YFIV - BACSU - GREMLIN Contacts

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YFIV - Uncharacterized HTH-type transcriptional regulator YfiV

UniProt:	O31564	Sequences: MEYNLHDTTVLNENILSSEEREIWVLYMKVLTSAGLGDVSEWMKLDMSMPQMKVLMLLNNHGTLKVSDIAEKMGASLSNTTGLLDRLEKSGFVKRSHSEEDRRSVVVQLTENAKKIFRGLYEKGHLKLKRSLELLSPEEKQAVYEGLSILSRALENAKKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (134)
Sequences:	24407 (18175)
Seq/√Len:	1570.1

ECOLI - SLYA MPRA MARR
BACSU - YFIV YWAE YCGE YETL YSMB YUSO MHQR YXAD YYBA YKOM OHRR YDGJ YDGG YWHA YPOP YHJH YDCH YWOH YVMB YVNA 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
63_T	108_Q	3.203	1.00
96_S	108_Q	3.198	1.00
139_E	149_I	2.910	1.00
94_K	108_Q	2.654	1.00
65_K	104_S	2.538	1.00
98_S	106_V	2.470	1.00
136_S	139_E	2.383	1.00
142_A	145_E	2.148	1.00
142_A	146_G	2.047	1.00
97_H	105_V	1.998	1.00
59_N	117_F	1.957	1.00
51_Q	90_S	1.929	1.00
135_L	146_G	1.874	1.00
65_K	68_D	1.871	1.00
98_S	104_S	1.858	1.00
59_N	109_L	1.835	1.00
139_E	142_A	1.776	1.00
63_T	106_V	1.751	1.00
134_L	153_A	1.697	1.00
139_E	145_E	1.639	1.00
91_G	112_N	1.629	1.00
66_V	84_L	1.629	1.00
26_L	148_S	1.617	1.00
88_E	95_R	1.604	1.00
112_N	116_I	1.577	1.00
51_Q	86_R	1.559	1.00
84_L	107_V	1.555	1.00
143_V	146_G	1.545	1.00
61_H	72_K	1.523	1.00
54_V	83_L	1.498	1.00
48_S	51_Q	1.471	1.00
63_T	96_S	1.450	1.00
112_N	115_K	1.436	1.00
85_D	89_K	1.404	1.00
59_N	114_K	1.368	1.00
116_I	119_G	1.367	1.00
146_G	149_I	1.360	1.00
57_L	72_K	1.318	1.00
26_L	151_S	1.315	1.00
26_L	144_Y	1.272	1.00
67_S	77_L	1.262	1.00
68_D	71_E	1.259	1.00
45_L	123_K	1.242	1.00
145_E	149_I	1.223	1.00
54_V	80_T	1.220	1.00
76_S	79_N	1.216	1.00
66_V	105_V	1.202	1.00
41_E	123_K	1.201	1.00
30_V	151_S	1.190	1.00
67_S	71_E	1.187	1.00
85_D	102_R	1.152	1.00
115_K	119_G	1.147	1.00
45_L	119_G	1.133	1.00
75_A	79_N	1.115	1.00
29_K	151_S	1.106	1.00
95_R	105_V	1.097	1.00
140_K	144_Y	1.089	1.00
78_S	81_T	1.084	1.00
39_V	43_M	1.075	1.00
66_V	80_T	1.064	1.00
66_V	107_V	1.023	1.00
138_E	142_A	1.013	1.00
50_P	83_L	1.003	1.00
139_E	146_G	0.989	1.00
66_V	77_L	0.989	1.00
90_S	116_I	0.980	1.00
90_S	112_N	0.972	1.00
109_L	113_A	0.970	1.00
111_E	114_K	0.969	1.00
123_K	126_L	0.969	1.00
64_L	68_D	0.966	1.00
41_E	130_R	0.960	1.00
94_K	110_T	0.960	1.00
144_Y	148_S	0.958	1.00
81_T	85_D	0.958	1.00
111_E	115_K	0.951	1.00
92_F	116_I	0.950	1.00
30_V	147_L	0.947	1.00
85_D	88_E	0.941	1.00
76_S	82_G	0.938	1.00
68_D	72_K	0.937	1.00
23_I	144_Y	0.929	1.00
96_S	106_V	0.929	1.00
79_N	82_G	0.914	1.00
97_H	102_R	0.902	1.00
64_L	72_K	0.902	1.00
45_L	120_L	0.889	1.00
84_L	93_V	0.885	1.00
135_L	150_L	0.878	1.00
28_M	31_L	0.878	1.00
75_A	80_T	0.877	1.00
61_H	64_L	0.877	1.00
114_K	118_R	0.868	1.00
58_L	93_V	0.867	1.00
41_E	126_L	0.867	1.00
137_P	141_Q	0.850	1.00
59_N	118_R	0.845	1.00
31_L	35_G	0.843	1.00
