YHJH - BACSU - GREMLIN Contacts

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YHJH - Uncharacterized HTH-type transcriptional regulator YhjH

UniProt:	Q796S4	Sequences: MNTDHTKRNLFELYAELIHQQEKWEGLIKAFLSDELRKLDVEHGSKSQLTMTEIHVLSCVGDNEPINVTSIAEKMNTTKATVSRISTKLLGAGFLHRTQLSDNKKEVYFRLTPAGKKLHSLHKYYHQKAEQRFLSFFDRYTEEEILFAERLFRDLVTKWYPSSEEIEGGLPSIFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	175 (137)
Sequences:	2193 (1778)
Seq/√Len:	151.9

ECOLI - SLYA MARR MPRA
BACSU - YHJH YVNA YVMB YFIV YCGE MHQR YSMB YWHA YXAD YUSO YYBA YDGG YPOP YETL YKOM OHRR YWAE YDGJ YWOH YDCH
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
65_P	110_R	2.745	1.00
93_G	114_A	2.608	1.00
96_H	110_R	2.569	1.00
67_N	70_S	2.536	1.00
148_A	151_L	2.516	1.00
53_E	92_A	2.361	1.00
98_T	110_R	2.347	1.00
144_E	154_D	2.335	1.00
141_T	144_E	2.324	1.00
60_V	66_I	2.284	1.00
77_T	82_V	2.168	1.00
60_V	95_L	2.132	1.00
99_Q	107_V	2.041	1.00
147_F	150_R	1.976	1.00
81_T	84_R	1.949	1.00
86_S	95_L	1.949	1.00
114_A	117_K	1.944	1.00
87_T	104_K	1.929	1.00
140_Y	151_L	1.886	1.00
97_R	104_K	1.842	1.00
67_N	106_E	1.841	1.00
103_N	106_E	1.829	1.00
113_P	116_K	1.827	1.00
144_E	150_R	1.809	1.00
122_H	126_H	1.797	1.00
61_G	119_H	1.748	1.00
100_L	106_E	1.736	1.00
140_Y	154_D	1.721	1.00
100_L	103_N	1.617	1.00
63_N	66_I	1.607	1.00
86_S	90_L	1.603	1.00
116_K	120_S	1.602	1.00
71_I	109_F	1.564	1.00
68_V	109_F	1.511	1.00
90_L	97_R	1.499	1.00
56_V	85_I	1.498	1.00
84_R	88_K	1.446	1.00
55_H	122_H	1.441	1.00
50_T	53_E	1.432	1.00
56_V	71_I	1.420	1.00
61_G	116_K	1.416	1.00
66_I	74_K	1.374	1.00
57_L	119_H	1.373	1.00
57_L	111_L	1.370	1.00
68_V	86_S	1.335	1.00
78_T	81_T	1.334	1.00
86_S	109_F	1.330	1.00
139_R	158_K	1.312	1.00
87_T	97_R	1.295	1.00
78_T	84_R	1.294	1.00
29_K	33_S	1.287	1.00
100_L	108_Y	1.278	1.00
39_L	42_E	1.244	1.00
58_S	80_A	1.211	1.00
69_T	79_K	1.193	1.00
144_E	147_F	1.180	1.00
55_H	126_H	1.178	1.00
83_S	87_T	1.140	1.00
69_T	73_E	1.134	1.00
83_S	103_N	1.127	1.00
61_G	111_L	1.110	0.99
57_L	61_G	1.101	0.99
59_C	75_M	1.095	0.99
49_L	94_F	1.092	0.99
139_R	154_D	1.086	0.99
97_R	107_V	1.082	0.99
143_E	146_L	1.077	0.99
104_K	107_V	1.072	0.99
67_N	108_Y	1.060	0.99
124_Y	128_K	1.060	0.99
146_L	150_R	1.038	0.99
142_E	146_L	1.035	0.99
34_D	160_Y	1.005	0.99
100_L	105_K	1.001	0.99
147_F	151_L	0.990	0.99
128_K	131_Q	0.982	0.99
68_V	79_K	0.982	0.99
37_R	41_V	0.963	0.98
70_S	73_E	0.952	0.98
66_I	70_S	0.945	0.98
150_R	154_D	0.940	0.98
111_L	115_G	0.939	0.98
68_V	83_S	0.926	0.98
49_L	54_I	0.901	0.98
23_K	153_R	0.900	0.98
56_V	75_M	0.888	0.97
27_L	153_R	0.866	0.97
36_L	40_D	0.865	0.97
99_Q	104_K	0.865	0.97
50_T	88_K	0.862	0.97
128_K	132_R	0.857	0.97
52_T	81_T	0.855	0.97
149_E	153_R	0.846	0.97
120_S	124_Y	0.830	0.96
113_P	117_K	0.829	0.96
27_L	149_E	0.824	0.96
64_E	109_F	0.823	0.96
28_I	31_F	0.822	0.96
117_K	121_L	0.817	0.96
52_T	85_I	0.814	0.96
