YWRC - BACSU - GREMLIN Contacts

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YWRC - Uncharacterized HTH-type transcriptional regulator YwrC

UniProt:	O05217	Sequences: MSHEYQIPNLVLDETDKQILTILHEEGRISYTDLGKRVDLSRVAVQARINQLIEAGVIEKFTAVINPAKIGIHVSVFFNVEVEPQFLEEVALKLEEEPAVTSLYHMTGPSKLHMHGIFTNDQEMEEFLTKRLYPLRGVVSVDCQMLIKRYKSRMGMKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	158 (139)
Sequences:	13671 (8788)
Seq/√Len:	745.4

ECOLI - LRP YBAO ASNC
BACSU - YWRC AZLB LRPB YUGG LRPC YEZC LRPA
HALSA - Q9HQ13 Q9HNI1 Q9HQ33 Q9HQB6 Q9HP41 Q9HQG1 Q9HNW8 Q9HP70
SULSO - Q7LXS6 Q97W90 Q7LX67 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
22_I	37_R	2.952	1.00
53_I	61_F	2.869	1.00
109_P	142_D	2.562	1.00
81_E	140_S	2.553	1.00
102_S	115_H	2.551	1.00
31_Y	49_I	2.292	1.00
119_T	123_E	2.285	1.00
68_A	122_Q	2.100	1.00
16_D	48_R	2.093	1.00
22_I	29_I	2.053	1.00
59_E	66_N	1.990	1.00
51_Q	55_A	1.984	1.00
83_E	139_V	1.905	1.00
75_S	115_H	1.813	1.00
59_E	64_V	1.808	1.00
97_E	131_R	1.805	1.00
77_F	104_Y	1.797	1.00
101_T	117_I	1.752	1.00
15_T	40_L	1.723	1.00
97_E	127_F	1.709	1.00
22_I	25_E	1.701	1.00
50_N	54_E	1.701	1.00
40_L	44_A	1.653	1.00
32_T	36_K	1.596	1.00
79_N	144_Q	1.564	1.00
29_I	37_R	1.555	1.00
93_K	96_E	1.545	1.00
120_N	123_E	1.542	1.00
123_E	126_E	1.532	1.00
33_D	36_K	1.505	1.00
32_T	42_R	1.500	1.00
99_A	123_E	1.477	1.00
93_K	135_L	1.473	1.00
40_L	45_V	1.456	1.00
31_Y	46_Q	1.437	1.00
41_S	44_A	1.430	1.00
90_V	94_L	1.426	1.00
19_I	34_L	1.406	1.00
80_V	114_M	1.402	1.00
91_A	95_E	1.385	1.00
28_R	61_F	1.381	1.00
88_E	92_L	1.358	1.00
86_F	89_E	1.346	1.00
38_V	45_V	1.341	1.00
81_E	109_P	1.337	1.00
126_E	130_K	1.298	1.00
78_F	116_G	1.268	1.00
81_E	139_V	1.266	1.00
14_E	18_Q	1.258	1.00
79_N	110_S	1.247	1.00
125_E	148_K	1.240	1.00
72_I	119_T	1.236	1.00
29_I	34_L	1.235	1.00
33_D	37_R	1.233	1.00
23_L	49_I	1.231	1.00
74_V	121_D	1.226	1.00
82_V	90_V	1.220	1.00
25_E	37_R	1.215	1.00
91_A	148_K	1.212	1.00
15_T	18_Q	1.197	1.00
50_N	53_I	1.187	1.00
30_S	33_D	1.169	1.00
13_D	48_R	1.166	1.00
99_A	131_R	1.138	1.00
26_E	37_R	1.107	1.00
15_T	38_V	1.087	1.00
75_S	117_I	1.081	1.00
22_I	34_L	1.081	1.00
79_N	142_D	1.079	1.00
31_Y	35_G	1.068	1.00
60_K	64_V	1.057	1.00
18_Q	21_T	1.048	1.00
100_V	116_G	1.023	1.00
18_Q	22_I	1.018	1.00
103_L	114_M	1.007	1.00
118_F	123_E	0.992	1.00
89_E	93_K	0.990	1.00
66_N	69_K	0.988	1.00
91_A	112_L	0.984	1.00
29_I	33_D	0.981	1.00
35_G	45_V	0.972	1.00
21_T	25_E	0.971	1.00
27_G	61_F	0.969	1.00
77_F	113_H	0.967	1.00
28_R	53_I	0.956	1.00
92_L	95_E	0.950	1.00
118_F	124_M	0.934	1.00
106_M	113_H	0.933	1.00
42_R	46_Q	0.932	1.00
46_Q	50_N	0.928	1.00
92_L	96_E	0.912	1.00
31_Y	42_R	0.905	1.00
118_F	127_F	0.904	1.00
116_G	127_F	0.901	1.00
104_Y	115_H	0.900	1.00
73_H	120_N	0.899	1.00
18_Q	38_V	0.886	1.00
77_F	115_H	0.886	1.00
35_G	40_L	0.875	1.00
32_T	46_Q	0.873	1.00
12_L	17_K	0.868	1.00
