YTTP - BACSU - GREMLIN Contacts

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YTTP - Probable HTH-type transcriptional regulator YttP

UniProt:	O34970	Sequences: MKVSTKDKIIESAVMLFNQKGFSGTSVREIAKSADVNVAHISYYFKGKGGLMEHLVSEFYEGYSKTLETAASNISTQSTQEQLLQLVFDILSYQHNHRQLTRFVYREVTIDSTLIREIMSTYLMKEKYIFQLIIEEGEKQREYLTLPLPHFILQLKSLLMMPYLQPQYISEVLYMQPHEPYFYKMYFEEIKIWIRSVFRTGDVALTN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	207 (178)
Sequences:	40378 (31956)
Seq/√Len:	2395.2

ECOLI - RUTR SLMA YBIH ACRR FABR NEMR COMR ENVR UIDR BETI BDCR YJDC RCDA
BACSU - YTTP YHGD FADR YFIR YVKB YVDT BSCR PKSA LMRA YXAF YEZE YCNC YVAF YUXN YERO YDGC YOBS YDES YXBF
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
28_R	38_V	3.988	1.00
20_K	29_E	3.884	1.00
15_M	33_S	3.405	1.00
46_K	50_G	2.687	1.00
17_F	25_T	2.387	1.00
131_Q	149_P	2.282	1.00
47_G	50_G	2.090	1.00
12_S	33_S	2.031	1.00
31_A	41_I	2.022	1.00
16_L	25_T	2.017	1.00
5_T	8_K	1.999	1.00
82_Q	136_E	1.973	1.00
16_L	33_S	1.956	1.00
16_L	29_E	1.938	1.00
131_Q	135_E	1.926	1.00
16_L	20_K	1.918	1.00
135_E	148_L	1.907	1.00
7_D	58_E	1.886	1.00
19_Q	33_S	1.873	1.00
78_S	81_E	1.834	1.00
8_K	12_S	1.799	1.00
28_R	32_K	1.797	1.00
6_K	54_H	1.783	1.00
12_S	15_M	1.768	1.00
14_V	58_E	1.719	1.00
10_I	54_H	1.660	1.00
37_N	40_H	1.653	1.00
13_A	17_F	1.604	1.00
7_D	11_E	1.577	1.00
27_V	42_S	1.569	1.00
29_E	32_K	1.551	1.00
57_S	118_I	1.513	1.00
27_V	38_V	1.492	1.00
58_E	62_G	1.491	1.00
14_V	55_L	1.458	1.00
138_E	145_T	1.455	1.00
54_H	57_S	1.440	1.00
135_E	139_K	1.437	1.00
135_E	138_E	1.425	1.00
15_M	19_Q	1.416	1.00
13_A	51_L	1.410	1.00
45_F	54_H	1.405	1.00
154_Q	158_L	1.404	1.00
21_G	25_T	1.403	1.00
68_E	129_I	1.398	1.00
14_V	59_F	1.393	1.00
137_G	142_E	1.373	1.00
40_H	43_Y	1.370	1.00
29_E	33_S	1.363	1.00
27_V	41_I	1.359	1.00
42_S	47_G	1.351	1.00
21_G	24_G	1.348	1.00
136_E	140_Q	1.330	1.00
12_S	16_L	1.319	1.00
25_T	30_I	1.315	1.00
26_S	29_E	1.307	1.00
53_E	57_S	1.304	1.00
20_K	24_G	1.280	1.00
84_L	184_K	1.274	1.00
11_E	58_E	1.271	1.00
138_E	146_L	1.255	1.00
73_N	76_T	1.246	1.00
127_K	153_L	1.236	1.00
137_G	143_Y	1.231	1.00
4_S	8_K	1.229	1.00
36_V	40_H	1.222	1.00
99_Q	102_R	1.212	1.00
50_G	54_H	1.210	1.00
84_L	88_F	1.176	1.00
127_K	131_Q	1.173	1.00
49_G	53_E	1.160	1.00
22_F	52_M	1.133	1.00
53_E	118_I	1.130	1.00
80_Q	84_L	1.124	1.00
10_I	45_F	1.122	1.00
12_S	34_A	1.119	1.00
