COMR - ECOLI - GREMLIN Contacts

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COMR - HTH-type transcriptional repressor ComR

UniProt:	P75952	Sequences: MATDSTQCVKKSRGRPKVFDRDAALDKAMKLFWQHGYEATSLADLVEATGAKAPTLYAEFTNKEGLFRAVLDRYIDRFAAKHEAQLFCEEKSVESALADYFAAIANCFTSKDTPAGCFMINNCTTLSPDSGDIANTLKSRHAMQERTLQQFLCQRQARGEIPPHCDVTHLAEFLNCIIQGMSISAREGASLEKLMQIAGTTLRLWPELVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13435
Length:	210 (186)
Sequences:	46035 (36080)
Seq/√Len:	2645.5

ECOLI - COMR SLMA RUTR NEMR ACRR BDCR UIDR ENVR FABR BETI YJDC YBIH RCDA
BACSU - YFIR YEZE FADR YHGD YVDT LMRA PKSA BSCR YTTP YXAF YVKB YDGC YDES YCNC YVAF YUXN YOBS YERO
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
35_H	44_D	3.956	1.00
43_A	53_A	3.861	1.00
30_K	48_A	3.493	1.00
61_T	65_G	2.704	1.00
32_F	40_T	2.373	1.00
62_N	65_G	2.314	1.00
149_Q	168_T	2.192	1.00
46_V	56_L	2.127	1.00
21_R	69_A	2.011	1.00
31_L	48_A	1.979	1.00
34_Q	48_A	1.977	1.00
31_L	40_T	1.957	1.00
149_Q	153_C	1.957	1.00
27_K	48_A	1.951	1.00
20_D	23_A	1.933	1.00
22_D	73_R	1.930	1.00
96_A	154_Q	1.905	1.00
23_A	27_K	1.892	1.00
31_L	44_D	1.891	1.00
31_L	35_H	1.876	1.00
92_S	95_S	1.862	1.00
43_A	47_E	1.826	1.00
14_G	17_K	1.734	1.00
153_C	167_V	1.715	1.00
153_C	157_A	1.698	1.00
27_K	30_K	1.695	1.00
52_K	55_T	1.685	1.00
29_M	73_R	1.629	1.00
22_D	26_D	1.595	1.00
153_C	156_Q	1.581	1.00
44_D	48_A	1.551	1.00
25_L	69_A	1.538	1.00
41_S	44_D	1.534	1.00
29_M	74_Y	1.520	1.00
30_K	34_Q	1.518	1.00
21_R	59_E	1.491	1.00
42_L	57_Y	1.490	1.00
69_A	72_D	1.488	1.00
83_E	147_T	1.458	1.00
28_A	32_F	1.453	1.00
72_D	136_T	1.443	1.00
44_D	47_E	1.441	1.00
73_R	77_R	1.437	1.00
154_Q	158_R	1.412	1.00
68_R	72_D	1.387	1.00
42_L	53_A	1.386	1.00
173_F	177_I	1.362	1.00
40_T	45_L	1.348	1.00
36_G	40_T	1.336	1.00
102_A	195_M	1.319	1.00
29_M	70_V	1.309	1.00
60_F	69_A	1.301	1.00
19_F	23_A	1.278	1.00
28_A	66_L	1.273	1.00
68_R	136_T	1.271	1.00
26_D	73_R	1.265	1.00
156_Q	163_P	1.264	1.00
55_T	58_A	1.230	1.00
98_A	199_G	1.224	1.00
81_K	103_A	1.215	1.00
145_E	172_E	1.214	1.00
155_R	161_I	1.212	1.00
102_A	198_A	1.207	1.00
42_L	56_L	1.203	1.00
169_H	196_Q	1.200	1.00
35_H	39_A	1.196	1.00
36_G	39_A	1.187	1.00
95_S	99_D	1.159	1.00
19_F	22_D	1.158	1.00
51_A	55_T	1.149	1.00
94_E	98_A	1.147	1.00
166_D	169_H	1.147	1.00
27_K	31_L	1.146	1.00
145_E	149_Q	1.141	1.00
98_A	202_L	1.138	1.00
155_R	160_E	1.138	1.00
64_E	68_R	1.136	1.00
96_A	151_F	1.133	1.00
56_L	66_L	1.132	1.00
65_G	69_A	1.126	1.00
32_F	37_Y	1.124	1.00
