YEZC - BACSU - GREMLIN Contacts

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YEZC - Uncharacterized HTH-type transcriptional regulator YezC

UniProt:	O31497	Sequences: MDDTDLQILSHLQRNGRLTMVELGKLVGLSSPSAAERVRKLEDKGVITGYSANICYEKLNKHVTAFILMEPKSCKHYAAFATSHPDVAENHRITGMYSYVTKVVTESVHTLEDFIDTSMAHGKPTTLVVLSSSSCHPAF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	139 (134)
Sequences:	13363 (8814)
Seq/√Len:	761.4

ECOLI - LRP YBAO ASNC
BACSU - YEZC LRPB LRPC AZLB YWRC LRPA YUGG
HALSA - Q9HQ13 Q9HQ33 Q9HNI1 Q9HQB6 Q9HP41 Q9HQG1 Q9HNW8 Q9HP70
SULSO - Q7LX67 Q7LXS6 Q97W90 Q97XP7 LYSM Q97X78 Q980P3 Q97VN7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_H	26_L	2.978	1.00
42_E	50_Y	2.926	1.00
96_M	125_T	2.590	1.00
89_E	102_K	2.545	1.00
70_E	123_K	2.320	1.00
20_M	38_V	2.277	1.00
106_E	110_T	2.223	1.00
57_E	109_H	2.109	1.00
40_K	44_K	2.026	1.00
11_H	18_L	1.998	1.00
5_D	37_R	1.995	1.00
48_T	55_C	1.983	1.00
73_S	76_H	1.956	1.00
64_T	102_K	1.804	1.00
88_A	104_V	1.788	1.00
48_T	53_N	1.776	1.00
4_T	29_L	1.723	1.00
66_F	91_H	1.716	1.00
39_R	43_D	1.691	1.00
21_V	25_K	1.688	1.00
84_H	114_F	1.668	1.00
29_L	33_S	1.642	1.00
11_H	14_R	1.611	1.00
68_L	127_L	1.556	1.00
29_L	34_A	1.544	1.00
30_S	33_S	1.538	1.00
18_L	26_L	1.536	1.00
110_T	113_D	1.529	1.00
21_V	31_S	1.528	1.00
113_D	117_T	1.523	1.00
22_E	25_K	1.521	1.00
107_S	110_T	1.486	1.00
77_Y	81_A	1.485	1.00
8_I	23_L	1.449	1.00
80_F	83_S	1.439	1.00
78_A	82_T	1.428	1.00
20_M	35_A	1.374	1.00
86_D	110_T	1.372	1.00
17_R	50_Y	1.358	1.00
112_E	131_S	1.329	1.00
27_V	34_A	1.309	1.00
22_E	26_L	1.299	1.00
75_K	79_A	1.292	1.00
70_E	122_G	1.290	1.00
61_K	106_E	1.279	1.00
3_D	7_Q	1.268	1.00
12_L	38_V	1.266	1.00
18_L	23_L	1.263	1.00
67_I	103_V	1.263	1.00
68_L	97_Y	1.245	1.00
69_M	101_T	1.222	1.00
4_T	7_Q	1.211	1.00
15_N	26_L	1.201	1.00
39_R	42_E	1.184	1.00
78_A	131_S	1.157	1.00
19_T	22_E	1.151	1.00
49_G	53_N	1.148	1.00
70_E	96_M	1.132	1.00
63_V	108_V	1.120	1.00
14_R	26_L	1.101	1.00
20_M	24_G	1.092	1.00
4_T	27_V	1.092	1.00
11_H	23_L	1.071	1.00
7_Q	11_H	1.050	1.00
80_F	118_S	1.049	1.00
24_G	34_A	1.043	1.00
76_H	80_F	1.021	1.00
18_L	22_E	1.020	1.00
55_C	58_K	1.010	1.00
68_L	125_T	1.010	1.00
2_D	37_R	1.009	1.00
16_G	50_Y	1.007	1.00
10_S	14_R	1.000	1.00
7_Q	10_S	0.989	1.00
68_L	96_M	0.987	1.00
84_H	117_T	0.986	1.00
105_T	110_T	0.986	1.00
93_I	100_V	0.982	1.00
64_T	104_V	0.977	1.00
105_T	111_L	0.977	1.00
90_N	101_T	0.975	1.00
87_V	103_V	0.972	1.00
78_A	99_Y	0.968	1.00
112_E	116_D	0.966	1.00
105_T	114_F	0.961	1.00
91_H	102_K	0.952	1.00
103_V	114_F	0.947	1.00
31_S	35_A	0.945	1.00
35_A	39_R	0.942	1.00
7_Q	27_V	0.942	1.00
62_H	107_S	0.919	1.00
92_R	116_D	0.918	1.00
79_A	82_T	0.918	1.00
66_F	100_V	0.905	1.00
20_M	31_S	0.901	1.00
24_G	29_L	0.884	1.00
