YVMB - BACSU - GREMLIN Contacts

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YVMB - Uncharacterized HTH-type transcriptional regulator YvmB

UniProt:	P40762	Sequences: MSDLTKQMIYDIYVRLLHLNEQKANTSLQQFFKEAAEEDVAEIPKNMTSIHVIDCIGQHEPINNAGIARKMNLSKANVTKISTKLIKEEFINSYQLTDNKKEVYFKLTRKGRRIFDLHEKLHKKKELAFYQFLDSFSQEEQKAVLKFLEQLTSTLEAEQTDGTPDKPVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	169 (131)
Sequences:	1843 (1499)
Seq/√Len:	131.0

ECOLI - SLYA MARR MPRA
BACSU - YVMB YVNA YHJH YSMB YDGG YCGE YYBA MHQR YUSO YFIV YWHA YKOM YDGJ YXAD YWAE YPOP YETL YWOH OHRR YDCH 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
92_N	106_K	2.847	1.00
56_I	62_I	2.689	1.00
140_E	150_Q	2.484	1.00
137_S	140_E	2.450	1.00
144_V	147_F	2.429	1.00
89_E	110_K	2.371	1.00
110_K	113_R	2.370	1.00
94_Y	106_K	2.341	1.00
99_N	102_E	2.300	1.00
57_G	115_F	2.291	1.00
63_N	66_G	2.268	1.00
56_I	91_I	2.233	1.00
49_S	88_E	2.210	1.00
136_F	147_F	2.207	1.00
143_A	146_K	2.184	1.00
109_R	112_R	2.182	1.00
82_S	91_I	2.166	1.00
63_N	102_E	2.072	1.00
96_L	99_N	2.054	1.00
93_S	100_K	2.041	1.00
61_P	106_K	2.030	1.00
51_H	118_H	1.897	1.00
136_F	150_Q	1.880	1.00
140_E	146_K	1.822	1.00
73_L	78_V	1.794	1.00
46_N	49_S	1.767	1.00
82_S	86_I	1.696	1.00
59_H	62_I	1.681	1.00
62_I	70_K	1.629	1.00
77_N	80_K	1.609	1.00
140_E	143_A	1.568	1.00
64_N	105_F	1.534	1.00
67_I	105_F	1.468	1.00
118_H	122_H	1.459	1.00
95_Q	103_V	1.411	1.00
93_S	103_V	1.396	1.00
57_G	107_L	1.374	1.00
96_L	101_K	1.367	1.00
53_I	107_L	1.352	1.00
53_I	115_F	1.350	1.00
86_I	105_F	1.349	1.00
135_S	154_T	1.318	1.00
54_D	76_A	1.312	1.00
86_I	93_S	1.312	1.00
52_V	81_I	1.309	1.00
74_S	77_N	1.297	1.00
96_L	102_E	1.294	1.00
64_N	82_S	1.242	1.00
120_K	124_K	1.227	1.00
80_K	84_K	1.225	1.00
112_R	116_D	1.213	1.00
53_I	57_G	1.199	0.99
83_T	100_K	1.199	0.99
74_S	80_K	1.198	0.99
46_N	84_K	1.164	0.99
59_H	70_K	1.155	0.99
134_D	142_K	1.104	0.99
143_A	147_F	1.099	0.99
52_V	78_V	1.096	0.99
96_L	104_Y	1.061	0.99
83_T	93_S	1.060	0.99
138_Q	142_K	1.044	0.99
130_Y	134_D	1.040	0.98
142_K	146_K	1.036	0.98
145_L	149_E	1.025	0.98
52_V	67_I	1.022	0.98
79_T	83_T	1.007	0.98
55_C	62_I	1.004	0.98
68_A	74_S	0.997	0.98
62_I	66_G	0.985	0.98
27_S	31_F	0.985	0.98
44_P	88_E	0.977	0.98
53_I	85_L	0.958	0.97
60_E	106_K	0.951	0.97
65_A	75_K	0.944	0.97
100_K	103_V	0.930	0.97
57_G	112_R	0.922	0.97
82_S	105_F	0.915	0.97
55_C	71_M	0.897	0.96
76_A	82_S	0.883	0.96
80_K	99_N	0.877	0.96
46_N	129_F	0.867	0.95
64_N	79_T	0.862	0.95
66_G	69_R	0.858	0.95
51_H	122_H	0.857	0.95
36_A	39_D	0.849	0.95
109_R	113_R	0.837	0.94
50_I	56_I	0.830	0.94
54_D	58_Q	0.827	0.94
65_A	102_E	0.822	0.94
113_R	116_D	0.811	0.93
73_L	80_K	0.811	0.93
52_V	56_I	0.811	0.93
32_F	35_A	0.804	0.93
45_K	131_Q	0.787	0.92
65_A	77_N	0.786	0.92
