YJDC - ECOLI - GREMLIN Contacts

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YJDC - HTH-type transcriptional regulator YjdC

UniProt:	P0ACU7	Sequences: MQREDVLGEALKLLELQGIANTTLEMVAERVDYPLDELRRFWPDKEAILYDALRYLSQQIDVWRRQLMLDETQTAEQKLLARYQALSECVKNNRYPGCLFIAACTFYPDPGHPIHQLADQQKSAAYDFTHELLTTLEVDDPAMVAKQMELVLEGCLSRMLVNRSQADVDTAHRLAEDILRFARCRQGGALT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12176
Length:	191 (174)
Sequences:	36121 (28516)
Seq/√Len:	2161.8

ECOLI - YJDC BDCR NEMR BETI COMR ACRR SLMA RCDA UIDR ENVR FABR RUTR YBIH
BACSU - YXAF LMRA YEZE YFIR PKSA YVDT YHGD FADR YCNC YTTP YVKB YUXN BSCR YDGC YERO YVAF YOBS YDES
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
17_Q	26_M	4.253	1.00
25_E	35_L	4.139	1.00
12_K	30_R	3.655	1.00
43_P	47_A	2.732	1.00
132_L	138_V	2.288	1.00
14_L	22_T	2.281	1.00
130_H	134_T	2.213	1.00
4_E	55_Y	2.144	1.00
28_A	38_L	2.100	1.00
44_D	47_A	2.068	1.00
34_P	37_E	2.065	1.00
13_L	22_T	2.057	1.00
16_L	30_R	2.027	1.00
80_L	176_E	2.014	1.00
54_R	117_L	1.995	1.00
9_E	30_R	1.977	1.00
13_L	30_R	1.901	1.00
74_T	77_Q	1.899	1.00
5_D	9_E	1.894	1.00
11_L	55_Y	1.871	1.00
84_Q	172_H	1.792	1.00
10_A	14_L	1.776	1.00
25_E	29_E	1.748	1.00
24_L	39_R	1.612	1.00
126_Y	130_H	1.604	1.00
13_L	26_M	1.595	1.00
130_H	142_A	1.581	1.00
4_E	8_G	1.555	1.00
7_L	51_D	1.549	1.00
50_Y	54_R	1.546	1.00
126_Y	142_A	1.540	1.00
13_L	17_Q	1.534	1.00
51_D	54_R	1.532	1.00
24_L	35_L	1.529	1.00
133_L	136_L	1.521	1.00
12_K	16_L	1.501	1.00
11_L	52_A	1.498	1.00
8_G	55_Y	1.495	1.00
9_E	12_K	1.477	1.00
55_Y	59_Q	1.471	1.00
47_A	51_D	1.446	1.00
10_A	48_I	1.413	1.00
26_M	29_E	1.406	1.00
26_M	30_R	1.403	1.00
133_L	138_V	1.398	1.00
134_T	138_V	1.366	1.00
18_G	22_T	1.364	1.00
147_Q	151_V	1.354	1.00
19_I	49_L	1.345	1.00
37_E	40_R	1.333	1.00
24_L	38_L	1.329	1.00
140_D	143_M	1.313	1.00
37_E	41_F	1.300	1.00
128_F	132_L	1.289	1.00
23_T	26_M	1.284	1.00
42_W	51_D	1.278	1.00
80_L	84_Q	1.260	1.00
33_Y	37_E	1.256	1.00
11_L	56_L	1.224	1.00
102_A	106_F	1.201	1.00
34_P	40_R	1.197	1.00
14_L	19_I	1.183	1.00
7_L	52_A	1.182	1.00
36_D	40_R	1.175	1.00
134_T	141_P	1.160	1.00
22_T	27_V	1.160	1.00
46_E	50_Y	1.150	1.00
9_E	31_V	1.149	1.00
143_M	170_T	1.142	1.00
78_K	132_L	1.139	1.00
131_E	135_T	1.132	1.00
50_Y	113_P	1.125	1.00
9_E	13_L	1.121	1.00
39_R	44_D	1.121	1.00
54_R	58_Q	1.120	1.00
