BAER - ECOLI - GREMLIN Contacts

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BAER - Transcriptional regulatory protein BaeR

UniProt:	P69228	Sequences: MTELPIDENTPRILIVEDEPKLGQLLIDYLRAASYAPTLISHGDQVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFSDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRCKPQRELQQQDAESPLIIDEGRFQASWRGKMLDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESLDAEQSFIRAVYGVGYRWEADACRIV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11618
Length:	240 (207)
Sequences:	72923 (51440)
Seq/√Len:	3575.3

ECOLI - BAER CREB KDPE ARCA RSTA YEDW OMPR CPXR PHOP TORR CUSR QSEB PHOB BASR DPIA FIMZ DCUR NARL NARP UVRY EVGA YGEK YJJQ YHJB BGLJ RCSB BARA CSGD UHPA TORS RSSB RCSA RCSC CHEB ARCB EVGS YEHT YPDB GLRR NTRC ZRAR ATOC RCSD
BACSU - YVRH YCBL YYCF YVCP YXDJ YRKP RESD YKOG PHOP YCLJ BCER CSSR CITT MALR DCTR YFIK YXJL DEGU CMPA YBDJ LIAR YDFI YVFU YHCZ DESR GLNL CHEB YESN LYTT SP0A NATR CHEV
HALSA - CHEB Q9HR09 Q9HNM3 BAT Q9HRE5 O51970 Q9HP91

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_G	39_L	3.680	1.00
23_G	41_S	3.201	1.00
27_I	39_L	3.114	1.00
16_V	46_V	2.697	1.00
47_L	75_E	2.596	1.00
44_D	66_G	2.564	1.00
38_T	55_P	2.414	1.00
67_T	75_E	2.380	1.00
43_G	67_T	2.365	1.00
42_H	66_G	2.336	1.00
51_R	79_F	2.329	1.00
12_R	38_T	2.207	1.00
12_R	36_A	2.115	1.00
29_Y	114_P	2.091	1.00
27_I	31_R	2.068	1.00
33_A	118_V	2.018	1.00
40_I	49_Y	1.970	1.00
96_R	116_E	1.891	1.00
63_M	90_K	1.862	1.00
41_S	45_Q	1.853	1.00
199_R	202_D	1.837	1.00
164_A	167_R	1.820	1.00
42_H	45_Q	1.767	1.00
38_T	49_Y	1.756	1.00
60_L	72_L	1.730	1.00
86_M	99_G	1.728	1.00
73_C	84_I	1.711	1.00
93_E	113_S	1.706	1.00
77_R	105_D	1.699	1.00
14_L	40_I	1.674	1.00
182_R	202_D	1.637	1.00
75_E	79_F	1.628	1.00
11_P	125_L	1.588	1.00
170_K	174_H	1.571	1.00
67_T	71_T	1.569	1.00
171_T	188_H	1.555	1.00
86_M	104_A	1.549	1.00
49_Y	53_T	1.543	1.00
30_L	121_V	1.532	1.00
38_T	53_T	1.521	1.00
43_G	72_L	1.519	1.00
68_D	71_T	1.490	1.00
106_D	120_R	1.468	1.00
181_S	184_Q	1.463	1.00
204_H	207_N	1.457	1.00
49_Y	52_Q	1.456	1.00
90_K	95_D	1.449	1.00
75_E	78_R	1.433	1.00
58_I	82_I	1.422	1.00
74_R	102_I	1.420	1.00
180_F	188_H	1.411	1.00
44_D	67_T	1.404	1.00
50_V	76_I	1.402	1.00
71_T	74_R	1.389	1.00
85_V	124_I	1.387	1.00
57_L	121_V	1.372	1.00
20_P	41_S	1.361	1.00
73_C	86_M	1.361	1.00
165_E	211_K	1.357	1.00
47_L	72_L	1.341	1.00
144_I	153_S	1.326	1.00
175_E	178_K	1.305	1.00
151_Q	158_M	1.268	1.00
142_P	155_R	1.253	1.00
17_E	23_G	1.247	1.00
62_L	70_L	1.244	1.00
35_Y	122_K	1.230	1.00
16_V	64_L	1.230	1.00
48_P	52_Q	1.225	1.00
105_D	127_R	1.220	1.00
49_Y	55_P	1.220	1.00
60_L	73_C	1.220	1.00
12_R	53_T	1.219	1.00
47_L	67_T	1.212	1.00
14_L	55_P	1.207	1.00
62_L	86_M	1.207	1.00
18_D	61_D	1.206	1.00
45_Q	48_P	1.200	1.00
139_A	144_I	1.193	1.00
40_I	46_V	1.176	1.00
