NEMR - ECOLI - GREMLIN Contacts

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NEMR - HTH-type transcriptional repressor NemR

UniProt:	P67430	Sequences: MNKHTEHDTREHLLATGEQLCLQRGFTGMGLSELLKTAEVPKGSFYHYFRSKEAFGVAMLERHYAAYHQRLTELLQSGEGNYRDRILAYYQQTLNQFCQHGTISGCLTVKLSAEVCDLSEDMRSAMDKGARGVIALLSQALENGRENHCLTFCGEPLQQAQVLYALWLGANLQAKISRSFEPLENALAHVKNIIATPAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13947
Length:	199 (180)
Sequences:	47841 (37937)
Seq/√Len:	2827.6

ECOLI - NEMR COMR ACRR SLMA RUTR UIDR ENVR YJDC FABR BDCR RCDA BETI YBIH
BACSU - YEZE YFIR FADR YXAF LMRA YHGD PKSA YTTP YVDT BSCR YVKB YCNC YDES YVAF YDGC YUXN YERO YOBS YXBF
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
32_S	42_K	4.106	1.00
24_R	33_E	3.991	1.00
19_Q	37_T	3.504	1.00
50_R	54_A	2.714	1.00
21_C	29_M	2.477	1.00
35_L	45_F	2.174	1.00
51_S	54_A	2.156	1.00
138_S	157_L	2.134	1.00
23_Q	37_T	2.016	1.00
20_L	29_M	2.016	1.00
20_L	37_T	1.984	1.00
9_T	12_H	1.977	1.00
11_E	62_R	1.963	1.00
16_T	37_T	1.929	1.00
85_R	143_N	1.911	1.00
138_S	142_E	1.904	1.00
20_L	33_E	1.896	1.00
20_L	24_R	1.878	1.00
12_H	16_T	1.864	1.00
81_N	84_D	1.822	1.00
10_R	58_A	1.803	1.00
32_S	36_K	1.793	1.00
41_P	44_S	1.758	1.00
16_T	19_Q	1.684	1.00
142_E	156_P	1.669	1.00
18_E	62_R	1.659	1.00
11_E	15_A	1.597	1.00
87_L	191_K	1.587	1.00
31_L	46_Y	1.586	1.00
31_L	42_K	1.585	1.00
17_G	21_C	1.583	1.00
14_L	58_A	1.558	1.00
58_A	61_E	1.490	1.00
142_E	146_E	1.484	1.00
33_E	37_T	1.479	1.00
142_E	145_R	1.468	1.00
18_E	63_H	1.433	1.00
33_E	36_K	1.424	1.00
19_Q	23_Q	1.424	1.00
30_G	33_E	1.421	1.00
91_Q	187_L	1.417	1.00
18_E	59_M	1.390	1.00
17_G	55_F	1.378	1.00
62_R	66_A	1.375	1.00
57_V	61_E	1.370	1.00
61_E	125_A	1.363	1.00
162_V	166_L	1.343	1.00
25_G	29_M	1.333	1.00
72_T	136_L	1.319	1.00
57_V	125_A	1.315	1.00
29_M	34_L	1.315	1.00
10_R	48_Y	1.313	1.00
8_D	12_H	1.312	1.00
31_L	45_F	1.311	1.00
15_A	62_R	1.307	1.00
49_F	58_A	1.305	1.00
44_S	47_H	1.289	1.00
134_I	161_Q	1.282	1.00
143_N	147_N	1.241	1.00
25_G	28_G	1.232	1.00
21_C	26_F	1.231	1.00
45_F	55_F	1.211	1.00
24_R	28_G	1.206	1.00
145_R	152_F	1.204	1.00
144_G	149_C	1.193	1.00
144_G	150_L	1.189	1.00
145_R	154_G	1.180	1.00
70_R	92_Q	1.175	1.00
16_T	20_L	1.170	1.00
42_K	46_Y	1.164	1.00
85_R	140_A	1.155	1.00
81_N	149_C	1.149	1.00
41_P	47_H	1.123	1.00
44_S	48_Y	1.118	1.00
54_A	58_A	1.116	1.00
6_E	47_H	1.115	1.00
87_L	91_Q	1.106	1.00