46_E	111_G	1.117	1.00
78_K	135_T	1.117	1.00
3_R	51_D	1.113	1.00
47_A	50_Y	1.102	1.00
126_Y	146_K	1.099	1.00
77_Q	81_A	1.096	1.00
27_V	48_I	1.091	1.00
173_R	176_E	1.091	1.00
63_W	85_A	1.082	1.00
172_H	176_E	1.082	1.00
18_G	21_N	1.070	1.00
7_L	42_W	1.067	1.00
122_K	126_Y	1.046	1.00
123_S	127_D	1.039	1.00
76_E	80_L	1.033	1.00
65_R	128_F	1.027	1.00
17_Q	21_N	1.023	1.00
35_L	39_R	1.021	1.00
130_H	141_P	1.006	1.00
117_L	120_Q	1.003	1.00
134_T	137_E	1.002	1.00
51_D	55_Y	0.994	1.00
61_D	124_A	0.992	1.00
150_L	154_G	0.988	1.00
103_A	106_F	0.988	1.00
46_E	113_P	0.985	1.00
166_A	170_T	0.972	1.00
81_A	84_Q	0.969	1.00
167_D	170_T	0.964	1.00
127_D	131_E	0.963	1.00
142_A	146_K	0.951	1.00
128_F	131_E	0.944	1.00
58_Q	62_V	0.927	1.00
35_L	40_R	0.927	1.00
28_A	35_L	0.926	1.00
77_Q	80_L	0.921	1.00
116_Q	120_Q	0.918	1.00
55_Y	58_Q	0.906	1.00
89_C	93_N	0.905	1.00
112_H	116_Q	0.903	1.00
143_M	173_R	0.902	1.00
87_S	169_D	0.897	1.00
132_L	137_E	0.889	1.00
63_W	66_Q	0.887	1.00
38_L	48_I	0.887	1.00
11_L	15_E	0.887	1.00
12_K	95_Y	0.884	1.00
131_E	134_T	0.882	1.00
8_G	12_K	0.881	1.00
14_L	49_L	0.877	1.00
84_Q	176_E	0.870	1.00
61_D	65_R	0.868	1.00
20_A	106_F	0.868	1.00
67_L	85_A	0.866	1.00
115_H	119_D	0.864	1.00
119_D	123_S	0.859	1.00
10_A	52_A	0.859	1.00
67_L	81_A	0.840	1.00
159_M	162_N	0.837	1.00
73_Q	81_A	0.835	1.00
124_A	127_D	0.829	1.00
120_Q	124_A	0.828	1.00
84_Q	88_E	0.822	1.00
62_V	66_Q	0.820	1.00
85_A	88_E	0.818	1.00
127_D	130_H	0.817	1.00
84_Q	169_D	0.811	1.00
29_E	35_L	0.809	1.00
25_E	39_R	0.806	1.00
5_D	31_V	0.802	1.00
56_L	59_Q	0.802	1.00
19_I	45_K	0.799	1.00
80_L	173_R	0.798	1.00
24_L	28_A	0.794	1.00
113_P	116_Q	0.790	1.00
17_Q	30_R	0.781	1.00
123_S	126_Y	0.780	1.00
72_T	77_Q	0.770	1.00
147_Q	150_L	0.767	1.00
72_T	78_K	0.765	1.00
6_V	31_V	0.760	1.00
133_L	137_E	0.760	1.00
97_G	102_A	0.755	1.00
88_E	92_N	0.744	1.00
132_L	136_L	0.740	1.00
78_K	131_E	0.738	1.00
81_A	85_A	0.734	1.00
132_L	135_T	0.733	1.00
93_N	96_P	0.733	1.00
50_Y	117_L	0.733	1.00
103_A	107_Y	0.720	1.00
106_F	110_P	0.720	1.00
6_V	41_F	0.720	1.00
19_I	46_E	0.712	1.00
98_C	101_I	0.706	1.00
31_V	34_P	0.703	1.00
73_Q	77_Q	0.701	1.00
28_A	34_P	0.699	1.00
150_L	158_R	0.693	1.00
33_Y	41_F	0.691	1.00
99_L	103_A	0.676	1.00
17_Q	22_T	0.676	1.00
121_Q	125_A	0.675	1.00
169_D	173_R	0.674	1.00
65_R	124_A	0.666	1.00
