YKOM - BACSU - GREMLIN Contacts

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YKOM - Uncharacterized HTH-type transcriptional regulator YkoM

UniProt:	O34949	Sequences: MMRLSFNEEEVERAMNLYRVFARAFKSVSEHSIRDSKEHGFNPTEFAVLELLYTRGPQKLQQIGSRLLLVSGNVTYVIDKLERNGFLVREQDPKDKRSVYAHLTDKGNEYLDKIYPIHALRIARAFSGLSPDEQDQLIVLLKKAGIHSQHLLFR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	154 (133)
Sequences:	24153 (17854)
Seq/√Len:	1548.1

ECOLI - MARR SLYA MPRA
BACSU - YKOM YCGE YSMB YXAD YWAE YUSO YFIV OHRR YYBA MHQR YETL YWHA YPOP YDCH YDGJ YWOH YDGG YHJH 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
90_E	102_H	3.113	1.00
133_E	143_K	2.925	1.00
88_V	102_H	2.661	1.00
59_K	98_S	2.528	1.00
57_P	102_H	2.495	1.00
92_D	100_Y	2.464	1.00
130_S	133_E	2.388	1.00
136_Q	139_V	2.159	1.00
136_Q	140_L	2.054	1.00
91_Q	99_V	2.007	1.00
53_Y	111_L	1.996	1.00
45_E	84_N	1.974	1.00
59_K	62_Q	1.901	1.00
92_D	98_S	1.886	1.00
129_L	140_L	1.847	1.00
133_E	136_Q	1.806	1.00
53_Y	103_L	1.777	1.00
128_G	147_H	1.709	1.00
60_L	78_I	1.644	1.00
82_E	89_R	1.643	1.00
133_E	139_V	1.631	1.00
106_K	110_Y	1.607	1.00
20_V	142_K	1.593	1.00
85_G	106_K	1.593	1.00
45_E	80_K	1.586	1.00
137_L	140_L	1.570	1.00
78_I	101_A	1.551	1.00
55_R	66_R	1.535	1.00
42_N	45_E	1.496	1.00
48_V	77_V	1.475	1.00
110_Y	113_K	1.460	1.00
79_D	83_R	1.448	1.00
106_K	109_E	1.446	1.00
140_L	143_K	1.406	1.00
53_Y	108_N	1.361	1.00
20_V	145_G	1.313	1.00
70_V	73_N	1.292	1.00
20_V	138_I	1.283	1.00
62_Q	65_S	1.283	1.00
51_L	66_R	1.280	1.00
39_H	117_I	1.275	1.00
60_L	99_V	1.233	1.00
61_Q	71_S	1.216	1.00
48_V	74_V	1.211	1.00
139_V	143_K	1.207	1.00
35_D	117_I	1.191	1.00
109_E	113_K	1.174	1.00
79_D	96_K	1.155	1.00
24_A	145_G	1.154	1.00
39_H	113_K	1.149	1.00
61_Q	65_S	1.143	1.00
69_L	73_N	1.122	1.00
89_R	99_V	1.097	1.00
38_E	117_I	1.096	1.00
72_G	75_T	1.090	1.00
132_D	136_Q	1.086	1.00
33_I	37_K	1.082	1.00
60_L	74_V	1.070	1.00
133_E	140_L	1.063	1.00
23_R	145_G	1.038	1.00
134_Q	138_I	1.038	1.00
86_F	110_Y	1.027	1.00
60_L	101_A	1.026	1.00
79_D	82_E	1.024	1.00
60_L	71_S	1.011	1.00
84_N	106_K	1.006	1.00
105_D	108_N	1.005	1.00
138_I	142_K	0.996	1.00
57_P	100_Y	0.983	1.00
75_T	79_D	0.977	1.00
44_T	77_V	0.967	1.00
58_Q	62_Q	0.957	1.00
84_N	110_Y	0.954	1.00
35_D	124_R	0.953	1.00
117_I	120_L	0.953	1.00
103_L	107_G	0.952	1.00
62_Q	66_R	0.946	1.00
105_D	109_E	0.944	1.00
24_A	141_L	0.942	1.00
88_V	104_T	0.938	1.00
91_Q	96_K	0.932	1.00
73_N	76_Y	0.924	1.00
129_L	144_A	0.924	1.00
78_I	87_L	0.924	1.00
70_V	76_Y	0.910	1.00
22_A	25_F	0.910	1.00
69_L	74_V	0.897	1.00
108_N	112_D	0.896	1.00
58_Q	66_R	0.894	1.00
56_G	108_N	0.890	1.00
90_E	100_Y	0.888	1.00
53_Y	112_D	0.887	1.00
27_S	145_G	0.874	1.00
17_L	138_I	0.868	1.00
86_F	106_K	0.863	1.00
33_I	43_P	0.860	1.00
118_H	122_I	0.859	1.00
55_R	58_Q	0.856	1.00
