YVAF - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YVAF - Uncharacterized HTH-type transcriptional regulator YvaF

UniProt:	O32228	Sequences: MDKRILAETFRLIKQKGFSFTMNDLAAALGTSKRTLYAYYSSKDQLVEAVVEQFIAEMKQIERDIYENESLNVLEKVKQMLISLPQGMELLNMGLLNELKKYHYDAWLTLDAFIKEEWAIVLALLNECKQQKRIRNINPDLFVHMYIGSINQVYDPEYPLKHQFTTGEVLESIVDVLFNGITADEEADAT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	190 (174)
Sequences:	36345 (28764)
Seq/√Len:	2180.6

ECOLI - ACRR RUTR ENVR SLMA COMR NEMR BDCR UIDR FABR YBIH BETI YJDC RCDA
BACSU - YVAF FADR YHGD BSCR YFIR YVDT YTTP LMRA YVKB PKSA YXAF YDGC YEZE YDES YCNC YOBS YUXN YERO
HALSA - Q9HRF3 Q9HM72
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
16_K	24_D	3.918	1.00
23_N	33_K	3.907	1.00
11_R	28_A	3.721	1.00
41_S	45_Q	2.800	1.00
122_L	140_D	2.310	1.00
13_I	20_F	2.309	1.00
76_K	127_E	2.171	1.00
26_A	36_L	2.169	1.00
12_L	20_F	2.139	1.00
15_Q	28_A	2.114	1.00
42_S	45_Q	2.092	1.00
32_S	35_T	2.080	1.00
72_N	75_E	1.911	1.00
3_K	53_Q	1.902	1.00
94_G	98_E	1.902	1.00
126_N	130_Q	1.864	1.00
122_L	126_N	1.863	1.00
4_R	8_E	1.736	1.00
22_M	33_K	1.729	1.00
23_N	27_A	1.714	1.00
126_N	139_P	1.696	1.00
12_L	28_A	1.693	1.00
8_E	28_A	1.690	1.00
129_K	136_N	1.681	1.00
10_F	53_Q	1.677	1.00
12_L	24_D	1.653	1.00
126_N	129_K	1.628	1.00
12_L	16_K	1.579	1.00
9_T	13_I	1.559	1.00
22_M	37_Y	1.530	1.00
3_K	7_A	1.496	1.00
49_A	52_E	1.471	1.00
6_L	49_A	1.470	1.00
78_K	171_E	1.464	1.00
8_E	11_R	1.456	1.00
17_G	20_F	1.434	1.00
35_T	38_A	1.421	1.00
128_C	134_I	1.420	1.00
82_I	167_G	1.404	1.00
128_C	133_R	1.398	1.00
22_M	36_L	1.390	1.00
40_Y	49_A	1.388	1.00
48_E	109_T	1.382	1.00
127_E	131_Q	1.372	1.00
52_E	109_T	1.369	1.00
72_N	133_R	1.356	1.00
24_D	27_A	1.353	1.00
10_F	50_V	1.339	1.00
63_R	120_I	1.337	1.00
20_F	25_L	1.331	1.00
7_A	53_Q	1.318	1.00
11_R	15_Q	1.315	1.00
32_S	38_A	1.293	1.00
141_L	172_S	1.291	1.00
21_T	24_D	1.286	1.00
129_K	137_I	1.279	1.00
10_F	54_F	1.262	1.00
138_N	141_L	1.248	1.00
24_D	28_A	1.238	1.00
82_I	170_L	1.236	1.00
118_W	144_H	1.236	1.00
145_M	149_S	1.235	1.00
82_I	171_E	1.234	1.00
53_Q	57_E	1.216	1.00
44_D	103_H	1.205	1.00
48_E	52_E	1.197	1.00
9_T	46_L	1.196	1.00
31_T	35_T	1.190	1.00
18_F	47_V	1.190	1.00
61_I	83_S	1.187	1.00
74_L	78_K	1.186	1.00
124_L	128_C	1.175	1.00
45_Q	49_A	1.172	1.00
78_K	82_I	1.163	1.00