66_F	129_V	0.881	1.00
17_R	42_E	0.868	1.00
56_Y	104_V	0.867	1.00
91_H	129_V	0.866	1.00
1_M	6_L	0.865	1.00
41_L	46_V	0.863	1.00
91_H	132_S	0.862	1.00
21_V	35_A	0.857	1.00
87_V	90_N	0.847	1.00
79_A	83_S	0.843	1.00
16_G	22_E	0.839	1.00
6_L	10_S	0.833	1.00
66_F	102_K	0.827	1.00
80_F	84_H	0.820	1.00
96_M	123_K	0.818	1.00
81_A	90_N	0.810	1.00
87_V	101_T	0.800	1.00
32_P	36_E	0.779	1.00
23_L	38_V	0.762	1.00
75_K	78_A	0.761	1.00
5_D	40_K	0.754	1.00
76_H	79_A	0.751	1.00
23_L	34_A	0.749	1.00
108_V	128_V	0.747	1.00
77_Y	99_Y	0.742	1.00
16_G	52_A	0.739	1.00
97_Y	125_T	0.733	1.00
94_T	128_V	0.733	1.00
46_V	58_K	0.722	1.00
78_A	133_S	0.715	1.00
86_D	114_F	0.713	1.00
3_D	6_L	0.704	1.00
8_I	34_A	0.703	1.00
61_K	104_V	0.699	1.00
61_K	86_D	0.699	1.00
115_I	124_P	0.697	1.00
8_I	37_R	0.696	1.00
15_N	18_L	0.694	1.00
11_H	15_N	0.694	1.00
36_E	40_K	0.681	1.00
8_I	18_L	0.677	1.00
73_S	120_A	0.677	1.00
109_H	112_E	0.672	1.00
92_R	99_Y	0.670	1.00
110_T	114_F	0.663	1.00
115_I	130_L	0.662	1.00
74_C	99_Y	0.661	1.00
8_I	38_V	0.656	1.00
8_I	11_H	0.654	1.00
115_I	126_T	0.653	1.00
65_A	128_V	0.648	1.00
67_I	101_T	0.647	1.00
68_L	100_V	0.643	1.00
64_T	129_V	0.643	1.00
69_M	77_Y	0.636	1.00
64_T	132_S	0.632	1.00
80_F	120_A	0.628	1.00
24_G	31_S	0.625	1.00
9_L	41_L	0.624	1.00
70_E	97_Y	0.621	1.00
93_I	97_Y	0.621	1.00
20_M	34_A	0.619	1.00
81_A	101_T	0.618	1.00
70_E	125_T	0.613	1.00
36_E	39_R	0.613	1.00
69_M	121_H	0.609	1.00
75_K	116_D	0.608	1.00
76_H	120_A	0.607	1.00
37_R	41_L	0.604	1.00
86_D	106_E	0.592	1.00
5_D	41_L	0.590	1.00
16_G	49_G	0.590	1.00
114_F	117_T	0.589	1.00
84_H	118_S	0.584	1.00
108_V	130_L	0.583	1.00
93_I	129_V	0.581	1.00
32_P	35_A	0.576	1.00
124_P	130_L	0.568	1.00
45_G	48_T	0.566	1.00
72_K	76_H	0.560	1.00
74_C	116_D	0.558	1.00
1_M	46_V	0.551	1.00
2_D	5_D	0.549	1.00
54_I	59_L	0.549	1.00
113_D	116_D	0.548	1.00
64_T	91_H	0.547	1.00
67_I	124_P	0.543	1.00
13_Q	51_S	0.541	1.00
103_V	111_L	0.541	1.00
47_I	50_Y	0.540	1.00
62_H	104_V	0.539	1.00
65_A	111_L	0.539	1.00
8_I	41_L	0.535	1.00
98_S	123_K	0.532	1.00
21_V	24_G	0.528	1.00
4_T	33_S	0.523	1.00
109_H	113_D	0.523	1.00
76_H	119_M	0.522	1.00
71_P	117_T	0.518	1.00
53_N	56_Y	0.517	1.00
69_M	124_P	0.517	1.00
44_K	58_K	0.512	1.00
74_C	92_R	0.505	1.00
29_L	37_R	0.500	1.00
66_F	69_M	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
4ch7A	1	0.9424	100	0.173	Contact Map
4un1B	1	1	100	0.21	Contact Map
4un1A	1	0.9856	100	0.215	Contact Map
2p5vA	5	1	100	0.224	Contact Map
4pcqA	2	0.9928	100	0.227	Contact Map
2e1cA	1	1	100	0.233	Contact Map
2ia0A	2	0.9712	100	0.236	Contact Map
3i4pA	5	0.9928	100	0.243	Contact Map
2cg4A	6	1	99.9	0.247	Contact Map
2pn6A	5	1	99.9	0.269	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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