YPOP - BACSU - GREMLIN Contacts

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YPOP - Uncharacterized HTH-type transcriptional regulator YpoP

UniProt:	P54182	Sequences: MKVRTQMMYDMETLLRKVFKQIRNEINEILDKELSRNEFTILRILSEQGPKKVTEFAPILEVSASHITAVTDALVEKEWITRIRSKEDRRIIRIHITEAGEKVLQHFNEKKTEYFFKRFDCYTDAELATLIELFSKLDKKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	141 (129)
Sequences:	22949 (17006)
Seq/√Len:	1497.3

ECOLI - SLYA MARR MPRA
BACSU - YPOP YWHA YUSO YXAD YCGE YDGG YSMB YWAE MHQR YKOM YFIV YYBA YDCH OHRR YETL YWOH YDGJ YHJH 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_I	95_H	3.150	1.00
126_E	136_K	2.855	1.00
85_S	93_R	2.750	1.00
52_K	91_I	2.731	1.00
50_P	95_H	2.686	1.00
81_T	95_H	2.652	1.00
123_T	126_E	2.440	1.00
129_T	132_E	2.325	1.00
129_T	133_L	2.273	1.00
46_S	104_L	2.102	1.00
84_R	92_I	2.068	1.00
52_K	55_E	2.059	1.00
38_E	77_K	1.982	1.00
122_Y	133_L	1.900	1.00
85_S	91_I	1.836	1.00
46_S	96_I	1.807	1.00
126_E	129_T	1.773	1.00
75_V	82_R	1.685	1.00
99_A	103_V	1.677	1.00
78_E	99_A	1.613	1.00
38_E	73_A	1.595	1.00
14_L	135_S	1.578	1.00
130_L	133_L	1.546	1.00
53_V	71_T	1.542	1.00
48_Q	59_I	1.482	1.00
35_S	38_E	1.482	1.00
72_D	76_E	1.468	1.00
46_S	101_E	1.454	1.00
126_E	132_E	1.450	1.00
103_V	106_H	1.449	1.00
99_A	102_K	1.449	1.00
71_T	94_I	1.448	1.00
41_I	70_V	1.446	1.00
133_L	136_K	1.416	1.00
44_I	59_I	1.345	1.00
14_L	131_I	1.342	1.00
14_L	138_D	1.283	1.00
55_E	58_P	1.269	1.00
29_I	110_K	1.262	1.00
50_P	93_R	1.261	1.00
72_D	89_R	1.252	1.00
54_T	64_A	1.239	1.00
41_I	67_I	1.231	1.00
102_K	106_H	1.205	1.00
53_V	92_I	1.176	1.00
132_E	136_K	1.173	1.00
63_S	66_H	1.165	1.00
82_R	92_I	1.157	1.00
62_V	66_H	1.138	1.00
53_V	94_I	1.134	1.00
48_Q	51_K	1.102	1.00
127_L	131_I	1.101	1.00
125_A	129_T	1.096	1.00
79_W	103_V	1.089	1.00
131_I	135_S	1.086	1.00
126_E	133_L	1.080	1.00
54_T	58_P	1.079	1.00
17_K	138_D	1.065	1.00
51_K	55_E	1.061	1.00
27_N	31_D	1.058	1.00
53_V	64_A	1.052	1.00
53_V	67_I	1.041	1.00
18_V	138_D	1.010	1.00
68_T	72_D	1.010	1.00
16_R	19_F	0.989	1.00
65_S	68_T	0.988	1.00
45_L	80_I	0.985	1.00
81_T	97_T	0.981	1.00
50_P	83_I	0.972	1.00
72_D	75_V	0.968	1.00
110_K	113_E	0.964	1.00
96_I	100_G	0.956	1.00
55_E	59_I	0.950	1.00
51_K	59_I	0.947	1.00
98_E	101_E	0.942	1.00
49_G	101_E	0.941	1.00
19_F	23_R	0.924	1.00
77_K	103_V	0.916	1.00
62_V	67_I	0.916	1.00
96_I	101_E	0.915	1.00
79_W	99_A	0.911	1.00
29_I	114_Y	0.905	1.00
33_E	77_K	0.904	1.00
37_N	70_V	0.902	1.00
101_E	105_Q	0.897	1.00
115_F	118_R	0.893	1.00
83_I	93_R	0.890	1.00
66_H	69_A	0.887	1.00
98_E	102_K	0.878	1.00
11_M	131_I	0.876	1.00
77_K	99_A	0.869	1.00
29_I	117_K	0.866	1.00
111_K	115_F	0.864	1.00
63_S	69_A	0.858	1.00
84_R	89_R	0.854	1.00
