YDFF - BACSU - GREMLIN Contacts

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

YDFF - Uncharacterized HTH-type transcriptional regulator YdfF

UniProt:	P96683	Sequences: MNPNIAKISSLLSDPSRSSILLSLMDGRIHPAGELAYLANIKPQTASFHLNKLLEAKLISVEKHGRHRYYRLADSDAANVIEQLLHIAPKAKVKSLKESKEKKDLHFARTCYDHLAGYVGVQMAHSLVEQGMLKKVDLNFEVTSEGALFFSKLGINEEQQRNKRRAFARCCLDWSERQHHIAGALGNALLVRMLEEEWIVRMPKTRAIRITQSGKIAFEKHLNVKI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	226 (217)
Sequences:	937 (628)
Seq/√Len:	42.6

BACSU - YDFF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
192_R	196_E	5.420	1.00
20_I	46_A	4.505	1.00
62_E	71_R	3.922	1.00
113_D	165_R	3.736	1.00
125_H	178_Q	3.703	1.00
113_D	187_N	3.400	1.00
115_L	208_I	3.298	1.00
143_T	146_G	3.117	1.00
199_I	208_I	3.096	1.00
11_L	56_A	2.949	1.00
80_V	83_Q	2.810	1.00
132_M	149_F	2.654	1.00
25_M	85_L	2.641	1.00
200_V	209_R	2.622	1.00
16_S	41_I	2.606	1.00
124_A	140_F	2.383	1.00
54_L	59_I	2.380	1.00
165_R	187_N	2.375	1.00
41_I	45_T	2.266	1.00
166_A	169_R	2.236	1.00
77_A	87_I	2.130	0.99
194_L	208_I	2.095	0.99
105_L	174_W	2.070	0.99
47_S	51_N	2.002	0.99
115_L	120_G	1.989	0.99
198_W	217_A	1.977	0.99
62_E	179_H	1.941	0.99
165_R	184_A	1.929	0.99
34_E	177_R	1.907	0.99
32_A	50_L	1.876	0.99
196_E	217_A	1.801	0.98
54_L	61_V	1.796	0.98
31_P	64_H	1.786	0.98
80_V	87_I	1.765	0.98
26_D	30_H	1.727	0.98
127_L	132_M	1.710	0.97
60_S	71_R	1.682	0.97
106_H	175_S	1.635	0.97
123_M	222_L	1.579	0.96
172_L	177_R	1.573	0.96
199_I	210_I	1.572	0.96
213_S	217_A	1.559	0.96
184_A	187_N	1.545	0.95
197_E	200_V	1.522	0.95
110_T	190_L	1.507	0.95
12_L	21_L	1.499	0.95
110_T	208_I	1.494	0.94
28_R	176_E	1.489	0.94
115_L	199_I	1.476	0.94
191_V	195_E	1.428	0.93
64_H	67_H	1.427	0.93
34_E	64_H	1.423	0.93
193_M	218_F	1.416	0.93
81_I	121_V	1.401	0.92
140_F	168_A	1.400	0.92
190_L	194_L	1.396	0.92
108_A	208_I	1.349	0.91
126_S	222_L	1.331	0.90
29_I	64_H	1.321	0.90
58_L	77_A	1.318	0.90
11_L	59_I	1.309	0.89
16_S	30_H	1.307	0.89
155_I	192_R	1.281	0.88
85_L	175_S	1.278	0.88
113_D	184_A	1.273	0.88
124_A	181_I	1.208	0.85
32_A	43_P	1.204	0.85
193_M	217_A	1.203	0.85
211_T	214_G	1.191	0.84
110_T	199_I	1.182	0.84
217_A	220_K	1.165	0.83
19_S	40_N	1.159	0.83
39_A	46_A	1.153	0.82
130_Q	145_E	1.146	0.82
31_P	172_L	1.139	0.82
25_M	34_E	1.137	0.81
69_Y	177_R	1.128	0.81
132_M	145_E	1.121	0.80
41_I	46_A	1.112	0.80
102_K	106_H	1.108	0.80
11_L	68_R	1.099	0.79
47_S	70_Y	1.096	0.79
42_K	48_F	1.076	0.78
71_R	85_L	1.068	0.77
26_D	68_R	1.066	0.77
147_A	167_F	1.048	0.76
29_I	69_Y	1.047	0.76
31_P	34_E	1.047	0.76
120_G	123_M	1.044	0.75
23_S	30_H	1.041	0.75
132_M	146_G	1.034	0.75
67_H	172_L	1.032	0.75
126_S	129_E	1.031	0.75
33_G	37_Y	1.021	0.74
21_L	70_Y	1.019	0.74
135_K	170_C	1.018	0.74
102_K	168_A	0.999	0.72
80_V	84_L	0.992	0.72
