88_V	147_H	1.894	1.00
23_L	27_Q	1.866	1.00
84_D	87_S	1.845	1.00
35_G	39_K	1.842	1.00
15_H	19_V	1.811	1.00
19_V	22_R	1.746	1.00
146_K	150_E	1.738	1.00
146_K	160_T	1.703	1.00
44_T	47_A	1.680	1.00
21_L	65_L	1.625	1.00
14_Q	18_D	1.602	1.00
17_L	61_E	1.567	1.00
146_K	149_I	1.563	1.00
20_A	24_F	1.554	1.00
34_L	49_Y	1.530	1.00
61_E	64_E	1.512	1.00
34_L	45_R	1.509	1.00
36_E	40_A	1.506	1.00
33_S	36_E	1.498	1.00
22_R	26_Q	1.497	1.00
162_R	193_D	1.484	1.00
21_L	66_S	1.465	1.00
36_E	39_K	1.464	1.00
75_L	140_R	1.453	1.00
13_R	51_H	1.450	1.00
65_L	69_N	1.436	1.00
32_T	37_I	1.423	1.00
60_S	64_E	1.419	1.00
90_R	192_R	1.413	1.00
147_H	151_A	1.406	1.00
166_I	170_Y	1.369	1.00
11_E	15_H	1.361	1.00
64_E	129_A	1.326	1.00
34_L	48_I	1.312	1.00
20_A	58_L	1.305	1.00
21_L	62_I	1.302	1.00
28_G	32_T	1.299	1.00
52_F	61_E	1.272	1.00
149_I	156_A	1.260	1.00
18_D	65_L	1.259	1.00
148_C	154_L	1.256	1.00
47_A	50_W	1.255	1.00
94_I	192_R	1.254	1.00
27_Q	31_S	1.239	1.00
94_I	191_A	1.235	1.00
90_R	94_I	1.232	1.00
73_L	95_H	1.224	1.00
138_Y	165_I	1.211	1.00
19_V	23_L	1.209	1.00
159_M	162_R	1.179	1.00
24_F	29_V	1.169	1.00
87_S	91_E	1.166	1.00
44_T	50_W	1.165	1.00
43_V	47_A	1.163	1.00
60_S	129_A	1.163	1.00
88_V	144_T	1.156	1.00
28_G	31_S	1.149	1.00
148_C	153_M	1.146	1.00
48_I	58_L	1.141	1.00
94_I	188_K	1.140	1.00
45_R	49_Y	1.140	1.00
86_L	199_L	1.138	1.00
86_L	90_R	1.124	1.00
196_A	200_E	1.124	1.00
91_E	94_I	1.119	1.00
138_Y	142_E	1.106	1.00
11_E	14_Q	1.096	1.00
12_T	51_H	1.094	1.00
57_D	61_E	1.077	1.00
46_G	50_W	1.075	1.00
29_V	59_F	1.062	1.00
56_S	125_V	1.061	1.00
56_S	60_S	1.060	1.00
144_T	148_C	1.059	1.00
140_R	143_Q	1.057	1.00
47_A	51_H	1.054	1.00
57_D	60_S	1.049	1.00
162_R	189_K	1.046	1.00
56_S	123_M	1.041	1.00
178_W	181_A	1.041	1.00
90_R	195_V	1.033	1.00
17_L	52_F	1.030	1.00
18_D	22_R	1.030	1.00
19_V	41_A	1.024	1.00
27_Q	40_A	1.024	1.00
17_L	62_I	1.023	1.00
20_A	62_I	1.020	1.00
37_I	58_L	1.018	1.00
64_E	68_S	1.009	1.00
186_D	189_K	1.007	1.00
110_M	113_I	1.004	1.00
21_L	25_S	1.004	1.00
83_G	91_E	1.004	1.00
169_G	173_G	0.995	1.00
73_L	76_E	0.992	1.00
77_Y	95_H	0.989	1.00
9_A	50_W	0.974	1.00
49_Y	54_D	0.974	1.00
129_A	132_N	0.964	1.00
71_G	136_E	0.957	1.00
85_P	151_A	0.950	1.00
142_E	160_T	0.945	1.00
61_E	65_L	0.941	1.00
113_I	116_K	0.935	1.00
149_I	157_D	0.926	1.00
135_L	139_D	0.926	1.00
84_D	153_M	0.924	1.00
90_R	196_A	0.921	1.00
87_S	90_R	0.920	1.00
91_E	95_H	0.915	1.00
10_Q	14_Q	0.911	1.00
143_Q	147_H	0.910	1.00
65_L	68_S	0.909	1.00
138_Y	161_R	0.905	1.00
132_N	136_E	0.903	1.00
95_H	98_E	0.901	1.00
38_A	45_R	0.898	1.00
110_M	114_F	0.889	1.00
103_E	106_R	0.889	1.00
195_V	199_L	0.888	1.00
144_T	147_H	0.887	1.00
149_I	152_K	0.880	1.00
149_I	160_T	0.880	1.00
99_S	103_E	0.880	1.00
12_T	43_V	0.874	1.00
142_E	164_A	0.869	1.00
7_Q	11_E	0.868	1.00
82_P	88_V	0.863	1.00
161_R	165_I	0.860	1.00
139_D	143_Q	0.856	1.00
45_R	50_W	0.853	1.00
94_I	98_E	0.850	1.00
128_Q	132_N	0.849	1.00
39_K	45_R	0.847	1.00
77_Y	91_E	0.846	1.00
192_R	196_A	0.845	1.00
149_I	154_L	0.844	1.00
193_D	196_A	0.842	1.00
75_L	79_A	0.840	1.00
72_E	76_E	0.840	1.00
90_R	199_L	0.833	1.00
143_Q	146_K	0.832	1.00
8_E	11_E	0.828	1.00
189_K	193_D	0.826	1.00
177_N	180_F	0.822	1.00
147_H	150_E	0.821	1.00