98_A	102_A	1.123	1.00
64_E	130_S	1.097	1.00
99_D	102_A	1.092	1.00
20_D	59_E	1.080	1.00
156_Q	165_C	1.075	1.00
27_K	49_T	1.066	1.00
136_T	139_S	1.063	1.00
45_L	66_L	1.062	1.00
52_K	58_A	1.059	1.00
53_A	57_Y	1.059	1.00
25_L	60_F	1.058	1.00
64_E	132_D	1.054	1.00
54_P	58_A	1.045	1.00
26_D	30_K	1.042	1.00
147_T	150_Q	1.039	1.00
72_D	76_D	1.033	1.00
25_L	70_V	1.028	1.00
55_T	59_E	1.028	1.00
149_Q	167_V	1.016	1.00
37_Y	67_F	1.004	1.00
29_M	33_W	1.001	1.00
65_G	68_R	1.000	1.00
162_P	165_C	0.997	1.00
91_K	99_D	0.991	1.00
28_A	70_V	0.985	1.00
35_H	48_A	0.983	1.00
92_S	160_E	0.970	1.00
151_F	155_R	0.949	1.00
199_G	203_R	0.942	1.00
156_Q	167_V	0.942	1.00
198_A	202_L	0.939	1.00
73_R	76_D	0.938	1.00
117_C	121_N	0.935	1.00
146_R	150_Q	0.932	1.00
17_K	58_A	0.931	1.00
168_T	172_E	0.931	1.00
90_E	96_A	0.929	1.00
79_A	143_M	0.929	1.00
93_V	158_R	0.924	1.00
57_Y	62_N	0.918	1.00
156_Q	159_G	0.917	1.00
69_A	73_R	0.915	1.00
107_C	111_K	0.914	1.00
185_A	188_G	0.913	1.00
150_Q	154_Q	0.912	1.00
81_K	84_A	0.908	1.00
80_A	84_A	0.907	1.00
46_V	53_A	0.906	1.00
151_F	154_Q	0.903	1.00
95_S	98_A	0.902	1.00
135_N	139_S	0.902	1.00
142_A	146_R	0.902	1.00
139_S	143_M	0.898	1.00
18_V	22_D	0.895	1.00
176_C	180_G	0.891	1.00
149_Q	171_A	0.889	1.00
99_D	103_A	0.882	1.00
193_K	196_Q	0.876	1.00
145_E	168_T	0.870	1.00
31_L	34_Q	0.870	1.00
165_C	170_L	0.865	1.00
192_E	196_Q	0.865	1.00
20_D	51_A	0.861	1.00
156_Q	161_I	0.854	1.00
102_A	106_N	0.853	1.00
150_Q	153_C	0.849	1.00
85_Q	99_D	0.847	1.00
103_A	106_N	0.847	1.00
79_A	83_E	0.841	1.00
74_Y	77_R	0.841	1.00
134_A	138_K	0.833	1.00
15_R	19_F	0.829	1.00
154_Q	157_A	0.824	1.00
191_L	195_M	0.822	1.00
129_D	132_D	0.813	1.00
14_G	18_V	0.803	1.00
169_H	172_E	0.802	1.00
76_D	80_A	0.801	1.00
38_E	125_T	0.800	1.00
195_M	199_G	0.793	1.00
136_T	140_R	0.785	1.00
23_A	49_T	0.785	1.00
16_P	19_F	0.783	1.00
93_V	155_R	0.782	1.00
169_H	200_T	0.782	1.00
24_A	56_L	0.777	1.00
23_A	26_D	0.776	1.00
116_G	120_I	0.776	1.00
72_D	140_R	0.773	1.00
176_C	179_Q	0.768	1.00
197_I	201_T	0.760	1.00
30_K	113_T	0.756	1.00
192_E	195_M	0.754	1.00
91_K	95_S	0.754	1.00
146_R	149_Q	0.752	1.00
194_L	197_I	0.751	1.00
131_G	135_N	0.748	1.00
37_Y	63_K	0.747	1.00
42_L	46_V	0.744	1.00
196_Q	199_G	0.744	1.00
47_E	53_A	0.742	1.00
169_H	173_F	0.740	1.00
101_F	174_L	0.739	1.00
17_K	20_D	0.731	1.00
152_L	174_L	0.722	1.00
24_A	49_T	0.721	1.00
77_R	80_A	0.720	1.00
199_G	202_L	0.719	1.00
85_Q	103_A	0.719	1.00
25_L	73_R	0.718	1.00
16_P	20_D	0.718	1.00
