YCBG - BACSU - GREMLIN Contacts

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YCBG - Uncharacterized HTH-type transcriptional regulator YcbG

UniProt:	P42239	Sequences: MYEGLEDLKVDTVNRKTLAKQVIERIVHLLSSGQLRAGDKLPTEMELMDILHVSRPVLREALSSLETLGVITRKTRGGTYFNDKIGMQPFSVMLALATDNLPAIIEARMALELGLVTIAAEKINEEELQRLQKTIDDIANSTDNHYGEADKEFHRIIALSANNPVVEGMIQSLLITHAKIDSQIPYRERDVTVEYHKKIYDALAKRDPYKAHYHMYEHLKFVRDKILKGMDEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	233 (200)
Sequences:	24143 (17978)
Seq/√Len:	1271.2

ECOLI - NANR PDHR EXUR LLDR GLCC UXUR MCBR YDFH DGOR FADR YIEP YJJM CSIR FRLR YEGW YIDP PHNF YIHL MNGR
BACSU - YCBG YDHC GNTR LUTR YMFC YVOA YURK TRER YYDK YBGA GMUR
SULSO - Q97YR4

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
132_Q	204_A	3.691	1.00
117_T	212_H	3.323	1.00
207_D	210_K	2.929	1.00
36_R	39_D	2.820	1.00
139_A	197_K	2.807	1.00
29_L	34_Q	2.742	1.00
29_L	50_I	2.400	1.00
110_A	114_G	2.306	1.00
44_E	55_R	2.268	1.00
130_R	156_I	2.145	1.00
23_I	64_S	2.123	1.00
103_A	164_P	2.091	1.00
27_V	68_L	2.091	1.00
72_T	82_N	2.064	1.00
109_M	220_K	2.025	1.00
22_V	53_V	1.957	1.00
121_E	208_P	1.946	1.00
106_E	118_I	1.928	1.00
73_R	79_T	1.868	1.00
202_A	210_K	1.791	1.00
22_V	51_L	1.783	1.00
127_E	162_N	1.746	1.00
159_L	167_E	1.734	1.00
128_L	204_A	1.731	1.00
156_I	159_L	1.724	1.00
124_N	127_E	1.712	1.00
25_R	29_L	1.683	1.00
135_I	200_Y	1.653	1.00
113_L	216_Y	1.635	1.00
16_K	24_E	1.632	1.00
195_Y	221_F	1.612	1.00
107_A	169_M	1.577	1.00
113_L	212_H	1.574	1.00
28_H	32_S	1.571	1.00
117_T	208_P	1.570	1.00
212_H	216_Y	1.564	1.00
114_G	117_T	1.531	1.00
210_K	214_H	1.529	1.00
154_H	196_H	1.508	1.00
201_D	205_K	1.460	1.00
23_I	68_L	1.449	1.00
198_K	214_H	1.447	1.00
155_R	171_Q	1.409	1.00
165_V	176_T	1.402	1.00
74_K	77_G	1.392	1.00
116_V	211_A	1.392	1.00
168_G	172_S	1.368	1.00
127_E	160_S	1.365	1.00
139_A	193_V	1.352	1.00
109_M	216_Y	1.343	1.00
137_D	149_A	1.340	1.00
205_K	210_K	1.332	1.00
134_T	149_A	1.330	1.00
158_A	170_I	1.326	1.00
132_Q	136_D	1.325	1.00
45_M	49_D	1.315	1.00
123_I	128_L	1.306	1.00
132_Q	200_Y	1.299	1.00
46_E	50_I	1.292	1.00
208_P	212_H	1.288	1.00
40_K	80_Y	1.279	1.00
197_K	201_D	1.269	1.00
133_K	137_D	1.265	1.00
109_M	223_R	1.264	1.00
103_A	165_V	1.234	1.00
109_M	113_L	1.215	1.00
43_T	46_E	1.207	1.00
134_T	156_I	1.202	1.00
137_D	152_E	1.199	1.00
108_R	112_E	1.191	1.00
74_K	80_Y	1.191	1.00
21_Q	25_R	1.184	1.00
213_Y	217_E	1.178	1.00
25_R	28_H	1.178	1.00
195_Y	218_H	1.162	1.00
102_P	227_L	1.161	1.00
135_I	197_K	1.151	1.00
25_R	51_L	1.147	1.00
47_L	58_L	1.146	1.00
123_I	206_R	1.137	1.00
155_R	159_L	1.131	1.00
35_L	81_F	1.123	1.00
66_E	73_R	1.114	1.00
216_Y	220_K	1.108	1.00
152_E	156_I	1.108	1.00
