LMRA - BACSU - GREMLIN Contacts

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LMRA - HTH-type transcriptional regulator LmrA

UniProt:	O34619	Sequences: MSYGDSREKILSAATRLFQLQGYYGTGLNQIIKESGAPKGSLYYHFPGGKEQLAIEAVNEMKEYIRQKIADCMEACTDPAEGIQAFLKELSCQFSCTEDIEGLPVGLLAAETSLKSEPLREACHEAYKEWASVYEEKLRQTGCSESRAKEASTVVNAMIEGGILLSLTAKNSTPLLHISSCIPDLLKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	188 (174)
Sequences:	43254 (34050)
Seq/√Len:	2581.3

ECOLI - NEMR SLMA COMR ACRR RUTR YJDC BETI BDCR UIDR ENVR FABR YBIH RCDA
BACSU - LMRA YXAF YHGD YEZE FADR YFIR YTTP YVDT PKSA YVKB BSCR YVAF YDGC YCNC YDES YUXN YERO YOBS
HALSA - Q9HRF3 Q9HM72
SULSO - Q97VV1

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_N	39_K	4.131	1.00
21_Q	30_Q	4.130	1.00
16_R	34_E	3.538	1.00
47_P	52_Q	2.737	1.00
18_F	26_T	2.461	1.00
48_G	52_Q	2.174	1.00
13_A	34_E	2.149	1.00
6_S	9_K	2.112	1.00
32_I	42_L	2.106	1.00
131_A	149_K	2.031	1.00
17_L	34_E	2.008	1.00
20_L	34_E	2.003	1.00
9_K	13_A	1.983	1.00
8_E	60_E	1.968	1.00
17_L	30_Q	1.960	1.00
17_L	26_T	1.954	1.00
78_D	81_E	1.866	1.00
15_T	60_E	1.858	1.00
131_A	135_E	1.854	1.00
17_L	21_Q	1.822	1.00
7_R	56_E	1.804	1.00
38_P	41_S	1.783	1.00
13_A	16_R	1.781	1.00
29_N	33_K	1.770	1.00
135_E	148_A	1.768	1.00
11_L	56_E	1.746	1.00
135_E	139_R	1.719	1.00
82_G	136_E	1.670	1.00
14_A	18_F	1.650	1.00
28_L	39_K	1.635	1.00
8_E	12_S	1.626	1.00
28_L	43_Y	1.585	1.00
135_E	138_L	1.530	1.00
136_E	140_Q	1.522	1.00
60_E	64_Y	1.515	1.00
14_A	53_L	1.514	1.00
154_V	158_M	1.506	1.00
30_Q	34_E	1.501	1.00
15_T	57_A	1.492	1.00
30_Q	33_K	1.488	1.00
59_N	122_A	1.483	1.00
56_E	59_N	1.472	1.00
138_L	145_E	1.445	1.00
46_F	56_E	1.435	1.00
88_K	179_S	1.414	1.00
55_I	59_N	1.413	1.00
12_S	60_E	1.406	1.00
15_T	61_M	1.392	1.00
5_D	9_K	1.392	1.00
16_R	20_L	1.384	1.00
41_S	44_Y	1.367	1.00
22_G	26_T	1.366	1.00
27_G	30_Q	1.334	1.00
133_V	137_K	1.318	1.00
22_G	25_G	1.311	1.00
138_L	146_S	1.279	1.00
26_T	31_I	1.258	1.00
28_L	42_L	1.257	1.00
52_Q	56_E	1.246	1.00
55_I	118_P	1.242	1.00
37_A	41_S	1.233	1.00
127_Y	131_A	1.230	1.00
41_S	45_H	1.229	1.00
137_K	142_G	1.213	1.00
23_Y	54_A	1.208	1.00
40_G	44_Y	1.207	1.00
13_A	17_L	1.204	1.00
81_E	85_A	1.202	1.00
51_E	55_I	1.191	1.00
18_F	23_Y	1.179	1.00
38_P	44_Y	1.158	1.00
21_Q	25_G	1.154	1.00
68_K	89_E	1.151	1.00
137_K	143_C	1.147	1.00
