MPRA - ECOLI - GREMLIN Contacts

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MPRA - Transcriptional repressor MprA

UniProt:	P0ACR9	Sequences: MDSSFTPIEQMLKFRASRHEDFPYQEILLTRLCMHMQSKLLENRNKMLKAQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQHNCLHQLWSALSTTEKDQLEQITRKLLSRLDQMEQDGVVLEAMS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10603
Length:	176 (138)
Sequences:	20590 (15066)
Seq/√Len:	1282.5

ECOLI - MPRA SLYA MARR
BACSU - YETL YWAE YFIV YCGE MHQR YUSO YSMB YYBA YXAD YKOM YDGJ OHRR YDGG YWHA YPOP YWOH 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
104_R	116_Q	3.101	1.00
147_E	157_K	3.097	1.00
106_S	114_H	2.851	1.00
73_Q	112_C	2.819	1.00
102_E	116_Q	2.678	1.00
150_Q	154_I	2.517	1.00
144_S	147_E	2.455	1.00
150_Q	153_Q	2.279	1.00
69_N	116_Q	2.209	1.00
142_A	161_R	2.204	1.00
73_Q	76_E	2.008	1.00
57_L	98_R	2.003	1.00
105_E	113_L	1.965	1.00
65_E	125_L	1.936	1.00
143_L	154_I	1.916	1.00
65_E	117_L	1.906	1.00
147_E	150_Q	1.870	1.00
106_S	112_C	1.858	1.00
32_L	156_R	1.808	1.00
120_K	124_F	1.729	1.00
151_L	154_I	1.714	1.00
96_E	103_R	1.658	1.00
57_L	94_E	1.617	1.00
32_L	159_L	1.605	1.00
147_E	153_Q	1.600	1.00
67_Q	80_A	1.577	1.00
54_N	57_L	1.564	1.00
99_G	120_K	1.555	1.00
92_A	115_L	1.531	1.00
120_K	123_E	1.530	1.00
74_P	92_A	1.519	1.00
124_F	127_E	1.513	1.00
60_A	91_I	1.438	1.00
32_L	152_E	1.434	1.00
65_E	122_H	1.427	1.00
154_I	157_K	1.414	1.00
147_E	154_I	1.393	1.00
63_T	80_A	1.372	1.00
93_D	97_K	1.371	1.00
51_Q	131_P	1.360	1.00
47_M	131_P	1.340	1.00
123_E	127_E	1.325	1.00
93_D	110_R	1.300	1.00
153_Q	157_K	1.275	1.00
60_A	88_A	1.273	1.00
75_S	85_R	1.268	1.00
76_E	79_C	1.251	1.00
75_S	79_C	1.212	1.00
51_Q	127_E	1.210	1.00
35_H	159_L	1.205	1.00
36_M	159_L	1.147	1.00
64_L	101_I	1.142	1.00
45_N	49_K	1.138	1.00
84_S	87_N	1.131	1.00
74_P	113_L	1.130	1.00
103_R	113_L	1.128	1.00
152_E	156_R	1.125	1.00
74_P	115_L	1.117	1.00
86_T	89_T	1.087	1.00
50_A	131_P	1.078	1.00
67_Q	72_I	1.038	1.00
148_K	152_E	1.037	1.00
89_T	93_D	1.034	1.00
100_W	124_F	1.030	1.00
34_M	37_Q	1.027	1.00
83_S	87_N	1.022	1.00
56_T	91_I	1.021	1.00
69_N	114_H	1.019	1.00
36_M	155_T	1.009	1.00
122_H	126_R	0.997	1.00
102_E	118_T	0.983	1.00
146_T	150_Q	0.977	1.00
74_P	85_R	0.964	1.00
37_Q	41_L	0.959	1.00
39_K	163_D	0.957	1.00
74_P	88_A	0.952	1.00
72_I	76_E	0.950	1.00
29_L	152_E	0.948	1.00
145_T	149_D	0.946	1.00
83_S	88_A	0.946	1.00
92_A	101_I	0.946	1.00
131_P	134_N	0.940	1.00
98_R	120_K	0.940	1.00
100_W	120_K	0.938	1.00
43_N	135_C	0.931	1.00
119_E	122_H	0.930	1.00
104_R	114_H	0.928	1.00
96_E	102_E	0.896	1.00
51_Q	128_V	0.890	1.00
132_Q	136_L	0.886	1.00
39_K	159_L	0.884	1.00
47_M	138_Q	0.882	1.00
98_R	124_F	0.873	1.00
117_L	121_G	0.871	1.00
68_E	122_H	0.866	1.00
150_Q	157_K	0.866	1.00
47_M	135_C	0.865	1.00
87_N	90_R	0.855	1.00
72_I	80_A	0.853	1.00
25_Q	149_D	0.847	1.00
45_N	55_E	0.846	1.00