82_E	88_V	0.855	1.00
131_P	135_D	0.852	1.00
35_D	120_L	0.851	1.00
52_L	87_L	0.849	1.00
116_P	120_L	0.838	1.00
46_F	114_I	0.837	1.00
122_I	125_A	0.826	1.00
39_H	114_I	0.825	1.00
40_G	84_N	0.824	1.00
25_F	29_S	0.820	1.00
113_K	117_I	0.819	1.00
92_D	95_D	0.808	1.00
47_A	67_L	0.799	1.00
120_L	124_R	0.796	1.00
76_Y	80_K	0.792	1.00
93_P	100_Y	0.787	1.00
95_D	98_S	0.780	1.00
49_L	111_L	0.779	1.00
136_Q	143_K	0.777	1.00
56_G	102_H	0.777	1.00
124_R	127_S	0.777	1.00
76_Y	79_D	0.776	1.00
22_A	26_K	0.771	1.00
135_D	139_V	0.768	1.00
121_R	124_R	0.765	1.00
57_P	90_E	0.764	1.00
53_Y	115_Y	0.763	1.00
120_L	123_A	0.760	1.00
48_V	67_L	0.756	1.00
31_H	121_R	0.744	1.00
35_D	121_R	0.739	1.00
55_R	62_Q	0.735	1.00
109_E	112_D	0.735	1.00
51_L	67_L	0.732	1.00
26_K	30_E	0.732	1.00
82_E	87_L	0.730	1.00
79_D	89_R	0.726	1.00
116_P	119_A	0.725	1.00
119_A	123_A	0.724	1.00
78_I	82_E	0.721	1.00
46_F	118_H	0.721	1.00
130_S	134_Q	0.716	1.00
103_L	108_N	0.716	1.00
60_L	75_T	0.716	1.00
48_V	63_I	0.712	1.00
132_D	135_D	0.711	1.00
142_K	146_I	0.709	1.00
126_F	134_Q	0.708	1.00
52_L	58_Q	0.704	1.00
51_L	58_Q	0.704	1.00
64_G	71_S	0.702	1.00
51_L	55_R	0.698	1.00
35_D	38_E	0.698	1.00
135_D	138_I	0.697	1.00
80_K	83_R	0.697	1.00
44_T	73_N	0.692	1.00
24_A	144_A	0.691	1.00
80_K	84_N	0.690	1.00
21_F	25_F	0.683	1.00
51_L	63_I	0.682	1.00
52_L	103_L	0.676	1.00
29_S	32_S	0.666	1.00
20_V	23_R	0.651	1.00
64_G	74_V	0.644	1.00
29_S	33_I	0.639	1.00
31_H	124_R	0.618	1.00
113_K	116_P	0.618	1.00
31_H	34_R	0.615	1.00
50_E	54_T	0.613	1.00
46_F	111_L	0.611	1.00
74_V	78_I	0.600	1.00
45_E	77_V	0.599	1.00
81_L	86_F	0.595	1.00
143_K	147_H	0.595	1.00
47_A	51_L	0.589	1.00
104_T	107_G	0.587	1.00
129_L	134_Q	0.585	1.00
139_V	142_K	0.585	1.00
21_F	24_A	0.583	1.00
85_G	88_V	0.578	1.00
140_L	144_A	0.570	1.00
21_F	141_L	0.566	1.00
140_L	147_H	0.561	1.00
71_S	75_T	0.554	1.00
50_E	115_Y	0.550	1.00
32_S	35_D	0.547	1.00
23_R	27_S	0.545	1.00
112_D	116_P	0.543	1.00
130_S	143_K	0.542	1.00
49_L	53_Y	0.541	1.00
111_L	115_Y	0.537	1.00
59_K	92_D	0.535	1.00
89_R	101_A	0.534	1.00
34_R	37_K	0.533	1.00
60_L	98_S	0.529	1.00
32_S	118_H	0.523	1.00
115_Y	119_A	0.520	1.00
126_F	130_S	0.518	1.00
129_L	133_E	0.516	1.00
44_T	69_L	0.508	1.00
59_K	100_Y	0.506	1.00
123_A	127_S	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
4rguA	4	0.9351	99.9	0.271	Contact Map
2nyxA	2	0.961	99.9	0.271	Contact Map
2fbkA	2	0.9156	99.9	0.279	Contact Map
3cjnA	2	0.9351	99.9	0.28	Contact Map
3s2wA	3	0.9351	99.9	0.284	Contact Map
3e6mA	2	0.9545	99.9	0.287	Contact Map
3oopA	2	0.8896	99.9	0.288	Contact Map
3bj6A	2	0.9675	99.9	0.291	Contact Map
3u2rA	4	0.8571	99.9	0.294	Contact Map
3boqA	2	0.8831	99.9	0.296	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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