YWHA - BACSU - GREMLIN Contacts

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YWHA - Uncharacterized HTH-type transcriptional regulator YwhA

UniProt:	P70993	Sequences: MDHDKLEANLLDHALTKYLKSTKQLDEATVPKHVNNVRGFILRIIYRHGSCTIKDILKEVTLSPSATTTALNHLEQEGFIERSRNNNDRRTVWITLSESGRGAAEQMIENRQQLIDGMFERLTAEEKKTFLAIIAKLAQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	139 (127)
Sequences:	21985 (16108)
Seq/√Len:	1429.4

ECOLI - SLYA MARR MPRA
BACSU - YWHA YPOP YUSO YXAD YCGE YSMB YWAE YKOM YFIV YDGG YYBA MHQR YETL YDGJ OHRR YDCH YHJH YWOH YVMB YVNA YBFA
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
83_S	95_T	3.025	1.00
50_S	95_T	2.918	1.00
126_E	136_K	2.758	1.00
81_E	95_T	2.576	1.00
85_N	93_W	2.450	1.00
52_T	91_T	2.421	1.00
123_T	126_E	2.337	1.00
129_T	132_A	2.245	1.00
84_R	92_V	2.035	1.00
46_Y	104_A	2.032	1.00
52_T	55_D	1.978	1.00
129_T	133_I	1.967	1.00
38_R	77_E	1.901	1.00
122_L	133_I	1.886	1.00
85_N	91_T	1.779	1.00
46_Y	96_L	1.729	1.00
126_E	129_T	1.679	1.00
53_I	71_L	1.655	1.00
78_G	99_S	1.609	1.00
38_R	73_H	1.561	1.00
99_S	103_A	1.557	1.00
35_N	38_R	1.523	1.00
71_L	94_I	1.519	1.00
48_H	59_E	1.518	1.00
130_F	133_I	1.513	1.00
75_E	82_R	1.488	1.00
126_E	132_A	1.483	1.00
72_N	76_Q	1.465	1.00
14_A	135_A	1.456	1.00
41_I	70_A	1.455	1.00
99_S	102_G	1.424	1.00
103_A	106_Q	1.420	1.00
32_K	110_N	1.412	1.00
46_Y	101_R	1.349	1.00
72_N	89_R	1.338	1.00
133_I	136_K	1.307	1.00
55_D	58_K	1.276	1.00
50_S	93_W	1.271	1.00
14_A	131_L	1.251	1.00
44_I	59_E	1.244	1.00
102_G	106_Q	1.221	1.00
63_S	66_A	1.197	1.00
53_I	92_V	1.194	1.00
32_K	106_Q	1.194	1.00
54_K	64_P	1.179	1.00
54_K	58_K	1.162	1.00
41_I	67_T	1.134	1.00
62_L	66_A	1.132	1.00
132_A	136_K	1.127	1.00
53_I	67_T	1.104	1.00
50_S	83_S	1.099	1.00
125_E	129_T	1.097	1.00
53_I	94_I	1.076	1.00
49_G	101_R	1.052	1.00
48_H	51_C	1.045	1.00
127_K	131_L	1.037	1.00
79_F	103_A	1.025	1.00
51_C	55_D	1.020	1.00
68_T	72_N	1.015	1.00
98_E	101_R	1.009	1.00
27_E	30_V	1.007	1.00
32_K	107_M	1.007	1.00
33_H	77_E	0.992	1.00
51_C	59_E	0.990	1.00
55_D	59_E	0.989	1.00
31_P	110_N	0.987	1.00
110_N	113_Q	0.979	1.00
65_S	68_T	0.974	1.00
77_E	99_S	0.968	1.00
72_N	75_E	0.967	1.00
53_I	64_P	0.963	1.00
122_L	137_L	0.963	1.00
96_L	100_G	0.958	1.00
98_E	102_G	0.951	1.00
82_R	92_V	0.942	1.00
16_T	19_L	0.942	1.00
49_G	95_T	0.939	1.00
66_A	69_T	0.939	1.00
84_R	89_R	0.930	1.00
71_L	80_I	0.925	1.00
46_Y	105_E	0.919	1.00
63_S	69_T	0.915	1.00
39_G	107_M	0.903	1.00
45_I	80_I	0.892	1.00
111_R	115_I	0.889	1.00
37_V	70_A	0.881	1.00
77_E	103_A	0.873	1.00
115_I	118_M	0.867	1.00
83_S	93_W	0.866	1.00
79_F	99_S	0.865	1.00
126_E	133_I	0.864	1.00
46_Y	108_I	0.863	1.00
131_L	135_A	0.858	1.00
