YETL - BACSU - GREMLIN Contacts

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YETL - Uncharacterized HTH-type transcriptional regulator YetL

UniProt:	O31541	Sequences: MELKHLPKYKHITEHAETYANIDAGSLELFLSLFDISKKMNHVMEHYFAGRGLSEGKFKILMLLFDAKDHRLSPTELAKRSNVTKATITGLLDGLARDGFVSRRHHTEDKRKISIELTTEGKARLEQFLPGHFSKISAVMENYSDEEKDMFVKMLGDLFERLSVFKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	167 (135)
Sequences:	22513 (16637)
Seq/√Len:	1431.9

ECOLI - MPRA SLYA MARR
BACSU - YETL YWAE YFIV MHQR YCGE YXAD YSMB YYBA YUSO YKOM YDGJ OHRR YWOH YDGG YWHA YPOP YDCH 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
71_R	116_E	2.969	1.00
147_E	157_D	2.964	1.00
104_R	116_E	2.940	1.00
73_S	112_K	2.645	1.00
106_H	114_S	2.626	1.00
102_S	116_E	2.569	1.00
150_M	154_M	2.328	1.00
144_S	147_E	2.326	1.00
150_M	153_K	2.155	1.00
71_R	114_S	1.937	1.00
105_H	113_I	1.930	1.00
142_N	161_R	1.928	1.00
57_K	98_D	1.908	1.00
73_S	76_E	1.897	1.00
65_F	125_L	1.893	1.00
147_E	150_M	1.832	1.00
143_Y	154_M	1.812	1.00
68_K	71_R	1.805	1.00
106_H	112_K	1.781	1.00
96_A	103_R	1.699	1.00
65_F	117_L	1.693	1.00
32_S	156_G	1.628	1.00
120_E	124_R	1.573	1.00
151_F	154_M	1.549	1.00
67_A	80_R	1.528	1.00
57_K	94_G	1.508	1.00
99_G	120_E	1.507	1.00
71_R	104_R	1.494	1.00
124_R	127_Q	1.472	1.00
120_E	123_A	1.466	1.00
54_S	57_K	1.461	1.00
74_P	92_L	1.457	1.00
147_E	153_K	1.452	1.00
32_S	159_F	1.448	1.00
92_L	115_I	1.404	1.00
60_I	91_L	1.395	1.00
32_S	152_V	1.387	1.00
65_F	122_K	1.372	1.00
63_L	80_R	1.372	1.00
93_D	97_R	1.342	1.00
51_R	131_G	1.339	1.00
47_Y	131_G	1.301	1.00
154_M	157_D	1.301	1.00
51_R	127_Q	1.270	1.00
147_E	154_M	1.230	1.00
75_T	85_K	1.228	1.00
93_D	110_K	1.202	1.00
76_E	79_K	1.200	1.00
153_K	157_D	1.187	1.00
123_A	127_Q	1.186	1.00
60_I	88_I	1.169	1.00
74_P	113_I	1.166	1.00
103_R	113_I	1.148	1.00
75_T	79_K	1.144	1.00
35_D	159_F	1.093	1.00
84_T	87_T	1.086	1.00
74_P	115_I	1.085	1.00
100_F	124_R	1.085	1.00
83_V	87_T	1.073	1.00
36_I	159_F	1.065	1.00
152_V	156_G	1.059	1.00
64_L	101_V	1.057	1.00
72_L	76_E	1.050	1.00
50_G	131_G	1.048	1.00
86_A	89_T	1.042	1.00
45_E	49_A	1.040	1.00
89_T	93_D	1.038	1.00
148_K	152_V	1.029	1.00
146_E	150_M	1.024	1.00
67_A	72_L	1.012	1.00
83_V	88_I	0.970	1.00
98_D	124_R	0.967	1.00
36_I	155_L	0.962	1.00
34_F	37_S	0.955	1.00
74_P	85_K	0.947	1.00
56_G	91_L	0.943	1.00
102_S	118_T	0.936	1.00
29_L	152_V	0.929	1.00
131_G	134_S	0.924	1.00
98_D	120_E	0.914	1.00
74_P	88_I	0.913	1.00
72_L	80_R	0.912	1.00
25_G	149_D	0.903	1.00
122_K	126_E	0.900	1.00
104_R	114_S	0.892	1.00
150_M	157_D	0.888	1.00
92_L	101_V	0.887	1.00
47_Y	138_A	0.880	1.00
100_F	120_E	0.879	1.00
119_T	122_K	0.870	1.00
117_L	121_G	0.868	1.00
87_T	90_G	0.865	1.00
47_Y	135_K	0.861	1.00
37_S	41_N	0.860	1.00
43_V	135_K	0.859	1.00
68_K	122_K	0.858	1.00
132_H	136_I	0.855	1.00
51_R	128_F	0.854	1.00