143_M	147_Q	0.665	1.00
5_D	8_G	0.665	1.00
140_D	144_V	0.664	1.00
110_P	114_I	0.664	1.00
112_H	115_H	0.660	1.00
141_P	145_A	0.660	1.00
158_R	162_N	0.654	1.00
28_A	31_V	0.654	1.00
88_E	168_V	0.653	1.00
116_Q	119_D	0.651	1.00
113_P	117_L	0.646	1.00
174_L	177_D	0.644	1.00
7_L	55_Y	0.636	1.00
97_G	100_F	0.626	1.00
169_D	172_H	0.625	1.00
153_E	158_R	0.622	1.00
76_E	176_E	0.620	1.00
151_V	154_G	0.620	1.00
83_Y	148_M	0.620	1.00
54_R	120_Q	0.618	1.00
168_V	172_H	0.618	1.00
11_L	59_Q	0.611	1.00
8_G	11_L	0.609	1.00
143_M	174_L	0.607	1.00
117_L	121_Q	0.603	1.00
146_K	158_R	0.601	1.00
72_T	81_A	0.596	1.00
102_A	105_T	0.594	1.00
146_K	170_T	0.590	1.00
118_A	122_K	0.590	1.00
122_K	153_E	0.588	1.00
74_T	78_K	0.582	1.00
120_Q	123_S	0.579	1.00
133_L	141_P	0.579	1.00
62_V	65_R	0.579	1.00
13_L	16_L	0.579	1.00
135_T	139_D	0.579	1.00
57_S	121_Q	0.576	1.00
59_Q	62_V	0.575	1.00
75_A	132_L	0.568	1.00
85_A	89_C	0.568	1.00
98_C	102_A	0.564	1.00
31_V	35_L	0.560	1.00
173_R	177_D	0.560	1.00
130_H	133_L	0.558	1.00
80_L	172_H	0.558	1.00
84_Q	173_R	0.557	1.00
25_E	34_P	0.557	1.00
98_C	106_F	0.554	1.00
6_V	38_L	0.554	1.00
25_E	40_R	0.552	1.00
28_A	33_Y	0.551	1.00
83_Y	152_L	0.549	1.00
171_A	174_L	0.549	1.00
111_G	114_I	0.548	1.00
165_Q	169_D	0.547	1.00
108_P	111_G	0.540	1.00
16_L	26_M	0.537	1.00
36_D	39_R	0.534	1.00
171_A	175_A	0.532	1.00
104_C	108_P	0.528	1.00
100_F	103_A	0.526	1.00
19_I	22_T	0.526	1.00
144_V	148_M	0.525	1.00
129_T	133_L	0.520	1.00
150_L	153_E	0.520	1.00
66_Q	85_A	0.516	1.00
125_A	132_L	0.516	1.00
60_I	89_C	0.513	1.00
118_A	121_Q	0.512	1.00
166_A	169_D	0.511	1.00
101_I	104_C	0.510	1.00
111_G	115_H	0.508	1.00
170_T	173_R	0.507	1.00
172_H	175_A	0.507	1.00
158_R	161_V	0.506	1.00
144_V	147_Q	0.506	1.00
70_D	73_Q	0.506	1.00
115_H	118_A	0.506	1.00
3_R	41_F	0.504	1.00
13_L	23_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
3g7rA	2	0.9581	100	0.241	Contact Map
4udsA	2	0.9476	100	0.256	Contact Map
4kwaA	2	0.9634	100	0.259	Contact Map
3dpjA	4	0.9738	100	0.259	Contact Map
3jsjA	2	0.9529	100	0.261	Contact Map
2ibdA	2	0.9634	100	0.275	Contact Map
2xdnA	2	1	100	0.275	Contact Map
3eupA	2	0.9686	100	0.276	Contact Map
2g7sA	2	0.9424	100	0.277	Contact Map
2hyjA	2	0.9476	100	0.278	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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