11_L	46_F	1.136	1.00
84_Q	88_K	1.135	1.00
107_L	111_E	1.130	1.00
7_R	45_H	1.121	1.00
52_Q	55_I	1.095	1.00
11_L	57_A	1.087	1.00
147_R	150_E	1.082	1.00
138_L	148_A	1.082	1.00
39_K	43_Y	1.079	1.00
5_D	8_E	1.072	1.00
85_A	88_K	1.061	1.00
78_D	142_G	1.056	1.00
80_A	84_Q	1.053	1.00
59_N	63_E	1.051	1.00
13_A	35_S	1.033	1.00
150_E	177_H	1.032	1.00
174_P	177_H	1.028	1.00
31_I	53_L	1.026	1.00
93_Q	97_T	1.014	1.00
70_A	129_E	1.009	1.00
157_A	161_G	1.003	1.00
12_S	16_R	0.999	1.00
42_L	53_L	0.996	1.00
138_L	141_T	0.994	1.00
15_T	19_Q	0.982	1.00
6_S	45_H	0.982	1.00
21_Q	34_E	0.980	1.00
14_A	57_A	0.976	1.00
72_C	89_E	0.965	1.00
48_G	51_E	0.957	1.00
72_C	85_A	0.949	1.00
61_M	64_Y	0.948	1.00
81_E	84_Q	0.939	1.00
32_I	39_K	0.934	1.00
127_Y	153_T	0.933	1.00
149_K	153_T	0.931	1.00
133_V	136_E	0.930	1.00
60_E	63_E	0.900	1.00
85_A	89_E	0.899	1.00
39_K	44_Y	0.896	1.00
6_S	37_A	0.895	1.00
89_E	92_C	0.892	1.00
129_E	132_S	0.888	1.00
11_L	60_E	0.888	1.00
68_K	71_D	0.885	1.00
43_Y	48_G	0.875	1.00
56_E	60_E	0.872	1.00
76_C	82_G	0.866	1.00
103_L	107_L	0.865	1.00
88_K	176_L	0.865	1.00
136_E	139_R	0.862	1.00
128_K	132_S	0.854	1.00
132_S	136_E	0.847	1.00
132_S	135_E	0.839	1.00
9_K	12_S	0.836	1.00
70_A	74_E	0.834	1.00
166_S	169_A	0.833	1.00
88_K	92_C	0.829	1.00
79_P	140_Q	0.817	1.00
9_K	35_S	0.815	1.00
23_Y	50_K	0.815	1.00
79_P	137_K	0.809	1.00
67_Q	71_D	0.808	1.00
118_P	122_A	0.803	1.00
117_E	121_E	0.801	1.00
118_P	121_E	0.788	1.00
173_T	177_H	0.785	1.00
63_E	67_Q	0.771	1.00
107_L	110_A	0.770	1.00
66_R	70_A	0.767	1.00
104_P	107_L	0.764	1.00
28_L	32_I	0.759	1.00
128_K	131_A	0.752	1.00
131_A	148_A	0.744	1.00
124_H	128_K	0.744	1.00
150_E	180_S	0.742	1.00
66_R	129_E	0.740	1.00
29_N	43_Y	0.740	1.00
148_A	152_S	0.740	1.00
91_S	176_L	0.740	1.00
84_Q	180_S	0.733	1.00
122_A	125_E	0.732	1.00
87_L	155_V	0.731	1.00
150_E	154_V	0.730	1.00
33_K	39_K	0.730	1.00
17_L	20_L	0.724	1.00
76_C	85_A	0.719	1.00
12_S	15_T	0.718	1.00
20_L	30_Q	0.714	1.00
135_E	149_K	0.713	1.00
138_L	143_C	0.713	1.00
10_I	35_S	0.708	1.00
113_S	116_S	0.699	1.00
92_C	96_C	0.692	1.00
75_A	85_A	0.688	1.00
18_F	54_A	0.687	1.00
51_E	116_S	0.687	1.00
112_T	116_S	0.686	1.00
102_G	107_L	0.681	1.00
111_E	115_K	0.681	1.00
131_A	152_S	0.681	1.00
64_Y	67_Q	0.680	1.00
176_L	180_S	0.680	1.00
102_G	106_G	0.677	1.00
121_E	125_E	0.673	1.00