76_E	80_A	0.840	1.00
107_D	114_H	0.838	1.00
65_E	129_L	0.836	1.00
47_M	134_N	0.836	1.00
60_A	77_L	0.829	1.00
52_G	98_R	0.815	1.00
59_M	81_L	0.804	1.00
117_L	122_H	0.804	1.00
109_D	112_C	0.792	1.00
105_E	110_R	0.788	1.00
143_L	158_L	0.785	1.00
78_S	85_R	0.783	1.00
65_E	126_R	0.782	1.00
130_P	134_N	0.776	1.00
67_Q	76_E	0.775	1.00
84_S	90_R	0.773	1.00
134_N	137_H	0.772	1.00
60_A	81_L	0.771	1.00
149_D	153_Q	0.770	1.00
96_E	101_I	0.768	1.00
119_E	123_E	0.768	1.00
93_D	96_E	0.767	1.00
127_E	131_P	0.767	1.00
156_R	160_S	0.763	1.00
34_M	38_S	0.757	1.00
90_R	93_D	0.753	1.00
130_P	133_H	0.750	1.00
157_K	161_R	0.747	1.00
135_C	138_Q	0.742	1.00
32_L	35_H	0.737	1.00
90_R	94_E	0.732	1.00
93_D	103_R	0.731	1.00
68_E	72_I	0.729	1.00
134_N	138_Q	0.726	1.00
106_S	109_D	0.721	1.00
94_E	97_K	0.718	1.00
47_M	50_A	0.716	1.00
146_T	149_D	0.710	1.00
74_P	89_T	0.708	1.00
58_F	128_V	0.706	1.00
64_L	117_L	0.702	1.00
140_W	148_K	0.693	1.00
92_A	96_E	0.691	1.00
94_E	98_R	0.689	1.00
63_T	67_Q	0.674	1.00
63_T	81_L	0.671	1.00
61_L	125_L	0.667	1.00
68_E	116_Q	0.666	1.00
127_E	130_P	0.664	1.00
149_D	152_E	0.663	1.00
36_M	158_L	0.659	1.00
64_L	72_I	0.652	1.00
33_C	155_T	0.652	1.00
154_I	158_L	0.651	1.00
138_Q	141_S	0.648	1.00
44_R	47_M	0.648	1.00
63_T	77_L	0.647	1.00
123_E	126_R	0.643	1.00
33_C	36_M	0.633	1.00
33_C	37_Q	0.630	1.00
88_A	92_A	0.629	1.00
136_L	139_L	0.628	1.00
77_L	115_L	0.623	1.00
133_H	137_H	0.617	1.00
159_L	163_D	0.609	1.00
63_T	72_I	0.608	1.00
42_E	46_K	0.590	1.00
75_S	78_S	0.590	1.00
38_S	42_E	0.590	1.00
57_L	91_I	0.581	1.00
56_T	87_N	0.581	1.00
43_N	138_Q	0.576	1.00
59_M	63_T	0.576	1.00
144_S	148_K	0.571	1.00
58_F	132_Q	0.571	1.00
143_L	148_K	0.570	1.00
95_L	100_W	0.570	1.00
101_I	115_L	0.560	1.00
143_L	157_K	0.560	1.00
41_L	45_N	0.549	1.00
75_S	112_C	0.549	1.00
78_S	88_A	0.546	1.00
99_G	102_E	0.540	1.00
154_I	161_R	0.536	1.00
56_T	83_S	0.532	1.00
73_Q	114_H	0.530	1.00
143_L	147_E	0.530	1.00
78_S	81_L	0.529	1.00
43_N	46_K	0.527	1.00
129_L	133_H	0.524	1.00
77_L	88_A	0.519	1.00
58_F	125_L	0.519	1.00
44_R	132_Q	0.518	1.00
36_M	41_L	0.517	1.00
25_Q	28_L	0.517	1.00
62_I	129_L	0.510	1.00
73_Q	106_S	0.509	1.00
118_T	121_G	0.508	1.00
29_L	151_L	0.507	1.00
41_L	55_E	0.507	1.00
62_I	66_S	0.506	1.00
124_F	128_V	0.506	1.00
144_S	157_K	0.506	1.00
34_M	55_E	0.502	1.00
74_P	112_C	0.500	1.00
120_K	127_E	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	0.8523	99.9	0.286	Contact Map
4rguA	4	0.8182	99.9	0.313	Contact Map
3u2rA	4	0.767	99.9	0.314	Contact Map
3zplA	2	0.9091	99.9	0.319	Contact Map
3deuA	2	0.7443	99.9	0.319	Contact Map
3cjnA	2	0.8295	99.9	0.32	Contact Map
3e6mA	2	0.858	99.9	0.323	Contact Map
3boqA	2	0.7727	99.9	0.324	Contact Map
4yifA	2	0.8011	99.9	0.328	Contact Map
2ethA	4	0.8011	99.9	0.334	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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