153_L	192_R	0.980	0.71
151_S	158_E	0.964	0.69
107_F	119_V	0.964	0.69
194_L	201_R	0.964	0.69
149_F	222_L	0.961	0.69
108_A	185_L	0.961	0.69
25_M	78_A	0.956	0.69
150_F	185_L	0.939	0.67
107_F	215_K	0.933	0.67
11_L	22_L	0.930	0.67
56_A	59_I	0.928	0.66
45_T	72_L	0.926	0.66
107_F	210_I	0.925	0.66
13_S	30_H	0.924	0.66
16_S	99_S	0.920	0.66
10_S	106_H	0.919	0.66
31_P	170_C	0.918	0.66
127_L	189_L	0.910	0.65
92_K	95_S	0.908	0.65
79_N	83_Q	0.904	0.64
25_M	172_L	0.902	0.64
95_S	98_E	0.901	0.64
153_L	196_E	0.890	0.63
16_S	45_T	0.888	0.63
99_S	102_K	0.884	0.63
216_I	220_K	0.877	0.62
181_I	218_F	0.872	0.62
28_R	98_E	0.872	0.62
50_L	70_Y	0.871	0.62
63_K	70_Y	0.865	0.61
148_L	152_K	0.864	0.61
45_T	49_H	0.860	0.61
78_A	82_E	0.849	0.60
30_H	44_Q	0.849	0.60
28_R	68_R	0.846	0.59
11_L	18_S	0.840	0.59
31_P	69_Y	0.837	0.58
120_G	190_L	0.836	0.58
5_I	72_L	0.832	0.58
61_V	68_R	0.831	0.58
14_D	18_S	0.831	0.58
156_N	159_Q	0.831	0.58
192_R	195_E	0.826	0.57
108_A	210_I	0.825	0.57
21_L	106_H	0.824	0.57
30_H	99_S	0.824	0.57
149_F	152_K	0.815	0.56
85_L	222_L	0.810	0.56
213_S	216_I	0.809	0.56
4_N	7_K	0.806	0.56
71_R	154_G	0.796	0.55
42_K	45_T	0.796	0.55
127_L	150_F	0.792	0.54
50_L	59_I	0.790	0.54
15_P	185_L	0.789	0.54
70_Y	185_L	0.789	0.54
112_Y	173_D	0.786	0.54
16_S	39_A	0.786	0.54
128_V	135_K	0.785	0.54
61_V	70_Y	0.783	0.53
138_L	168_A	0.782	0.53
78_A	172_L	0.781	0.53
12_L	81_I	0.778	0.53
147_A	158_E	0.774	0.53
146_G	149_F	0.774	0.53
101_E	168_A	0.773	0.52
116_A	177_R	0.772	0.52
113_D	164_R	0.771	0.52
158_E	197_E	0.766	0.52
112_Y	116_A	0.763	0.51
190_L	208_I	0.761	0.51
159_Q	195_E	0.757	0.51
12_L	80_V	0.754	0.51
69_Y	172_L	0.753	0.51
115_L	181_I	0.753	0.51
155_I	188_A	0.751	0.50
110_T	207_A	0.747	0.50
200_V	203_P	0.736	0.49
10_S	86_H	0.736	0.49
26_D	59_I	0.731	0.48
31_P	59_I	0.730	0.48
55_E	178_Q	0.728	0.48
190_L	199_I	0.727	0.48
126_S	130_Q	0.727	0.48
194_L	199_I	0.727	0.48
63_K	89_P	0.725	0.48
152_K	191_V	0.723	0.48
24_L	121_V	0.718	0.47
5_I	108_A	0.718	0.47
120_G	220_K	0.716	0.47
80_V	169_R	0.715	0.47
189_L	193_M	0.711	0.47
144_S	151_S	0.698	0.45
217_A	221_H	0.692	0.45
112_Y	206_R	0.690	0.45
13_S	26_D	0.689	0.45
127_L	218_F	0.688	0.44
118_Y	122_Q	0.685	0.44
29_I	67_H	0.681	0.44
57_K	130_Q	0.679	0.44
26_D	110_T	0.678	0.43
97_K	106_H	0.672	0.43
151_S	162_N	0.671	0.43
20_I	27_G	0.670	0.43
133_L	140_F	0.665	0.42
150_F	165_R	0.664	0.42
13_S	19_S	0.662	0.42
67_H	198_W	0.662	0.42
75_S	79_N	0.662	0.42
10_S	52_K	0.662	0.42
124_A	133_L	0.661	0.42
144_S	216_I	0.659	0.42
156_N	167_F	0.657	0.42
98_E	102_K	0.652	0.41
67_H	177_R	0.650	0.41
51_N	91_A	0.645	0.40
123_M	193_M	0.644	0.40
131_G	144_S	0.644	0.40
142_V	147_A	0.641	0.40
48_F	108_A	0.639	0.40
134_K	141_E	0.637	0.40
45_T	198_W	0.635	0.40
44_Q	52_K	0.633	0.39
8_I	175_S	0.629	0.39
148_L	201_R	0.628	0.39