10_I	42_L	0.667	1.00
120_R	123_C	0.666	1.00
147_R	151_A	0.662	1.00
125_E	129_E	0.646	1.00
6_S	38_P	0.643	1.00
6_S	41_S	0.642	1.00
137_K	141_T	0.637	1.00
71_D	89_E	0.635	1.00
23_Y	51_E	0.633	1.00
35_S	38_P	0.630	1.00
10_I	45_H	0.628	1.00
175_L	179_S	0.628	1.00
84_Q	87_L	0.628	1.00
171_N	174_P	0.624	1.00
150_E	153_T	0.620	1.00
165_L	168_T	0.619	1.00
134_Y	138_L	0.619	1.00
117_E	120_R	0.614	1.00
87_L	90_L	0.613	1.00
165_L	169_A	0.612	1.00
67_Q	70_A	0.611	1.00
157_A	165_L	0.611	1.00
21_Q	26_T	0.610	1.00
157_A	160_E	0.609	1.00
92_C	175_L	0.609	1.00
106_G	109_A	0.605	1.00
78_D	82_G	0.604	1.00
82_G	133_V	0.603	1.00
82_G	137_K	0.603	1.00
24_Y	111_E	0.603	1.00
127_Y	149_K	0.601	1.00
158_M	161_G	0.598	1.00
88_K	180_S	0.596	1.00
79_P	142_G	0.596	1.00
32_I	38_P	0.592	1.00
106_G	110_A	0.588	1.00
106_G	111_E	0.587	1.00
15_T	64_Y	0.581	1.00
59_N	118_P	0.581	1.00
160_E	165_L	0.577	1.00
90_L	94_F	0.577	1.00
24_Y	107_L	0.576	1.00
11_L	15_T	0.571	1.00
174_P	179_S	0.566	1.00
28_L	50_K	0.566	1.00
66_R	125_E	0.561	1.00
80_A	142_G	0.561	1.00
154_V	157_A	0.558	1.00
64_Y	68_K	0.556	1.00
92_C	95_S	0.553	1.00
172_S	176_L	0.553	1.00
103_L	106_G	0.549	1.00
6_S	44_Y	0.540	1.00
134_Y	155_V	0.539	1.00
37_A	45_H	0.539	1.00
23_Y	26_T	0.534	1.00
72_C	75_A	0.533	1.00
134_Y	137_K	0.533	1.00
71_D	75_A	0.533	1.00
77_T	85_A	0.533	1.00
35_S	39_K	0.530	1.00
116_S	120_R	0.528	1.00
32_I	37_A	0.527	1.00
137_K	140_Q	0.527	1.00
51_E	112_T	0.526	1.00
134_Y	151_A	0.526	1.00
87_L	159_I	0.525	1.00
72_C	76_C	0.524	1.00
175_L	178_I	0.523	1.00
17_L	27_G	0.522	1.00
14_A	31_I	0.522	1.00
153_T	165_L	0.521	1.00
71_D	74_E	0.521	1.00
93_Q	96_C	0.521	1.00
32_I	35_S	0.518	1.00
89_E	93_Q	0.517	1.00
90_L	160_E	0.511	1.00
29_N	44_Y	0.506	1.00
40_G	45_H	0.504	1.00
134_Y	148_A	0.503	1.00
51_E	118_P	0.502	1.00
29_N	38_P	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
1sgmA	2	0.9734	100	0.223	Contact Map
2genA	2	0.9681	100	0.224	Contact Map
3kz9A	2	0.9947	100	0.227	Contact Map
4kwaA	2	0.984	100	0.229	Contact Map
1vi0A	2	0.9734	100	0.233	Contact Map
4udsA	2	0.9574	100	0.234	Contact Map
2ibdA	2	0.9787	100	0.236	Contact Map
3himA	2	0.9894	100	0.236	Contact Map
3bruA	2	0.984	100	0.239	Contact Map
2hyjA	2	0.9947	100	0.242	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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