8_D	11_E	1.106	1.00
43_G	47_H	1.106	1.00
84_D	88_A	1.092	1.00
26_F	56_G	1.092	1.00
14_L	59_M	1.089	1.00
40_V	44_S	1.088	1.00
106_C	110_K	1.087	1.00
9_T	48_Y	1.078	1.00
134_I	138_S	1.072	1.00
53_E	57_V	1.069	1.00
155_E	158_Q	1.067	1.00
91_Q	184_E	1.067	1.00
88_A	91_Q	1.059	1.00
46_Y	51_S	1.057	1.00
83_R	87_L	1.042	1.00
151_T	154_G	1.040	1.00
53_E	121_D	1.036	1.00
158_Q	185_N	1.028	1.00
187_L	191_K	1.024	1.00
14_L	49_F	1.022	1.00
17_G	59_M	1.017	1.00
18_E	22_L	1.013	1.00
165_A	169_G	1.011	1.00
53_E	119_S	1.004	1.00
34_L	55_F	1.000	1.00
16_T	38_A	0.997	1.00
138_S	156_P	0.988	1.00
106_C	109_V	0.987	1.00
15_A	19_Q	0.983	1.00
54_A	57_V	0.982	1.00
35_L	42_K	0.971	1.00
182_P	185_N	0.967	1.00
110_K	114_E	0.966	1.00
140_A	144_G	0.961	1.00
136_L	139_Q	0.961	1.00
68_H	132_G	0.961	1.00
24_R	37_T	0.959	1.00
96_Q	100_H	0.950	1.00
80_G	88_A	0.949	1.00
125_A	128_K	0.947	1.00
61_E	65_A	0.945	1.00
87_L	188_A	0.945	1.00
84_D	87_L	0.944	1.00
139_Q	143_N	0.939	1.00
145_R	156_P	0.936	1.00
58_A	62_R	0.926	1.00
7_H	11_E	0.922	1.00
140_A	143_N	0.918	1.00
157_L	161_Q	0.917	1.00
9_T	40_V	0.905	1.00
74_L	92_Q	0.904	1.00
131_R	135_A	0.897	1.00
110_K	113_A	0.887	1.00
82_Y	147_N	0.887	1.00
62_R	65_A	0.872	1.00
88_A	92_Q	0.867	1.00
27_T	114_E	0.862	1.00
42_K	47_H	0.859	1.00
188_A	191_K	0.854	1.00
70_R	73_E	0.853	1.00
72_T	76_Q	0.851	1.00
79_E	85_R	0.845	1.00
135_A	139_Q	0.845	1.00
128_K	132_G	0.844	1.00
92_Q	95_N	0.836	1.00
138_S	160_A	0.835	1.00
63_H	66_A	0.832	1.00
74_L	88_A	0.832	1.00
69_Q	73_E	0.832	1.00
139_Q	142_E	0.830	1.00
134_I	157_L	0.828	1.00
124_S	128_K	0.817	1.00
181_E	185_N	0.811	1.00
65_A	69_Q	0.805	1.00
6_E	9_T	0.802	1.00
68_H	72_T	0.796	1.00
12_H	38_A	0.795	1.00
154_G	159_Q	0.791	1.00
20_L	23_Q	0.785	1.00
91_Q	95_N	0.782	1.00
82_Y	144_G	0.781	1.00
174_A	177_S	0.774	1.00
120_E	124_S	0.773	1.00
179_S	182_P	0.771	1.00
12_H	15_A	0.771	1.00
21_C	56_G	0.768	1.00
91_Q	191_K	0.765	1.00
36_K	42_K	0.761	1.00
123_R	127_D	0.758	1.00
38_A	41_P	0.757	1.00
158_Q	189_H	0.755	1.00
14_L	62_R	0.745	1.00
107_L	110_K	0.745	1.00
80_G	84_D	0.736	1.00
26_F	52_K	0.732	1.00
24_R	29_M	0.727	1.00
135_A	138_S	0.723	1.00
68_H	136_L	0.723	1.00
141_L	156_P	0.720	1.00
145_R	148_H	0.718	1.00
173_Q	176_I	0.708	1.00
156_P	160_A	0.703	1.00
109_V	112_S	0.703	1.00
13_L	38_A	0.701	1.00
111_L	114_E	0.701	1.00
165_A	168_L	0.700	1.00
145_R	150_L	0.696	1.00
13_L	45_F	0.696	1.00