150_D	154_H	1.107	1.00
123_I	160_S	1.105	1.00
117_T	209_Y	1.105	1.00
157_I	203_L	1.095	1.00
210_K	213_Y	1.093	1.00
29_L	51_L	1.092	1.00
223_R	227_L	1.074	1.00
102_P	223_R	1.074	1.00
135_I	138_I	1.070	1.00
200_Y	204_A	1.067	1.00
123_I	127_E	1.066	1.00
128_L	200_Y	1.066	1.00
113_L	117_T	1.065	1.00
72_T	80_Y	1.065	1.00
201_D	204_A	1.061	1.00
116_V	215_M	1.060	1.00
196_H	218_H	1.056	1.00
66_E	71_I	1.049	1.00
60_E	63_S	1.046	1.00
97_A	100_N	1.043	1.00
44_E	59_R	1.043	1.00
115_L	158_A	1.026	1.00
130_R	159_L	1.022	1.00
116_V	120_A	1.019	1.00
103_A	163_N	1.017	1.00
156_I	160_S	1.016	1.00
134_T	152_E	1.002	1.00
130_R	133_K	1.001	1.00
128_L	206_R	0.999	1.00
149_A	152_E	0.993	1.00
132_Q	197_K	0.989	1.00
106_E	163_N	0.985	1.00
16_K	21_Q	0.975	1.00
19_A	64_S	0.971	1.00
169_M	172_S	0.968	1.00
135_I	139_A	0.966	1.00
145_H	148_E	0.963	1.00
120_A	208_P	0.960	1.00
202_A	207_D	0.956	1.00
114_G	212_H	0.948	1.00
198_K	217_E	0.948	1.00
29_L	35_L	0.947	1.00
198_K	210_K	0.937	1.00
154_H	218_H	0.937	1.00
129_Q	133_K	0.933	1.00
136_D	139_A	0.933	1.00
194_E	198_K	0.932	1.00
161_A	167_E	0.924	1.00
130_R	134_T	0.923	1.00
118_I	122_K	0.923	1.00
30_L	81_F	0.916	1.00
148_E	152_E	0.910	1.00
40_K	78_G	0.909	1.00
62_L	79_T	0.907	1.00
209_Y	213_Y	0.906	1.00
27_V	70_V	0.902	1.00
128_L	132_Q	0.894	1.00
114_G	118_I	0.893	1.00
198_K	201_D	0.889	1.00
71_I	79_T	0.887	1.00
18_L	21_Q	0.885	1.00
153_F	200_Y	0.883	1.00
77_G	80_Y	0.879	1.00
120_A	203_L	0.877	1.00
74_K	78_G	0.875	1.00
64_S	67_T	0.869	1.00
48_M	58_L	0.868	1.00
167_E	171_Q	0.867	1.00
27_V	31_S	0.863	1.00
112_E	154_H	0.857	1.00
209_Y	212_H	0.856	1.00
134_T	137_D	0.847	1.00
62_L	71_I	0.845	1.00
107_A	165_V	0.844	1.00
46_E	49_D	0.839	1.00
137_D	140_N	0.837	1.00
199_I	215_M	0.836	1.00
63_S	66_E	0.834	1.00
23_I	27_V	0.834	1.00
54_S	57_V	0.830	1.00
108_R	219_L	0.826	1.00
100_N	165_V	0.822	1.00
136_D	140_N	0.822	1.00
122_K	162_N	0.822	1.00
125_E	129_Q	0.817	1.00
40_K	43_T	0.816	1.00
123_I	203_L	0.814	1.00
17_T	20_K	0.812	1.00
20_K	64_S	0.807	1.00
53_V	58_L	0.803	1.00
141_S	145_H	0.803	1.00
99_D	162_N	0.796	1.00
47_L	62_L	0.796	1.00
199_I	214_H	0.790	1.00
193_V	197_K	0.786	1.00
99_D	103_A	0.783	1.00
132_Q	201_D	0.777	1.00
120_A	211_A	0.771	1.00
120_A	206_R	0.769	1.00
127_E	130_R	0.769	1.00
63_S	73_R	0.766	1.00
106_E	223_R	0.765	1.00
18_L	57_V	0.764	1.00
220_K	224_D	0.764	1.00
165_V	169_M	0.763	1.00
190_D	194_E	0.762	1.00
19_A	23_I	0.755	1.00
138_I	146_Y	0.753	1.00
165_V	168_G	0.751	1.00
150_D	196_H	0.750	1.00
119_A	160_S	0.744	1.00
125_E	206_R	0.741	1.00
131_L	156_I	0.739	1.00
136_D	197_K	0.734	1.00
118_I	121_E	0.729	1.00
202_A	214_H	0.726	1.00
106_E	122_K	0.720	1.00
198_K	202_A	0.718	1.00
117_T	121_E	0.716	1.00