122_E	126_L	0.842	1.00
62_G	114_K	0.841	1.00
52_M	120_L	0.838	1.00
33_S	151_S	0.833	1.00
46_D	90_S	0.830	1.00
88_E	94_K	0.825	1.00
59_N	121_Y	0.823	1.00
92_F	112_N	0.821	1.00
39_V	49_M	0.820	1.00
98_S	101_D	0.820	1.00
124_G	128_L	0.817	1.00
101_D	104_S	0.815	1.00
53_K	73_M	0.811	1.00
119_G	123_K	0.811	1.00
128_L	131_S	0.796	1.00
57_L	73_M	0.793	1.00
126_L	130_R	0.791	1.00
82_G	85_D	0.791	1.00
55_L	117_F	0.788	1.00
54_V	73_M	0.788	1.00
28_M	32_T	0.785	1.00
44_K	123_K	0.779	1.00
141_Q	145_E	0.767	1.00
82_G	86_R	0.766	1.00
130_R	133_E	0.762	1.00
99_E	106_V	0.762	1.00
85_D	95_R	0.758	1.00
142_A	149_I	0.757	1.00
32_T	36_L	0.754	1.00
126_L	129_K	0.744	1.00
84_L	88_E	0.744	1.00
50_P	79_N	0.742	1.00
37_G	127_K	0.740	1.00
66_V	81_T	0.734	1.00
41_E	127_K	0.733	1.00
136_S	140_K	0.728	1.00
57_L	69_I	0.726	1.00
148_S	152_R	0.725	1.00
132_L	140_K	0.724	1.00
70_A	77_L	0.724	1.00
62_G	108_Q	0.724	1.00
57_L	61_H	0.720	1.00
58_L	64_L	0.720	1.00
61_H	68_D	0.717	1.00
138_E	141_Q	0.716	1.00
122_E	125_H	0.702	1.00
58_L	109_L	0.699	1.00
141_Q	144_Y	0.699	1.00
127_K	130_R	0.698	1.00
115_K	118_R	0.698	1.00
57_L	64_L	0.697	1.00
88_E	93_V	0.688	1.00
109_L	114_K	0.687	1.00
30_V	150_L	0.685	1.00
86_R	89_K	0.683	1.00
125_H	129_K	0.683	1.00
86_R	90_S	0.681	1.00
52_M	124_G	0.673	1.00
80_T	84_L	0.671	1.00
54_V	69_I	0.670	1.00
27_Y	31_L	0.660	1.00
70_A	80_T	0.656	1.00
37_G	130_R	0.637	1.00
52_M	117_F	0.615	1.00
38_D	41_E	0.613	1.00
26_L	29_K	0.612	1.00
41_E	44_K	0.610	1.00
135_L	140_K	0.605	1.00
149_I	153_A	0.591	1.00
91_G	94_K	0.586	1.00
35_G	39_V	0.576	1.00
119_G	122_E	0.576	1.00
40_S	43_M	0.575	1.00
35_G	38_D	0.572	1.00
77_L	81_T	0.572	1.00
56_M	60_N	0.570	1.00
146_G	150_L	0.566	1.00
53_K	57_L	0.563	1.00
110_T	113_A	0.562	1.00
27_Y	30_V	0.562	1.00
27_Y	147_L	0.561	1.00
87_L	92_F	0.557	1.00
118_R	122_E	0.547	1.00
37_G	40_S	0.543	1.00
121_Y	125_H	0.541	1.00
51_Q	83_L	0.540	1.00
146_G	153_A	0.534	1.00
145_E	148_S	0.533	1.00
65_K	98_S	0.532	1.00
117_F	121_Y	0.528	1.00
56_M	121_Y	0.526	1.00
136_S	149_I	0.526	1.00
50_P	75_A	0.526	1.00
66_V	104_S	0.523	1.00
134_L	149_I	0.523	1.00
22_E	144_Y	0.522	1.00
97_H	101_D	0.517	1.00
67_S	70_A	0.517	1.00
55_L	59_N	0.512	1.00
38_D	124_G	0.504	1.00
65_K	106_V	0.503	1.00
29_K	33_S	0.503	1.00
133_E	153_A	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
3cjnA	2	0.9125	99.9	0.277	Contact Map
3zplA	2	0.9437	99.9	0.284	Contact Map
2fbkA	2	0.8875	99.9	0.288	Contact Map
3u2rA	4	0.8313	99.9	0.289	Contact Map
3bj6A	2	0.9437	99.9	0.295	Contact Map
3e6mA	2	0.9437	99.9	0.297	Contact Map
3cdhA	4	0.85	99.9	0.297	Contact Map
3deuA	2	0.8187	99.9	0.298	Contact Map
3boqA	2	0.85	99.9	0.298	Contact Map
2ethA	4	0.8812	99.9	0.299	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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