39_A	43_Y	1.116	1.00
138_E	148_L	1.116	1.00
38_V	42_S	1.114	1.00
88_F	180_P	1.109	1.00
17_F	22_F	1.109	1.00
82_Q	133_I	1.099	1.00
66_T	89_D	1.096	1.00
157_S	161_M	1.081	1.00
13_A	55_L	1.078	1.00
146_L	151_F	1.071	1.00
6_K	44_Y	1.065	1.00
37_N	43_Y	1.062	1.00
81_E	85_Q	1.046	1.00
78_S	142_E	1.045	1.00
147_P	150_H	1.037	1.00
133_I	137_G	1.032	1.00
40_H	44_Y	1.031	1.00
11_E	15_M	1.027	1.00
10_I	55_L	1.020	1.00
50_G	53_E	1.017	1.00
180_P	184_K	1.014	1.00
85_Q	88_F	1.013	1.00
15_M	99_Q	1.013	1.00
10_I	58_E	1.000	1.00
14_V	18_N	0.997	1.00
64_S	125_K	0.996	1.00
70_A	89_D	0.981	1.00
77_Q	85_Q	0.978	1.00
81_E	84_L	0.977	1.00
57_S	61_E	0.972	1.00
129_I	132_L	0.969	1.00
131_Q	148_L	0.968	1.00
118_I	121_T	0.965	1.00
20_K	33_S	0.952	1.00
70_A	85_Q	0.948	1.00
49_G	114_L	0.946	1.00
124_M	128_Y	0.943	1.00
4_S	7_D	0.937	1.00
102_R	106_R	0.935	1.00
30_I	51_L	0.933	1.00
132_L	136_E	0.933	1.00
68_E	72_S	0.933	1.00
93_Y	97_H	0.929	1.00
121_T	125_K	0.923	1.00
54_H	58_E	0.909	1.00
66_T	69_T	0.906	1.00
101_T	104_V	0.905	1.00
76_T	82_Q	0.896	1.00
131_Q	152_I	0.894	1.00
58_E	61_E	0.882	1.00
31_A	38_V	0.880	1.00
59_F	62_G	0.876	1.00
38_V	43_Y	0.876	1.00
79_T	137_G	0.875	1.00
49_G	112_S	0.870	1.00
149_P	153_L	0.869	1.00
5_T	44_Y	0.853	1.00
89_D	92_S	0.853	1.00
73_N	85_Q	0.851	1.00
85_Q	89_D	0.850	1.00
132_L	135_E	0.848	1.00
64_S	68_E	0.843	1.00
127_K	149_P	0.843	1.00
138_E	141_R	0.841	1.00
117_E	121_T	0.840	1.00
128_Y	132_L	0.832	1.00
8_K	11_E	0.830	1.00
166_P	169_I	0.828	1.00
87_V	155_L	0.823	1.00
136_E	139_K	0.820	1.00
79_T	140_Q	0.816	1.00
9_I	41_I	0.815	1.00
8_K	34_A	0.814	1.00
18_N	99_Q	0.811	1.00
133_I	136_E	0.809	1.00
88_F	92_S	0.809	1.00
150_H	181_Y	0.803	1.00
64_S	129_I	0.801	1.00
41_I	51_L	0.796	1.00
5_T	36_V	0.791	1.00
61_E	65_K	0.791	1.00
65_K	69_T	0.786	1.00
128_Y	131_Q	0.778	1.00
32_K	38_V	0.778	1.00
116_R	120_S	0.774	1.00
70_A	73_N	0.773	1.00
125_K	129_I	0.772	1.00
150_H	154_Q	0.767	1.00
113_T	117_E	0.766	1.00
57_S	122_Y	0.763	1.00
111_D	114_L	0.761	1.00
148_L	152_I	0.759	1.00
20_K	25_T	0.748	1.00
22_F	48_K	0.734	1.00
76_T	81_E	0.731	1.00
113_T	116_R	0.729	1.00
84_L	87_V	0.726	1.00
11_E	14_V	0.724	1.00
99_Q	103_F	0.723	1.00
28_R	42_S	0.720	1.00
77_Q	81_E	0.716	1.00
134_I	155_L	0.715	1.00
125_K	128_Y	0.713	1.00
9_I	34_A	0.711	1.00
16_L	19_Q	0.710	1.00
62_G	65_K	0.702	1.00
107_E	110_I	0.696	1.00
73_N	77_Q	0.693	1.00