145_H	149_A	0.710	1.00
16_K	20_K	0.710	1.00
105_I	222_V	0.707	1.00
64_S	68_L	0.706	1.00
118_I	163_N	0.705	1.00
140_N	144_N	0.698	1.00
131_L	200_Y	0.696	1.00
155_R	174_L	0.696	1.00
214_H	217_E	0.695	1.00
34_Q	50_I	0.694	1.00
137_D	145_H	0.691	1.00
130_R	152_E	0.685	1.00
129_Q	132_Q	0.682	1.00
217_E	221_F	0.668	1.00
133_K	136_D	0.667	1.00
213_Y	216_Y	0.665	1.00
129_Q	204_A	0.663	1.00
155_R	167_E	0.662	1.00
139_A	143_D	0.662	1.00
199_I	211_A	0.661	1.00
107_A	166_V	0.659	1.00
137_D	141_S	0.658	1.00
221_F	225_K	0.656	1.00
119_A	123_I	0.648	1.00
199_I	218_H	0.635	1.00
127_E	159_L	0.635	1.00
135_I	193_V	0.633	1.00
116_V	208_P	0.633	1.00
151_K	178_A	0.629	1.00
76_R	79_T	0.628	1.00
127_E	156_I	0.621	1.00
57_V	61_A	0.616	1.00
151_K	174_L	0.616	1.00
152_E	155_R	0.615	1.00
107_A	111_L	0.614	1.00
128_L	203_L	0.613	1.00
109_M	219_L	0.609	1.00
141_S	149_A	0.608	1.00
220_K	223_R	0.602	1.00
195_Y	198_K	0.594	1.00
106_E	114_G	0.594	1.00
35_L	39_D	0.593	1.00
29_L	33_G	0.590	1.00
100_N	164_P	0.590	1.00
19_A	60_E	0.588	1.00
146_Y	192_T	0.580	1.00
125_E	204_A	0.580	1.00
37_A	83_D	0.579	1.00
115_L	161_A	0.578	1.00
51_L	58_L	0.577	1.00
63_S	67_T	0.572	1.00
110_A	166_V	0.568	1.00
224_D	227_L	0.567	1.00
98_T	102_P	0.563	1.00
138_I	193_V	0.562	1.00
82_N	179_K	0.555	1.00
15_R	21_Q	0.555	1.00
107_A	115_L	0.555	1.00
113_L	208_P	0.554	1.00
131_L	160_S	0.553	1.00
119_A	161_A	0.553	1.00
112_E	196_H	0.552	1.00
41_L	71_I	0.551	1.00
113_L	215_M	0.548	1.00
126_E	130_R	0.547	1.00
111_L	170_I	0.544	1.00
202_A	208_P	0.543	1.00
38_G	83_D	0.541	1.00
45_M	48_M	0.541	1.00
168_G	176_T	0.540	1.00
75_T	78_G	0.538	1.00
187_R	190_D	0.537	1.00
151_K	155_R	0.535	1.00
117_T	216_Y	0.533	1.00
115_L	166_V	0.531	1.00
188_E	225_K	0.530	1.00
188_E	191_V	0.530	1.00
35_L	41_L	0.528	1.00
141_S	144_N	0.527	1.00
96_L	179_K	0.527	1.00
150_D	192_T	0.521	1.00
110_A	113_L	0.518	1.00
49_D	52_H	0.518	1.00
158_A	174_L	0.517	1.00
217_E	220_K	0.513	1.00
119_A	157_I	0.511	1.00
140_N	143_D	0.510	1.00
146_Y	189_R	0.510	1.00
44_E	79_T	0.509	1.00
26_I	47_L	0.507	1.00
29_L	32_S	0.507	1.00
107_A	110_A	0.505	1.00
31_S	70_V	0.505	1.00
211_A	215_M	0.503	1.00
112_E	219_L	0.502	1.00
99_D	164_P	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
3sxyA	2	0.8541	100	0.188	Contact Map
4p96A	2	0.9528	100	0.202	Contact Map
3c7jA	4	0.9442	100	0.207	Contact Map
3ihuA	1	0.8584	100	0.207	Contact Map
4p9fA	1	0.8712	100	0.213	Contact Map
2hs5A	1	0.8627	100	0.217	Contact Map
2di3A	2	0.927	100	0.218	Contact Map
1hw1A	2	0.9313	100	0.235	Contact Map
3ic7A	2	0.4764	99.9	0.524	Contact Map
3by6A	2	0.5322	99.9	0.528	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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