143_M	146_R	0.717	1.00
79_A	147_T	0.716	1.00
26_D	29_M	0.714	1.00
49_T	52_K	0.713	1.00
193_K	197_I	0.708	1.00
35_H	40_T	0.704	1.00
53_A	58_A	0.703	1.00
90_E	95_S	0.699	1.00
200_T	203_R	0.698	1.00
167_V	171_A	0.697	1.00
196_Q	200_T	0.695	1.00
117_C	120_I	0.693	1.00
143_M	147_T	0.689	1.00
15_R	18_V	0.688	1.00
121_N	125_T	0.687	1.00
34_Q	44_D	0.686	1.00
72_D	139_S	0.679	1.00
152_L	167_V	0.678	1.00
43_A	57_Y	0.674	1.00
138_K	142_A	0.672	1.00
131_G	134_A	0.666	1.00
116_G	119_M	0.656	1.00
106_N	194_L	0.654	1.00
92_S	96_A	0.653	1.00
25_L	29_M	0.649	1.00
129_D	133_I	0.645	1.00
152_L	156_Q	0.643	1.00
184_S	188_G	0.626	1.00
20_D	55_T	0.623	1.00
32_F	67_F	0.619	1.00
80_A	83_E	0.615	1.00
106_N	110_S	0.610	1.00
102_A	199_G	0.610	1.00
37_Y	64_E	0.607	1.00
163_P	166_D	0.599	1.00
90_E	99_D	0.597	1.00
173_F	176_C	0.594	1.00
98_A	101_F	0.593	1.00
37_Y	40_T	0.589	1.00
104_I	108_F	0.588	1.00
84_A	103_A	0.585	1.00
42_L	63_K	0.584	1.00
170_L	173_F	0.573	1.00
193_K	198_A	0.571	1.00
18_V	21_R	0.571	1.00
29_M	77_R	0.570	1.00
198_A	201_T	0.565	1.00
24_A	59_E	0.563	1.00
75_I	140_R	0.560	1.00
156_Q	162_P	0.560	1.00
197_I	200_T	0.558	1.00
125_T	129_D	0.555	1.00
179_Q	183_I	0.555	1.00
116_G	121_N	0.554	1.00
75_I	143_M	0.553	1.00
118_F	121_N	0.551	1.00
68_R	132_D	0.550	1.00
121_N	124_T	0.545	1.00
107_C	110_S	0.544	1.00
184_S	187_E	0.543	1.00
166_D	170_L	0.542	1.00
132_D	136_T	0.541	1.00
94_E	160_E	0.540	1.00
49_T	53_A	0.540	1.00
180_G	183_I	0.538	1.00
103_A	107_C	0.535	1.00
17_K	59_E	0.533	1.00
179_Q	184_S	0.532	1.00
152_L	170_L	0.532	1.00
91_K	96_A	0.527	1.00
76_D	140_R	0.527	1.00
96_A	155_R	0.525	1.00
147_T	151_F	0.523	1.00
81_K	107_C	0.522	1.00
138_K	141_H	0.521	1.00
176_C	184_S	0.519	1.00
28_A	45_L	0.518	1.00
195_M	198_A	0.518	1.00
33_W	116_G	0.518	1.00
46_V	51_A	0.515	1.00
142_A	145_E	0.514	1.00
20_D	52_K	0.513	1.00
167_V	170_L	0.511	1.00
93_V	160_E	0.507	1.00
155_R	159_G	0.505	1.00
135_N	138_K	0.504	1.00
185_A	189_A	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
3bruA	2	0.9048	100	0.21	Contact Map
2hyjA	2	0.919	100	0.231	Contact Map
4udsA	2	0.8905	100	0.232	Contact Map
3g1oA	2	0.8952	100	0.233	Contact Map
2ibdA	2	0.9048	100	0.235	Contact Map
3kz9A	2	0.9619	100	0.236	Contact Map
3knwA	2	0.8667	100	0.238	Contact Map
2i10A	2	0.881	100	0.239	Contact Map
3eupA	2	0.9571	100	0.241	Contact Map
2xdnA	2	0.9381	100	0.244	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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