127_Q	131_Q	0.804	0.95
122_H	125_Y	0.786	0.95
56_V	82_V	0.785	0.95
63_N	74_K	0.778	0.94
58_S	62_D	0.775	0.94
117_K	120_S	0.774	0.94
82_V	90_L	0.771	0.94
150_R	153_R	0.766	0.94
83_S	106_E	0.763	0.94
87_T	91_G	0.760	0.94
151_L	154_D	0.759	0.94
123_K	127_Q	0.759	0.94
59_C	71_I	0.756	0.94
53_E	68_V	0.746	0.93
80_A	126_H	0.738	0.93
68_V	82_V	0.737	0.93
94_F	114_A	0.729	0.92
96_H	112_T	0.727	0.92
38_K	42_E	0.722	0.92
105_K	109_F	0.714	0.92
143_E	147_F	0.714	0.92
77_T	84_R	0.709	0.91
65_P	98_T	0.700	0.91
69_T	81_T	0.697	0.91
53_E	84_R	0.694	0.90
35_E	39_L	0.689	0.90
116_K	142_E	0.684	0.90
57_L	94_F	0.680	0.89
55_H	72_A	0.677	0.89
52_T	56_V	0.672	0.89
145_I	149_E	0.670	0.89
90_L	109_F	0.669	0.89
64_E	110_R	0.667	0.89
47_S	121_L	0.661	0.88
69_T	107_V	0.655	0.88
146_L	157_T	0.650	0.87
29_K	32_L	0.649	0.87
126_H	130_E	0.648	0.87
84_R	87_T	0.645	0.87
27_L	34_D	0.640	0.86
48_Q	114_A	0.637	0.86
59_C	66_I	0.636	0.86
141_T	145_I	0.636	0.86
37_R	40_D	0.634	0.86
55_H	58_S	0.631	0.86
27_L	32_L	0.626	0.85
72_A	79_K	0.617	0.84
69_T	106_E	0.610	0.84
48_Q	92_A	0.610	0.84
72_A	81_T	0.609	0.84
53_E	71_I	0.609	0.84
77_T	85_I	0.603	0.83
27_L	30_A	0.599	0.83
25_E	29_K	0.599	0.83
34_D	156_V	0.596	0.82
93_G	96_H	0.596	0.82
138_D	146_L	0.593	0.82
69_T	72_A	0.592	0.82
97_R	109_F	0.591	0.82
136_F	148_A	0.584	0.81
149_E	156_V	0.583	0.81
58_S	69_T	0.583	0.81
84_R	103_N	0.583	0.81
26_G	33_S	0.580	0.81
55_H	61_G	0.573	0.80
75_M	80_A	0.572	0.80
30_A	34_D	0.572	0.80
54_I	125_Y	0.571	0.80
114_A	157_T	0.570	0.79
77_T	81_T	0.567	0.79
74_K	128_K	0.565	0.79
42_E	46_K	0.563	0.79
54_I	122_H	0.560	0.78
50_T	130_E	0.556	0.78
85_I	88_K	0.550	0.77
87_T	95_L	0.549	0.77
41_V	119_H	0.543	0.76
35_E	38_K	0.542	0.76
81_T	152_F	0.541	0.76
116_K	150_R	0.541	0.76
24_W	33_S	0.539	0.76
81_T	136_F	0.539	0.76
65_P	108_Y	0.535	0.75
78_T	126_H	0.535	0.75
78_T	122_H	0.534	0.75
58_S	119_H	0.532	0.75
23_K	30_A	0.528	0.74
53_E	78_T	0.527	0.74
140_Y	148_A	0.527	0.74
153_R	161_P	0.525	0.74
145_I	158_K	0.522	0.73
124_Y	127_Q	0.521	0.73
72_A	78_T	0.520	0.73
59_C	83_S	0.520	0.73
62_D	120_S	0.519	0.73
52_T	77_T	0.518	0.73
55_H	107_V	0.518	0.73
62_D	119_H	0.510	0.72
69_T	90_L	0.510	0.72
148_A	154_D	0.510	0.72
53_E	88_K	0.509	0.71
23_K	93_G	0.508	0.71
75_M	82_V	0.508	0.71
83_S	126_H	0.503	0.71
120_S	146_L	0.501	0.70
149_E	155_L	0.500	0.70

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
1lj9A	2	0.8229	99.9	0.461	Contact Map
2fbkA	2	0.8171	99.9	0.465	Contact Map
3oopA	2	0.7886	99.9	0.469	Contact Map
3nqoA	2	0.8914	99.9	0.469	Contact Map
3bj6A	2	0.8514	99.9	0.47	Contact Map
1s3jA	2	0.8057	99.9	0.471	Contact Map
4mnuA	2	0.8629	99.9	0.477	Contact Map
3s2wA	3	0.8514	99.9	0.477	Contact Map
4yifA	2	0.8057	99.9	0.478	Contact Map
3deuA	2	0.7486	99.9	0.478	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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