44_D	48_P	1.166	1.00
92_E	95_D	1.165	1.00
184_Q	188_H	1.164	1.00
101_E	122_K	1.155	1.00
45_Q	49_Y	1.142	1.00
70_L	99_G	1.132	1.00
33_A	122_K	1.132	1.00
70_L	98_L	1.130	1.00
166_F	170_K	1.127	1.00
34_S	122_K	1.124	1.00
14_L	46_V	1.115	1.00
171_T	175_E	1.110	1.00
171_T	180_F	1.108	1.00
118_V	122_K	1.098	1.00
105_D	124_I	1.095	1.00
183_E	198_D	1.094	1.00
13_I	35_Y	1.094	1.00
147_E	170_K	1.088	1.00
146_D	149_R	1.083	1.00
93_E	97_L	1.077	1.00
57_L	125_L	1.060	1.00
145_I	173_S	1.058	1.00
203_S	206_K	1.057	1.00
98_L	102_I	1.051	1.00
199_R	203_S	1.028	1.00
94_I	98_L	1.025	1.00
119_A	123_T	1.017	1.00
116_E	119_A	1.016	1.00
40_I	45_Q	1.015	1.00
14_L	49_Y	1.014	1.00
74_R	98_L	1.014	1.00
167_R	170_K	1.013	1.00
163_P	167_R	1.006	1.00
47_L	51_R	0.998	1.00
96_R	109_C	0.998	1.00
15_I	26_L	0.983	1.00
200_T	204_H	0.982	1.00
11_P	35_Y	0.979	1.00
70_L	102_I	0.974	1.00
216_D	219_Q	0.972	1.00
46_V	50_V	0.966	1.00
46_V	72_L	0.965	1.00
171_T	185_L	0.965	1.00
27_I	37_P	0.964	1.00
60_L	84_I	0.960	1.00
215_L	219_Q	0.946	1.00
58_I	76_I	0.944	1.00
145_I	166_F	0.940	1.00
180_F	184_Q	0.938	1.00
97_L	101_E	0.937	1.00
24_Q	39_L	0.937	1.00
26_L	87_V	0.936	1.00
62_L	68_D	0.934	1.00
20_P	24_Q	0.930	1.00
153_S	158_M	0.927	1.00
21_K	25_L	0.926	1.00
12_R	56_D	0.912	1.00
14_L	50_V	0.911	1.00
16_V	40_I	0.906	1.00
148_G	178_K	0.905	1.00
124_I	127_R	0.902	1.00
16_V	58_I	0.902	1.00
35_Y	118_V	0.891	1.00
73_C	102_I	0.888	1.00
71_T	75_E	0.886	1.00
178_K	184_Q	0.882	1.00
15_I	37_P	0.878	1.00
199_R	206_K	0.876	1.00
48_P	51_R	0.872	1.00
20_P	23_G	0.865	1.00
60_L	86_M	0.857	1.00
198_D	202_D	0.847	1.00
64_L	72_L	0.841	1.00
205_I	209_R	0.839	1.00
73_C	104_A	0.836	1.00
162_T	211_K	0.836	1.00
93_E	96_R	0.833	1.00
28_D	32_A	0.830	1.00
150_F	167_R	0.830	1.00
97_L	115_R	0.828	1.00
72_L	76_I	0.825	1.00
24_Q	27_I	0.821	1.00
59_L	117_V	0.815	1.00
114_P	118_V	0.814	1.00
12_R	55_P	0.812	1.00
58_I	84_I	0.809	1.00
214_S	224_A	0.806	1.00
91_I	109_C	0.806	1.00
98_L	101_E	0.805	1.00
62_L	95_D	0.802	1.00
207_N	210_R	0.798	1.00
183_E	187_N	0.797	1.00
59_L	87_V	0.794	1.00
116_E	120_R	0.792	1.00
123_T	128_C	0.791	1.00
214_S	220_S	0.790	1.00
76_I	80_S	0.787	1.00
50_V	82_I	0.782	1.00
182_R	198_D	0.781	1.00
62_L	90_K	0.780	1.00
85_V	120_R	0.777	1.00
26_L	117_V	0.777	1.00
94_I	115_R	0.776	1.00
74_R	78_R	0.774	1.00
206_K	210_R	0.771	1.00
123_T	126_R	0.770	1.00
83_P	105_D	0.768	1.00
22_L	112_Y	0.766	1.00
67_T	72_L	0.765	1.00
63_M	89_A	0.764	1.00
11_P	129_K	0.759	1.00
50_V	55_P	0.750	1.00
100_L	120_R	0.748	1.00
87_V	112_Y	0.745	1.00
95_D	98_L	0.743	1.00
24_Q	28_D	0.737	1.00
43_G	47_L	0.734	1.00
213_E	216_D	0.728	1.00
16_V	72_L	0.721	1.00
171_T	174_H	0.720	1.00
150_F	166_F	0.717	1.00
209_R	214_S	0.716	1.00
113_S	116_E	0.715	1.00
93_E	115_R	0.715	1.00
59_L	121_V	0.709	1.00
184_Q	187_N	0.708	1.00