141_L	145_R	0.695	1.00
14_L	18_E	0.693	1.00
32_S	46_Y	0.691	1.00
118_L	121_D	0.688	1.00
141_L	163_L	0.687	1.00
184_E	188_A	0.685	1.00
75_L	136_L	0.681	1.00
158_Q	162_V	0.678	1.00
15_A	18_E	0.676	1.00
23_Q	33_E	0.675	1.00
125_A	129_G	0.667	1.00
31_L	35_L	0.667	1.00
79_E	84_D	0.666	1.00
132_G	136_L	0.665	1.00
90_Y	163_L	0.658	1.00
66_A	69_Q	0.649	1.00
9_T	44_S	0.645	1.00
31_L	52_K	0.644	1.00
183_L	186_A	0.636	1.00
61_E	129_G	0.636	1.00
87_L	90_Y	0.634	1.00
185_N	189_H	0.626	1.00
26_F	29_M	0.626	1.00
143_N	146_E	0.624	1.00
127_D	131_R	0.623	1.00
6_E	48_Y	0.623	1.00
69_Q	72_T	0.623	1.00
132_G	135_A	0.619	1.00
185_N	188_A	0.619	1.00
108_T	111_L	0.617	1.00
81_N	85_R	0.615	1.00
61_E	128_K	0.610	1.00
158_Q	161_Q	0.607	1.00
162_V	165_A	0.601	1.00
95_N	183_L	0.600	1.00
22_L	106_C	0.597	1.00
95_N	99_Q	0.596	1.00
173_Q	177_S	0.591	1.00
82_Y	149_C	0.589	1.00
186_A	190_V	0.586	1.00
118_L	122_M	0.585	1.00
38_A	42_K	0.585	1.00
182_P	186_A	0.583	1.00
26_F	53_E	0.582	1.00
93_T	97_F	0.579	1.00
79_E	88_A	0.570	1.00
158_Q	188_A	0.570	1.00
183_L	187_L	0.569	1.00
120_E	123_R	0.567	1.00
168_L	173_Q	0.565	1.00
168_L	172_L	0.559	1.00
85_R	144_G	0.556	1.00
35_L	40_V	0.555	1.00
64_Y	129_G	0.551	1.00
13_L	48_Y	0.549	1.00
182_P	187_L	0.547	1.00
186_A	189_H	0.545	1.00
83_R	149_C	0.542	1.00
187_L	190_V	0.542	1.00
9_T	41_P	0.542	1.00
91_Q	188_A	0.541	1.00
165_A	173_Q	0.541	1.00
78_G	88_A	0.539	1.00
94_L	184_E	0.536	1.00
18_E	66_A	0.533	1.00
32_S	41_P	0.532	1.00
72_T	132_G	0.532	1.00
35_L	41_P	0.527	1.00
65_A	129_G	0.524	1.00
83_R	191_K	0.522	1.00
155_E	159_Q	0.519	1.00
106_C	112_S	0.519	1.00
146_E	150_L	0.518	1.00
7_H	10_R	0.516	1.00
64_Y	132_G	0.516	1.00
73_E	92_Q	0.516	1.00
47_H	50_R	0.515	1.00
152_F	155_E	0.514	1.00
20_L	30_G	0.511	1.00
96_Q	99_Q	0.509	1.00
27_T	117_D	0.507	1.00
109_V	113_A	0.503	1.00
114_E	118_L	0.503	1.00
42_K	45_F	0.501	1.00
129_G	132_G	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
2hyjA	2	0.9698	100	0.193	Contact Map
3bruA	2	0.9598	100	0.195	Contact Map
4udsA	2	0.9246	100	0.202	Contact Map
3knwA	2	0.9095	100	0.205	Contact Map
2g7sA	2	0.9548	100	0.21	Contact Map
3eupA	2	0.995	100	0.213	Contact Map
2i10A	2	0.9296	100	0.214	Contact Map
3rd3A	2	0.9397	100	0.216	Contact Map
2xdnA	2	0.9899	100	0.22	Contact Map
4cgrA	2	0.9447	100	0.222	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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