145_D	149_D	0.851	1.00
39_K	159_F	0.845	1.00
76_E	80_R	0.831	1.00
84_T	90_G	0.827	1.00
130_P	134_S	0.820	1.00
59_K	81_S	0.819	1.00
105_H	110_K	0.812	1.00
52_G	98_D	0.803	1.00
45_E	55_E	0.800	1.00
93_D	96_A	0.796	1.00
127_Q	131_G	0.790	1.00
96_A	102_S	0.790	1.00
136_I	139_V	0.788	1.00
60_I	77_L	0.787	1.00
47_Y	134_S	0.778	1.00
119_T	123_A	0.776	1.00
140_M	148_K	0.776	1.00
34_F	38_K	0.772	1.00
90_G	93_D	0.772	1.00
135_K	138_A	0.770	1.00
117_L	122_K	0.767	1.00
109_D	112_K	0.764	1.00
94_G	97_R	0.759	1.00
68_K	72_L	0.758	1.00
58_F	128_F	0.752	1.00
106_H	109_D	0.747	1.00
61_L	125_L	0.739	1.00
134_S	137_S	0.732	1.00
47_Y	50_G	0.727	1.00
90_G	94_G	0.725	1.00
65_F	129_L	0.722	1.00
36_I	158_L	0.719	1.00
65_F	126_E	0.719	1.00
107_T	114_S	0.718	1.00
134_S	138_A	0.717	1.00
67_A	76_E	0.716	1.00
149_D	153_K	0.710	1.00
94_G	98_D	0.707	1.00
92_L	96_A	0.707	1.00
143_Y	158_L	0.706	1.00
32_S	35_D	0.705	1.00
138_A	141_E	0.704	1.00
63_L	81_S	0.701	1.00
78_A	85_K	0.700	1.00
93_D	103_R	0.698	1.00
63_L	67_A	0.696	1.00
33_L	36_I	0.688	1.00
96_A	101_V	0.687	1.00
146_E	149_D	0.683	1.00
58_F	132_H	0.673	1.00
130_P	133_F	0.669	1.00
144_S	148_K	0.666	1.00
156_G	160_E	0.663	1.00
56_G	87_T	0.661	1.00
133_F	137_S	0.660	1.00
157_D	161_R	0.658	1.00
60_I	81_S	0.658	1.00
88_I	92_L	0.657	1.00
64_L	72_L	0.653	1.00
74_P	89_T	0.652	1.00
149_D	152_V	0.651	1.00
64_L	117_L	0.651	1.00
63_L	77_L	0.650	1.00
33_L	37_S	0.649	1.00
68_K	116_E	0.646	1.00
77_L	115_I	0.637	1.00
78_A	88_I	0.636	1.00
38_K	42_H	0.630	1.00
44_M	47_Y	0.630	1.00
41_N	45_E	0.619	1.00
127_Q	130_P	0.619	1.00
43_V	138_A	0.619	1.00
123_A	126_E	0.615	1.00
33_L	155_L	0.609	1.00
59_K	63_L	0.598	1.00
62_M	66_D	0.579	1.00
62_M	129_L	0.579	1.00
43_V	46_H	0.578	1.00
63_L	72_L	0.573	1.00
95_L	100_F	0.565	1.00
125_L	129_L	0.564	1.00
129_L	133_F	0.563	1.00
154_M	158_L	0.563	1.00
143_Y	148_K	0.559	1.00
58_F	125_L	0.558	1.00
44_M	132_H	0.556	1.00
57_K	91_L	0.554	1.00
144_S	157_D	0.553	1.00
75_T	112_K	0.547	1.00
41_N	44_M	0.538	1.00
99_G	102_S	0.536	1.00
75_T	78_A	0.534	1.00
25_G	28_E	0.533	1.00
118_T	121_G	0.531	1.00
143_Y	147_E	0.527	1.00
103_R	115_I	0.527	1.00
73_S	106_H	0.526	1.00
53_L	128_F	0.522	1.00
74_P	112_K	0.519	1.00
42_H	46_H	0.518	1.00
142_N	157_D	0.516	1.00
54_S	91_L	0.511	1.00
34_F	55_E	0.506	1.00
38_K	41_N	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
2fbkA	2	0.8982	99.9	0.285	Contact Map
3zplA	2	0.9102	99.9	0.288	Contact Map
3u2rA	4	0.8084	99.9	0.289	Contact Map
3e6mA	2	0.9042	99.9	0.292	Contact Map
3deuA	2	0.7844	99.9	0.297	Contact Map
4rguA	4	0.8563	99.9	0.302	Contact Map
3cjnA	2	0.8743	99.9	0.304	Contact Map
3boqA	2	0.8204	99.9	0.315	Contact Map
4yifA	2	0.8443	99.9	0.316	Contact Map
3bj6A	2	0.8982	99.9	0.318	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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