91_L	98_E	1.160	1.00
34_R	38_A	1.142	1.00
165_T	168_E	1.122	1.00
75_E	79_Q	1.120	1.00
8_E	12_L	1.113	1.00
118_W	122_L	1.092	1.00
13_I	18_F	1.080	1.00
25_L	46_L	1.079	1.00
8_E	29_L	1.071	1.00
35_T	39_Y	1.049	1.00
37_Y	42_S	1.042	1.00
6_L	50_V	1.039	1.00
52_E	56_A	1.032	1.00
129_K	139_P	1.032	1.00
148_G	152_Q	1.012	1.00
74_L	178_F	1.010	1.00
137_I	142_F	1.001	1.00
44_D	48_E	0.984	1.00
73_V	131_Q	0.981	1.00
7_A	11_R	0.979	1.00
33_K	37_Y	0.978	1.00
45_Q	48_E	0.973	1.00
6_L	40_Y	0.966	1.00
61_I	64_D	0.959	1.00
78_K	174_V	0.956	1.00
83_S	86_Q	0.949	1.00
141_L	168_E	0.940	1.00
91_L	94_G	0.940	1.00
123_A	126_N	0.938	1.00
129_K	132_K	0.935	1.00
75_E	78_K	0.934	1.00
122_L	139_P	0.933	1.00
44_D	105_D	0.931	1.00
82_I	86_Q	0.924	1.00
78_K	175_D	0.924	1.00
73_V	128_C	0.916	1.00
76_K	124_L	0.914	1.00
92_N	98_E	0.912	1.00
93_M	98_E	0.909	1.00
123_A	127_E	0.908	1.00
109_T	112_A	0.906	1.00
120_I	123_A	0.900	1.00
119_A	123_A	0.898	1.00
127_E	130_Q	0.883	1.00
92_N	95_L	0.881	1.00
33_K	38_A	0.880	1.00
167_G	171_E	0.875	1.00
10_F	14_K	0.872	1.00
63_R	67_E	0.868	1.00
162_H	165_T	0.865	1.00
79_Q	82_I	0.864	1.00
112_A	116_E	0.859	1.00
94_G	97_N	0.855	1.00
5_I	36_L	0.855	1.00
49_A	53_Q	0.849	1.00
56_A	60_Q	0.848	1.00
98_E	101_K	0.847	1.00
118_W	140_D	0.843	1.00
53_Q	56_A	0.842	1.00
36_L	46_L	0.842	1.00
16_K	20_F	0.841	1.00
171_E	175_D	0.838	1.00
18_F	43_K	0.828	1.00
94_G	101_K	0.827	1.00
52_E	113_F	0.824	1.00
174_V	178_F	0.823	1.00
104_Y	107_W	0.810	1.00
139_P	143_V	0.807	1.00
109_T	113_F	0.806	1.00
170_L	174_V	0.799	1.00
65_I	83_S	0.794	1.00
125_L	139_P	0.789	1.00
140_D	144_H	0.789	1.00
146_Y	177_L	0.786	1.00
65_I	79_Q	0.783	1.00
59_K	120_I	0.781	1.00
26_A	33_K	0.779	1.00
95_L	99_L	0.774	1.00
108_L	112_A	0.774	1.00
16_K	28_A	0.770	1.00
168_E	172_S	0.769	1.00
122_L	143_V	0.769	1.00
54_F	57_E	0.768	1.00
73_V	133_R	0.767	1.00
59_K	116_E	0.759	1.00
68_N	79_Q	0.757	1.00
172_S	175_D	0.753	1.00
69_E	72_N	0.753	1.00
86_Q	167_G	0.752	1.00
104_Y	108_L	0.746	1.00
82_I	174_V	0.744	1.00
27_A	33_K	0.743	1.00
157_E	160_L	0.738	1.00
115_K	119_A	0.738	1.00
22_M	26_A	0.732	1.00
60_Q	64_D	0.730	1.00
9_T	50_V	0.729	1.00
81_L	146_Y	0.728	1.00
97_N	101_K	0.727	1.00
93_M	96_L	0.724	1.00
18_F	44_D	0.721	1.00
149_S	173_I	0.720	1.00
96_L	99_L	0.714	1.00
125_L	129_K	0.712	1.00
119_A	122_L	0.702	1.00