48_H	55_D	0.858	1.00
71_L	75_E	0.857	1.00
40_F	60_V	0.856	1.00
62_L	67_T	0.856	1.00
113_Q	116_D	0.852	1.00
81_E	97_S	0.851	1.00
86_N	93_W	0.848	1.00
101_R	105_E	0.845	1.00
69_T	73_H	0.841	1.00
124_A	128_K	0.841	1.00
109_E	113_Q	0.828	1.00
44_I	51_C	0.824	1.00
42_L	104_A	0.824	1.00
44_I	60_V	0.816	1.00
16_T	20_K	0.812	1.00
88_D	91_T	0.809	1.00
85_N	88_D	0.809	1.00
39_G	111_R	0.806	1.00
96_L	101_R	0.797	1.00
11_L	131_L	0.794	1.00
19_L	23_K	0.788	1.00
106_Q	110_N	0.788	1.00
18_Y	134_I	0.781	1.00
25_L	114_L	0.779	1.00
53_I	68_T	0.776	1.00
75_E	81_E	0.770	1.00
123_T	127_K	0.765	1.00
37_V	66_A	0.761	1.00
128_K	131_L	0.761	1.00
109_E	112_Q	0.724	1.00
15_L	19_L	0.723	1.00
44_I	56_I	0.721	1.00
73_H	76_Q	0.720	1.00
125_E	128_K	0.720	1.00
74_L	79_F	0.718	1.00
128_K	132_A	0.718	1.00
27_E	36_N	0.717	1.00
102_G	105_E	0.714	1.00
41_I	60_V	0.713	1.00
113_Q	117_G	0.713	1.00
41_I	56_I	0.712	1.00
45_I	51_C	0.711	1.00
75_E	80_I	0.707	1.00
129_T	136_K	0.706	1.00
112_Q	116_D	0.703	1.00
44_I	48_H	0.698	1.00
20_K	24_Q	0.692	1.00
117_G	120_E	0.688	1.00
114_L	117_G	0.687	1.00
72_N	82_R	0.683	1.00
38_R	70_A	0.679	1.00
67_T	71_L	0.679	1.00
57_L	64_P	0.677	1.00
25_L	28_A	0.670	1.00
57_L	67_T	0.665	1.00
14_A	17_K	0.664	1.00
23_K	27_E	0.664	1.00
45_I	96_L	0.663	1.00
69_T	72_N	0.662	1.00
15_L	18_Y	0.660	1.00
42_L	46_Y	0.656	1.00
106_Q	109_E	0.651	1.00
22_T	25_L	0.649	1.00
23_K	26_D	0.646	1.00
119_F	127_K	0.644	1.00
43_R	47_R	0.640	1.00
40_F	44_I	0.617	1.00
39_G	104_A	0.617	1.00
122_L	136_K	0.616	1.00
25_L	117_G	0.615	1.00
84_R	88_D	0.610	1.00
17_K	21_S	0.602	1.00
122_L	127_K	0.595	1.00
12_D	26_D	0.585	1.00
43_R	108_I	0.582	1.00
73_H	77_E	0.582	1.00
83_S	86_N	0.579	1.00
97_S	100_G	0.570	1.00
132_A	135_A	0.567	1.00
56_I	94_I	0.567	1.00
78_G	81_E	0.564	1.00
104_A	108_I	0.547	1.00
26_D	111_R	0.539	1.00
123_T	136_K	0.538	1.00
119_F	123_T	0.532	1.00
24_Q	28_A	0.532	1.00
54_K	57_L	0.531	1.00
105_E	109_E	0.528	1.00
111_R	114_L	0.527	1.00
108_I	112_Q	0.527	1.00
116_D	120_E	0.525	1.00
105_E	108_I	0.522	1.00
35_N	73_H	0.511	1.00
34_V	103_A	0.508	1.00
21_S	25_L	0.507	1.00
11_L	130_F	0.507	1.00
95_T	101_R	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
3bj6A	2	1	99.9	0.265	Contact Map
4rguA	4	0.9712	99.9	0.27	Contact Map
3fm5A	4	1	99.9	0.276	Contact Map
1s3jA	2	0.9928	99.9	0.279	Contact Map
2rdpA	2	0.9712	99.9	0.282	Contact Map
2gxgA	2	0.9568	99.9	0.287	Contact Map
3deuA	2	0.8993	99.9	0.287	Contact Map
4yifA	2	0.964	99.9	0.287	Contact Map
3cjnA	2	0.964	99.9	0.287	Contact Map
3e6mA	2	1	99.9	0.288	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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