36_A	46_A	0.626	0.39
75_S	133_L	0.626	0.39
13_S	56_A	0.625	0.39
21_L	175_S	0.624	0.39
38_L	83_Q	0.620	0.38
76_D	131_G	0.620	0.38
45_T	48_F	0.618	0.38
113_D	124_A	0.617	0.38
169_R	175_S	0.616	0.38
192_R	217_A	0.615	0.38
120_G	126_S	0.615	0.38
62_E	85_L	0.612	0.37
22_L	85_L	0.611	0.37
67_H	208_I	0.610	0.37
108_A	203_P	0.609	0.37
46_A	82_E	0.609	0.37
78_A	150_F	0.608	0.37
43_P	208_I	0.608	0.37
29_I	34_E	0.605	0.37
5_I	18_S	0.605	0.37
55_E	148_L	0.604	0.37
197_E	201_R	0.603	0.37
124_A	211_T	0.602	0.37
79_N	189_L	0.600	0.36
22_L	120_G	0.599	0.36
30_H	61_V	0.599	0.36
21_L	30_H	0.597	0.36
140_F	170_C	0.595	0.36
211_T	217_A	0.594	0.36
131_G	134_K	0.594	0.36
42_K	118_Y	0.590	0.36
34_E	172_L	0.587	0.35
20_I	101_E	0.587	0.35
188_A	192_R	0.579	0.35
25_M	31_P	0.579	0.35
28_R	96_L	0.579	0.35
122_Q	125_H	0.576	0.34
8_I	88_A	0.573	0.34
202_M	209_R	0.570	0.34
72_L	78_A	0.570	0.34
45_T	81_I	0.568	0.34
30_H	70_Y	0.567	0.34
68_R	106_H	0.566	0.33
12_L	87_I	0.566	0.33
112_Y	121_V	0.562	0.33
115_L	193_M	0.560	0.33
4_N	88_A	0.558	0.33
42_K	52_K	0.557	0.33
75_S	125_H	0.557	0.33
156_N	168_A	0.556	0.33
126_S	223_N	0.555	0.33
132_M	218_F	0.554	0.32
23_S	38_L	0.553	0.32
59_I	164_R	0.552	0.32
122_Q	223_N	0.551	0.32
145_E	148_L	0.550	0.32
181_I	185_L	0.550	0.32
31_P	70_Y	0.547	0.32
129_E	219_E	0.547	0.32
5_I	13_S	0.545	0.32
81_I	85_L	0.545	0.32
30_H	38_L	0.545	0.32
6_A	192_R	0.545	0.32
134_K	152_K	0.544	0.32
184_A	188_A	0.543	0.32
131_G	141_E	0.543	0.32
202_M	205_T	0.542	0.31
75_S	216_I	0.541	0.31
83_Q	190_L	0.540	0.31
64_H	69_Y	0.539	0.31
81_I	122_Q	0.538	0.31
44_Q	48_F	0.538	0.31
30_H	69_Y	0.535	0.31
28_R	110_T	0.534	0.31
12_L	216_I	0.532	0.31
154_G	197_E	0.531	0.31
80_V	147_A	0.530	0.31
7_K	88_A	0.528	0.30
187_N	198_W	0.526	0.30
132_M	143_T	0.526	0.30
4_N	83_Q	0.523	0.30
96_L	194_L	0.519	0.30
5_I	79_N	0.518	0.30
48_F	120_G	0.518	0.30
26_D	82_E	0.518	0.30
188_A	222_L	0.517	0.29
157_E	200_V	0.517	0.29
84_L	123_M	0.513	0.29
109_R	206_R	0.511	0.29
119_V	210_I	0.510	0.29
95_S	100_K	0.510	0.29
150_F	193_M	0.506	0.29
193_M	199_I	0.506	0.29
15_P	223_N	0.506	0.29
171_C	186_G	0.506	0.29
67_H	165_R	0.505	0.29
12_L	26_D	0.504	0.28
23_S	168_A	0.504	0.28
22_L	182_A	0.503	0.28
121_V	154_G	0.503	0.28
34_E	170_C	0.501	0.28
10_S	43_P	0.500	0.28
76_D	90_K	0.500	0.28

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
2kkoA	2	0.4336	99.4	0.828	Contact Map
1r1tA	2	0.3982	99.4	0.83	Contact Map
1u2wA	2	0.4071	99.4	0.831	Contact Map
1q1hA	1	0.3451	99.3	0.835	Contact Map
1r1uA	2	0.4071	99.3	0.837	Contact Map
2zkzA	2	0.3805	99.3	0.838	Contact Map
3pqkA	2	0.4115	99.3	0.838	Contact Map
3cuoA	2	0.3938	99.3	0.841	Contact Map
4k2eA	2	0.3938	99.2	0.841	Contact Map
3f6vA	2	0.4248	99.2	0.846	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 0.0078 seconds.