12_L	15_Q	0.702	1.00
79_Q	83_S	0.702	1.00
125_L	146_Y	0.702	1.00
95_L	98_E	0.701	1.00
126_N	140_D	0.701	1.00
13_I	47_V	0.701	1.00
86_Q	90_L	0.700	1.00
19_S	98_E	0.696	1.00
4_R	29_L	0.695	1.00
93_M	97_N	0.691	1.00
111_D	115_K	0.685	1.00
72_N	76_K	0.679	1.00
57_E	60_Q	0.679	1.00
84_L	88_M	0.673	1.00
23_N	37_Y	0.665	1.00
69_E	76_K	0.652	1.00
92_N	97_N	0.652	1.00
31_T	39_Y	0.647	1.00
60_Q	63_R	0.646	1.00
6_L	53_Q	0.641	1.00
86_Q	166_T	0.638	1.00
5_I	29_L	0.638	1.00
29_L	32_S	0.637	1.00
148_G	151_N	0.635	1.00
7_A	10_F	0.627	1.00
86_Q	170_L	0.623	1.00
166_T	170_L	0.622	1.00
116_E	119_A	0.619	1.00
59_K	63_R	0.619	1.00
56_A	113_F	0.616	1.00
111_D	114_I	0.616	1.00
5_I	39_Y	0.612	1.00
138_N	172_S	0.611	1.00
107_W	111_D	0.610	1.00
94_G	99_L	0.607	1.00
108_L	111_D	0.601	1.00
129_K	134_I	0.598	1.00
124_L	127_E	0.598	1.00
92_N	99_L	0.591	1.00
69_E	79_Q	0.588	1.00
64_D	68_N	0.584	1.00
91_L	95_L	0.582	1.00
78_K	178_F	0.580	1.00
148_G	156_P	0.580	1.00
83_S	87_G	0.579	1.00
92_N	96_L	0.577	1.00
125_L	142_F	0.577	1.00
4_R	7_A	0.575	1.00
138_N	142_F	0.571	1.00
103_H	106_A	0.570	1.00
66_Y	120_I	0.567	1.00
156_P	159_P	0.565	1.00
36_L	41_S	0.563	1.00
73_V	134_I	0.563	1.00
6_L	10_F	0.563	1.00
78_K	81_L	0.562	1.00
26_A	29_L	0.559	1.00
89_E	166_T	0.559	1.00
128_C	132_K	0.557	1.00
169_V	173_I	0.556	1.00
26_A	31_T	0.555	1.00
65_I	68_N	0.552	1.00
64_D	83_S	0.551	1.00
168_E	171_E	0.549	1.00
65_I	69_E	0.547	1.00
19_S	101_K	0.545	1.00
15_Q	24_D	0.541	1.00
91_L	97_N	0.538	1.00
141_L	145_M	0.538	1.00
145_M	148_G	0.536	1.00
73_V	76_K	0.530	1.00
52_E	112_A	0.526	1.00
76_K	128_C	0.525	1.00
172_S	176_V	0.524	1.00
170_L	173_I	0.523	1.00
164_F	168_E	0.519	1.00
66_Y	123_A	0.516	1.00
84_L	151_N	0.507	1.00
87_G	90_L	0.504	1.00
113_F	116_E	0.502	1.00
164_F	167_G	0.500	1.00
167_G	170_L	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
4udsA	2	0.9421	100	0.262	Contact Map
2ibdA	2	0.9579	100	0.266	Contact Map
1vi0A	2	0.9632	100	0.27	Contact Map
2rasA	2	0.9947	100	0.272	Contact Map
2xdnA	2	0.9947	100	0.272	Contact Map
2hytA	2	0.9684	100	0.274	Contact Map
4kwaA	2	0.9579	100	0.274	Contact Map
2genA	2	0.9632	100	0.275	Contact Map
3bqzB	3	0.9474	100	0.276	Contact Map
3dcfA	2	0.9368	100	0.277	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.

Page generated in 0.0066 seconds.