19_Q	29_E	0.691	1.00
5_T	37_N	0.682	1.00
71_A	129_I	0.679	1.00
173_L	177_P	0.676	1.00
27_V	31_A	0.674	1.00
103_F	106_R	0.670	1.00
87_V	90_I	0.669	1.00
134_I	148_L	0.665	1.00
57_S	121_T	0.663	1.00
120_S	124_M	0.662	1.00
69_T	73_N	0.654	1.00
118_I	122_Y	0.654	1.00
23_S	107_E	0.648	1.00
17_F	52_M	0.634	1.00
92_S	96_N	0.634	1.00
104_V	107_E	0.633	1.00
65_K	68_E	0.633	1.00
9_I	44_Y	0.632	1.00
154_Q	157_S	0.627	1.00
23_S	110_I	0.620	1.00
22_F	49_G	0.612	1.00
102_R	105_Y	0.609	1.00
10_I	14_V	0.600	1.00
34_A	37_N	0.600	1.00
106_R	110_I	0.597	1.00
138_E	143_Y	0.594	1.00
78_S	82_Q	0.587	1.00
181_Y	184_K	0.586	1.00
150_H	153_L	0.586	1.00
76_T	85_Q	0.584	1.00
134_I	138_E	0.581	1.00
5_T	40_H	0.580	1.00
31_A	36_V	0.579	1.00
79_T	142_E	0.579	1.00
100_L	103_F	0.573	1.00
134_I	151_F	0.572	1.00
158_L	161_M	0.572	1.00
88_F	183_Y	0.572	1.00
84_L	180_P	0.571	1.00
93_Y	96_N	0.569	1.00
147_P	151_F	0.568	1.00
80_Q	142_E	0.562	1.00
36_V	44_Y	0.559	1.00
117_E	120_S	0.558	1.00
97_H	100_L	0.557	1.00
90_I	94_Q	0.556	1.00
101_T	105_Y	0.555	1.00
101_T	106_R	0.555	1.00
174_Y	177_P	0.554	1.00
157_S	160_M	0.552	1.00
157_S	165_Q	0.552	1.00
22_F	25_T	0.551	1.00
135_E	149_P	0.550	1.00
79_T	143_Y	0.545	1.00
61_E	122_Y	0.544	1.00
71_A	132_L	0.542	1.00
107_E	111_D	0.540	1.00
165_Q	168_Y	0.536	1.00
60_Y	125_K	0.533	1.00
88_F	184_K	0.533	1.00
91_L	95_H	0.533	1.00
151_F	154_Q	0.532	1.00
100_L	106_R	0.532	1.00
69_T	89_D	0.529	1.00
66_T	93_Y	0.527	1.00
173_L	176_Q	0.524	1.00
62_G	66_T	0.523	1.00
5_T	43_Y	0.521	1.00
27_V	48_K	0.520	1.00
79_T	133_I	0.519	1.00
41_I	46_K	0.517	1.00
31_A	37_N	0.517	1.00
38_V	41_I	0.515	1.00
122_Y	126_E	0.515	1.00
99_Q	105_Y	0.514	1.00
53_E	117_E	0.512	1.00
34_A	38_V	0.510	1.00
14_V	62_G	0.509	1.00
92_S	95_H	0.506	1.00
120_S	123_L	0.504	1.00
178_H	181_Y	0.503	1.00
145_T	151_F	0.502	1.00
172_V	176_Q	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
4jykA	2	0.9372	100	0.253	Contact Map
3nrgA	2	0.9469	100	0.254	Contact Map
3npiA	2	0.9855	100	0.261	Contact Map
3f0cA	2	0.913	100	0.264	Contact Map
4kwaA	2	0.9227	100	0.266	Contact Map
2ibdA	2	0.9179	100	0.267	Contact Map
3dewA	2	0.9179	100	0.268	Contact Map
2qtqA	2	0.9372	100	0.268	Contact Map
3lsjA	2	0.9517	100	0.27	Contact Map
3himA	2	0.9227	100	0.27	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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