67_P	117_I	0.842	1.00
27_G	33_D	0.836	1.00
83_E	86_F	0.826	1.00
100_V	114_M	0.825	1.00
52_L	57_V	0.824	1.00
77_F	146_L	0.821	1.00
100_V	103_L	0.810	1.00
109_P	140_S	0.798	1.00
17_K	21_T	0.794	1.00
104_Y	146_L	0.791	1.00
16_D	51_Q	0.788	1.00
34_L	45_V	0.784	1.00
94_L	103_L	0.771	1.00
88_E	91_A	0.767	1.00
128_L	143_C	0.762	1.00
104_Y	149_R	0.762	1.00
110_S	142_D	0.758	1.00
19_I	48_R	0.757	1.00
79_N	113_H	0.752	1.00
80_V	90_V	0.751	1.00
126_E	131_R	0.749	1.00
43_V	47_A	0.747	1.00
87_L	112_L	0.746	1.00
93_K	97_E	0.745	1.00
19_I	45_V	0.740	1.00
27_G	63_A	0.738	1.00
34_L	49_I	0.725	1.00
12_L	57_V	0.723	1.00
89_E	92_L	0.721	1.00
13_D	16_D	0.720	1.00
79_N	109_P	0.715	1.00
133_Y	141_V	0.712	1.00
81_E	110_S	0.708	1.00
76_V	124_M	0.698	1.00
22_I	26_E	0.694	1.00
107_T	145_M	0.687	1.00
105_H	112_L	0.684	1.00
57_V	69_K	0.676	1.00
78_F	141_V	0.675	1.00
122_Q	125_E	0.674	1.00
99_A	127_F	0.670	1.00
19_I	29_I	0.670	1.00
26_E	29_I	0.664	1.00
47_A	51_Q	0.662	1.00
14_E	17_K	0.662	1.00
83_E	137_G	0.660	1.00
90_V	112_L	0.657	1.00
75_S	146_L	0.655	1.00
91_A	150_Y	0.654	1.00
72_I	117_I	0.652	1.00
72_I	99_A	0.651	1.00
121_D	145_M	0.644	1.00
76_V	145_M	0.636	1.00
89_E	137_G	0.633	1.00
43_V	46_Q	0.631	1.00
56_G	59_E	0.629	1.00
99_A	119_T	0.626	1.00
47_A	50_N	0.623	1.00
123_E	127_F	0.615	1.00
78_F	114_M	0.615	1.00
35_G	42_R	0.615	1.00
80_V	138_V	0.609	1.00
20_L	52_L	0.608	1.00
31_Y	45_V	0.607	1.00
48_R	52_L	0.607	1.00
106_M	110_S	0.607	1.00
16_D	52_L	0.600	1.00
128_L	141_V	0.599	1.00
122_Q	126_E	0.598	1.00
27_G	60_K	0.597	1.00
19_I	22_I	0.597	1.00
94_L	114_M	0.595	1.00
19_I	49_I	0.590	1.00
97_E	135_L	0.586	1.00
79_N	106_M	0.584	1.00
19_I	52_L	0.575	1.00
76_V	143_C	0.573	1.00
65_I	70_I	0.570	1.00
127_F	131_R	0.567	1.00
15_T	44_A	0.562	1.00
131_R	135_L	0.560	1.00
121_D	147_I	0.560	1.00
127_F	132_L	0.560	1.00
93_K	136_R	0.553	1.00
66_N	70_I	0.551	1.00
24_H	62_T	0.550	1.00
75_S	149_R	0.546	1.00
32_T	35_G	0.546	1.00
106_M	146_L	0.543	1.00
105_H	111_K	0.542	1.00
75_S	104_Y	0.540	1.00
58_I	61_F	0.539	1.00
88_E	134_P	0.537	1.00
124_M	145_M	0.536	1.00
82_V	111_K	0.534	1.00
106_M	144_Q	0.528	1.00
81_E	142_D	0.528	1.00
105_H	133_Y	0.524	1.00
64_V	67_P	0.516	1.00
86_F	136_R	0.512	1.00
93_K	137_G	0.512	1.00
128_L	147_I	0.509	1.00
109_P	144_Q	0.509	1.00
51_Q	54_E	0.507	1.00
105_H	125_E	0.505	1.00
38_V	44_A	0.502	1.00
101_T	115_H	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	0.8608	100	0.173	Contact Map
4un1A	1	0.8987	100	0.202	Contact Map
2e1cA	1	0.9304	100	0.211	Contact Map
4un1B	1	0.943	100	0.219	Contact Map
2p5vA	5	0.962	100	0.22	Contact Map
4pcqA	2	0.9367	100	0.221	Contact Map
3i4pA	5	0.9241	100	0.24	Contact Map
2ia0A	2	0.9114	100	0.245	Contact Map
2pn6A	5	0.9241	100	0.252	Contact Map
2cg4A	6	0.9367	100	0.258	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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