47_L	50_V	0.707	1.00
168_L	172_L	0.706	1.00
13_I	57_L	0.705	1.00
85_V	106_D	0.700	1.00
167_R	171_T	0.698	1.00
101_E	119_A	0.695	1.00
43_G	66_G	0.692	1.00
203_S	207_N	0.691	1.00
153_S	156_G	0.689	1.00
202_D	205_I	0.685	1.00
125_L	128_C	0.682	1.00
30_L	35_Y	0.682	1.00
13_I	30_L	0.680	1.00
112_Y	117_V	0.677	1.00
15_I	39_L	0.669	1.00
50_V	58_I	0.669	1.00
174_H	188_H	0.665	1.00
17_E	64_L	0.665	1.00
25_L	29_Y	0.664	1.00
213_E	220_S	0.663	1.00
196_V	201_I	0.662	1.00
31_R	37_P	0.662	1.00
137_Q	144_I	0.660	1.00
23_G	27_I	0.660	1.00
96_R	113_S	0.655	1.00
15_I	27_I	0.655	1.00
29_Y	118_V	0.652	1.00
83_P	125_L	0.649	1.00
99_G	104_A	0.648	1.00
164_A	204_H	0.647	1.00
147_E	174_H	0.645	1.00
47_L	79_F	0.642	1.00
174_H	180_F	0.638	1.00
43_G	64_L	0.635	1.00
143_L	154_W	0.634	1.00
51_R	75_E	0.633	1.00
138_D	141_S	0.633	1.00
197_T	200_T	0.633	1.00
61_D	110_K	0.632	1.00
172_L	205_I	0.631	1.00
115_R	119_A	0.625	1.00
19_E	89_A	0.616	1.00
11_P	56_D	0.614	1.00
213_E	219_Q	0.614	1.00
135_Q	138_D	0.613	1.00
128_C	132_R	0.608	1.00
18_D	88_T	0.605	1.00
76_I	84_I	0.604	1.00
77_R	82_I	0.601	1.00
70_L	95_D	0.601	1.00
154_W	213_E	0.599	1.00
31_R	36_A	0.597	1.00
81_D	130_P	0.594	1.00
112_Y	116_E	0.592	1.00
154_W	215_L	0.591	1.00
154_W	157_K	0.587	1.00
145_I	170_K	0.585	1.00
59_L	85_V	0.581	1.00
142_P	154_W	0.580	1.00
19_E	22_L	0.579	1.00
29_Y	33_A	0.579	1.00
88_T	110_K	0.577	1.00
62_L	99_G	0.575	1.00
81_D	131_Q	0.574	1.00
45_Q	66_G	0.573	1.00
88_T	96_R	0.571	1.00
50_V	79_F	0.569	1.00
171_T	189_L	0.568	1.00
73_C	77_R	0.563	1.00
120_R	124_I	0.563	1.00
13_I	121_V	0.555	1.00
145_I	152_A	0.552	1.00
54_P	80_S	0.551	1.00
83_P	128_C	0.551	1.00
119_A	122_K	0.550	1.00
60_L	64_L	0.546	1.00
154_W	214_S	0.544	1.00
91_I	111_P	0.544	1.00
215_L	220_S	0.540	1.00
146_D	151_Q	0.539	1.00
77_R	83_P	0.536	1.00
88_T	107_Y	0.532	1.00
122_K	126_R	0.531	1.00
106_D	123_T	0.529	1.00
15_I	23_G	0.526	1.00
50_V	80_S	0.523	1.00
97_L	100_L	0.522	1.00
94_I	97_L	0.522	1.00
169_L	220_S	0.521	1.00
46_V	58_I	0.520	1.00
50_V	72_L	0.520	1.00
162_T	165_E	0.520	1.00
57_L	124_I	0.516	1.00
18_D	64_L	0.516	1.00
144_I	156_G	0.515	1.00
47_L	76_I	0.512	1.00
76_I	82_I	0.512	1.00
99_G	107_Y	0.512	1.00
22_L	25_L	0.509	1.00
42_H	64_L	0.507	1.00
121_V	125_L	0.503	1.00
214_S	219_Q	0.500	1.00
143_L	152_A	0.500	1.00
115_R	118_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
4b09A	2	0.9	100	0.187	Contact Map
3r0jA	2	0.925	100	0.237	Contact Map
2gwrA	1	0.9375	100	0.243	Contact Map
4kfcA	2	0.9375	100	0.243	Contact Map
2oqrA	2	0.9333	100	0.246	Contact Map
1ys7A	2	0.9333	100	0.248	Contact Map
1kgsA	1	0.9083	100	0.271	Contact Map
3q9sA	1	0.875	100	0.286	Contact Map
1p2fA	1	0.9	100	0.29	Contact Map
2hqrA	2	0.9167	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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