139_E	142_K	0.783	0.92
137_S	141_Q	0.779	0.92
31_F	35_A	0.772	0.92
131_Q	157_A	0.754	0.91
28_L	36_A	0.751	0.90
51_H	76_A	0.750	0.90
142_K	153_S	0.718	0.88
81_I	84_K	0.716	0.88
145_L	152_T	0.716	0.88
63_N	104_Y	0.711	0.88
46_N	74_S	0.702	0.87
29_Q	33_K	0.700	0.87
36_A	40_V	0.693	0.87
45_K	90_F	0.689	0.86
68_A	77_N	0.687	0.86
107_L	111_G	0.687	0.86
26_T	35_A	0.686	0.86
87_K	98_D	0.685	0.86
44_P	110_K	0.685	0.86
139_E	143_A	0.676	0.85
87_K	114_I	0.671	0.85
64_N	78_V	0.669	0.85
48_T	77_N	0.666	0.84
73_L	144_V	0.665	0.84
65_A	69_R	0.662	0.84
146_K	150_Q	0.648	0.83
78_V	86_I	0.647	0.83
49_S	64_N	0.641	0.82
50_I	101_K	0.641	0.82
68_A	78_V	0.640	0.82
116_D	142_K	0.635	0.81
131_Q	134_D	0.635	0.81
87_K	137_S	0.635	0.81
85_L	90_F	0.630	0.81
37_E	40_V	0.630	0.81
79_T	102_E	0.628	0.81
83_T	87_K	0.623	0.80
58_Q	115_F	0.621	0.80
49_S	154_T	0.620	0.80
141_Q	145_L	0.616	0.79
27_S	34_E	0.612	0.79
46_N	100_K	0.611	0.79
147_F	150_Q	0.607	0.78
51_H	55_C	0.603	0.78
79_T	99_N	0.601	0.78
119_E	123_K	0.600	0.78
59_H	134_D	0.600	0.78
86_I	97_T	0.598	0.77
25_N	29_Q	0.594	0.77
95_Q	100_K	0.592	0.77
64_N	75_K	0.591	0.77
49_S	101_K	0.587	0.76
60_E	105_F	0.585	0.76
90_F	107_L	0.584	0.76
135_S	150_Q	0.578	0.75
39_D	42_E	0.576	0.75
136_F	155_L	0.574	0.75
68_A	83_T	0.572	0.74
49_S	74_S	0.572	0.74
43_I	117_L	0.570	0.74
48_T	81_I	0.569	0.74
150_Q	153_S	0.566	0.74
66_G	156_E	0.566	0.74
136_F	140_E	0.564	0.73
46_N	50_I	0.564	0.73
48_T	52_V	0.563	0.73
77_N	132_F	0.563	0.73
92_N	109_R	0.562	0.73
49_S	118_H	0.561	0.73
135_S	143_A	0.560	0.73
95_Q	102_E	0.560	0.73
68_A	75_K	0.558	0.72
78_V	83_T	0.549	0.71
149_E	152_T	0.548	0.71
122_H	125_K	0.546	0.71
80_K	105_F	0.545	0.71
148_L	156_E	0.545	0.71
49_S	114_I	0.544	0.71
119_E	146_K	0.543	0.70
82_S	119_E	0.542	0.70
51_H	68_A	0.542	0.70
48_T	71_M	0.539	0.70
35_A	40_V	0.534	0.69
62_I	67_I	0.534	0.69
73_L	77_N	0.532	0.69
44_P	90_F	0.532	0.69
37_E	41_A	0.532	0.69
130_Y	151_L	0.529	0.68
50_I	118_H	0.522	0.67
89_E	108_T	0.517	0.67
86_I	91_I	0.517	0.67
149_E	157_A	0.516	0.67
43_I	58_Q	0.512	0.66
55_C	153_S	0.511	0.66
63_N	75_K	0.509	0.66
93_S	105_F	0.506	0.65
90_F	110_K	0.503	0.65
80_K	83_T	0.502	0.64
31_F	72_N	0.501	0.64
56_I	85_L	0.500	0.64

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
2rdpA	2	0.8284	99.9	0.451	Contact Map
4mnuA	2	0.8876	99.9	0.46	Contact Map
1lj9A	2	0.8521	99.9	0.46	Contact Map
2fbkA	2	0.8107	99.8	0.462	Contact Map
4yifA	2	0.8343	99.8	0.462	Contact Map
3s2wA	3	0.8343	99.8	0.464	Contact Map
1s3jA	2	0.8521	99.8	0.464	Contact Map
3g3zA	2	0.8402	99.8	0.466	Contact Map
3tgnA	2	0.8639	99.8	0.466	Contact Map
3deuA	2	0.7751	99.8	0.467	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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