71_T	80_I	0.852	1.00
46_S	108_N	0.852	1.00
41_I	56_F	0.851	1.00
18_V	134_F	0.837	1.00
129_T	136_K	0.837	1.00
124_D	128_A	0.833	1.00
25_E	114_Y	0.831	1.00
46_S	105_Q	0.831	1.00
39_F	107_F	0.822	1.00
122_Y	137_L	0.819	1.00
109_E	113_E	0.818	1.00
21_Q	138_D	0.817	1.00
75_V	80_I	0.815	1.00
69_A	73_A	0.797	1.00
88_D	91_I	0.795	1.00
48_Q	55_E	0.786	1.00
44_I	48_Q	0.777	1.00
16_R	20_K	0.775	1.00
29_I	113_E	0.773	1.00
75_V	81_T	0.763	1.00
69_A	72_D	0.758	1.00
42_L	104_L	0.756	1.00
123_T	127_L	0.752	1.00
106_H	110_K	0.748	1.00
73_A	76_E	0.744	1.00
102_K	105_Q	0.742	1.00
114_Y	117_K	0.741	1.00
40_T	60_L	0.736	1.00
71_T	75_V	0.735	1.00
86_K	93_R	0.728	1.00
113_E	116_F	0.725	1.00
14_L	17_K	0.724	1.00
117_K	120_D	0.722	1.00
32_K	110_K	0.719	1.00
57_A	67_I	0.719	1.00
20_K	24_N	0.717	1.00
128_A	131_I	0.708	1.00
44_I	60_L	0.706	1.00
49_G	95_H	0.705	1.00
109_E	112_T	0.698	1.00
53_V	68_T	0.696	1.00
27_N	36_R	0.690	1.00
85_S	88_D	0.690	1.00
39_F	111_K	0.681	1.00
72_D	82_R	0.675	1.00
15_L	19_F	0.674	1.00
128_A	132_E	0.673	1.00
125_A	128_A	0.671	1.00
44_I	51_K	0.667	1.00
37_N	66_H	0.665	1.00
113_E	117_K	0.659	1.00
45_L	51_K	0.656	1.00
67_I	71_T	0.655	1.00
112_T	116_F	0.654	1.00
119_F	127_L	0.654	1.00
74_L	79_W	0.649	1.00
43_R	47_E	0.644	1.00
44_I	56_F	0.642	1.00
41_I	60_L	0.641	1.00
106_H	109_E	0.638	1.00
57_A	64_A	0.636	1.00
73_A	77_K	0.613	1.00
45_L	96_I	0.611	1.00
29_I	32_K	0.602	1.00
10_D	131_I	0.598	1.00
18_V	137_L	0.593	1.00
25_E	117_K	0.590	1.00
56_F	94_I	0.585	1.00
122_Y	127_L	0.580	1.00
40_T	44_I	0.577	1.00
132_E	135_S	0.577	1.00
25_E	28_E	0.575	1.00
15_L	18_V	0.574	1.00
23_R	26_I	0.572	1.00
38_E	70_V	0.571	1.00
108_N	112_T	0.568	1.00
17_K	21_Q	0.561	1.00
26_I	29_I	0.561	1.00
39_F	104_L	0.560	1.00
23_R	27_N	0.560	1.00
97_T	100_G	0.555	1.00
122_Y	136_K	0.548	1.00
105_Q	109_E	0.544	1.00
80_I	94_I	0.544	1.00
78_E	81_T	0.543	1.00
11_M	130_L	0.534	1.00
104_L	108_N	0.533	1.00
54_T	57_A	0.531	1.00
103_V	107_F	0.527	1.00
133_L	137_L	0.525	1.00
42_L	46_S	0.525	1.00
122_Y	126_E	0.513	1.00
43_R	108_N	0.513	1.00
15_L	134_F	0.512	1.00
105_Q	108_N	0.511	1.00
26_I	111_K	0.507	1.00
83_I	86_K	0.504	1.00
74_L	80_I	0.502	1.00
82_R	94_I	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	0.276	Contact Map
4rguA	4	0.9716	99.9	0.277	Contact Map
3fm5A	4	1	99.9	0.278	Contact Map
3cdhA	4	0.9362	99.9	0.283	Contact Map
2nnnA	2	0.9433	99.9	0.285	Contact Map
3cjnA	2	0.9504	99.9	0.287	Contact Map
1s3jA	2	0.9929	99.9	0.288	Contact Map
2gxgA	2	0.9574	99.9	0.291	Contact Map
3jw4A	2	0.9078	99.9	0.293	Contact Map
3boqA	2	0.922	99.9	0.295	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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