71_G	75_L	0.817	1.00
68_S	72_E	0.815	1.00
188_K	192_R	0.813	1.00
23_L	26_Q	0.806	1.00
177_N	181_A	0.803	1.00
85_P	148_C	0.796	1.00
136_E	140_R	0.794	1.00
15_H	41_A	0.790	1.00
16_I	41_A	0.789	1.00
16_I	48_I	0.784	1.00
29_V	55_K	0.778	1.00
66_S	69_N	0.774	1.00
9_A	12_T	0.769	1.00
107_R	110_M	0.759	1.00
129_A	133_L	0.755	1.00
17_L	65_L	0.754	1.00
191_A	194_Y	0.752	1.00
15_H	18_D	0.749	1.00
83_G	87_S	0.746	1.00
94_I	195_V	0.744	1.00
162_R	166_I	0.739	1.00
111_E	115_H	0.731	1.00
139_D	142_E	0.730	1.00
191_A	195_V	0.729	1.00
127_Q	131_R	0.726	1.00
111_E	114_F	0.725	1.00
71_G	140_R	0.722	1.00
116_K	119_F	0.711	1.00
160_T	164_A	0.711	1.00
27_Q	32_T	0.710	1.00
155_P	158_L	0.705	1.00
131_R	135_L	0.704	1.00
82_P	87_S	0.701	1.00
41_A	44_T	0.701	1.00
69_N	72_E	0.700	1.00
193_D	197_I	0.698	1.00
124_A	128_Q	0.694	1.00
136_E	139_D	0.693	1.00
169_G	172_S	0.692	1.00
34_L	38_A	0.683	1.00
158_L	163_A	0.683	1.00
98_E	188_K	0.680	1.00
166_I	169_G	0.674	1.00
30_S	119_F	0.671	1.00
124_A	127_Q	0.670	1.00
72_E	75_L	0.670	1.00
17_L	21_L	0.661	1.00
149_I	158_L	0.659	1.00
8_E	12_T	0.655	1.00
155_P	200_E	0.654	1.00
26_Q	36_E	0.652	1.00
35_G	49_Y	0.643	1.00
170_Y	194_Y	0.641	1.00
93_L	167_M	0.639	1.00
145_L	160_T	0.638	1.00
188_K	191_A	0.637	1.00
18_D	21_L	0.636	1.00
78_Q	140_R	0.632	1.00
101_V	187_L	0.632	1.00
159_M	193_D	0.631	1.00
22_R	105_R	0.629	1.00
98_E	102_T	0.624	1.00
185_F	188_K	0.621	1.00
162_R	165_I	0.620	1.00
145_L	149_I	0.619	1.00
12_T	47_A	0.619	1.00
64_E	132_N	0.616	1.00
34_L	55_K	0.614	1.00
145_L	167_M	0.613	1.00
29_V	32_T	0.613	1.00
122_E	125_V	0.612	1.00
190_E	194_Y	0.605	1.00
64_E	133_L	0.602	1.00
98_E	191_A	0.602	1.00
29_V	56_S	0.596	1.00
7_Q	10_Q	0.588	1.00
16_I	51_H	0.585	1.00
172_S	176_E	0.581	1.00
90_R	93_L	0.581	1.00
131_R	134_C	0.579	1.00
187_L	191_A	0.578	1.00
68_S	133_L	0.575	1.00
76_E	95_H	0.570	1.00
45_R	48_I	0.570	1.00
24_F	59_F	0.567	1.00
82_P	91_E	0.556	1.00
187_L	190_E	0.556	1.00
185_F	189_K	0.555	1.00
98_E	187_L	0.554	1.00
50_W	53_K	0.554	1.00
21_L	69_N	0.553	1.00
192_R	195_V	0.553	1.00
85_P	153_M	0.553	1.00
149_I	155_P	0.552	1.00
9_A	51_H	0.552	1.00
160_T	163_A	0.551	1.00
110_M	115_H	0.542	1.00
128_Q	131_R	0.538	1.00
84_D	88_V	0.538	1.00
146_K	161_R	0.533	1.00
41_A	45_R	0.528	1.00
73_L	99_S	0.528	1.00
20_A	37_I	0.524	1.00
95_H	99_S	0.523	1.00
38_A	43_V	0.523	1.00
159_M	163_A	0.521	1.00
81_F	91_E	0.521	1.00
140_R	144_T	0.519	1.00
134_C	138_Y	0.515	1.00
167_M	198_L	0.514	1.00
88_V	148_C	0.512	1.00
16_I	43_V	0.512	1.00
12_T	50_W	0.512	1.00
12_T	44_T	0.512	1.00
43_V	51_H	0.511	1.00
156_A	159_M	0.510	1.00
196_A	199_L	0.509	1.00
67_E	133_L	0.506	1.00
133_L	136_E	0.504	1.00
93_L	96_V	0.501	1.00
7_Q	12_T	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	0.9581	100	0.176	Contact Map
3lhqA	2	0.9814	100	0.203	Contact Map
2w53A	2	0.9349	100	0.207	Contact Map
2wuiA	2	0.9256	100	0.215	Contact Map
4udsA	2	0.8744	100	0.22	Contact Map
3vibA	2	0.9442	100	0.221	Contact Map
2ibdA	2	0.893	100	0.232	Contact Map
2gfnA	2	0.8977	100	0.235	Contact Map
3npiA	2	0.9349	100	0.245	Contact Map
4cgrA	2	0.893	100	0.246	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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