RUTR - ECOLI - GREMLIN Contacts

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RUTR - HTH-type transcriptional regulator RutR

UniProt:	P0ACU2	Sequences: MTQGAVKTTGKRSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12301
Length:	212 (176)
Sequences:	43158 (33051)
Seq/√Len:	2491.3

ECOLI - RUTR COMR FABR SLMA ACRR ENVR YBIH UIDR BDCR NEMR BETI YJDC RCDA
BACSU - YFIR YTTP FADR YHGD BSCR YVDT YVKB PKSA YOBS LMRA YDGC YXAF YEZE YVAF YDES YCNC YUXN YERO
HALSA - Q9HRF3
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
42_E	52_K	3.872	1.00
34_F	43_Q	3.843	1.00
29_D	47_L	3.482	1.00
60_P	64_A	2.675	1.00
31_F	39_T	2.421	1.00
61_S	64_A	2.257	1.00
30_T	47_L	2.143	1.00
142_S	160_Q	2.020	1.00
26_A	47_L	1.994	1.00
45_A	55_L	1.968	1.00
30_T	43_Q	1.965	1.00
30_T	34_F	1.946	1.00
30_T	39_T	1.922	1.00
33_Q	47_L	1.919	1.00
20_K	68_A	1.917	1.00
21_K	72_Q	1.881	1.00
26_A	29_D	1.847	1.00
22_A	26_A	1.844	1.00
89_A	92_A	1.844	1.00
19_K	22_A	1.802	1.00
93_A	147_G	1.779	1.00
146_A	159_P	1.777	1.00
42_E	46_E	1.774	1.00
142_S	146_A	1.739	1.00
13_S	16_V	1.656	1.00
28_L	72_Q	1.653	1.00
146_A	150_K	1.589	1.00
21_K	25_S	1.585	1.00
24_L	68_A	1.558	1.00
27_A	31_F	1.541	1.00
41_L	56_L	1.526	1.00
51_S	54_N	1.525	1.00
43_Q	47_L	1.509	1.00
29_D	33_Q	1.499	1.00
41_L	52_K	1.490	1.00
39_T	44_I	1.489	1.00
20_K	58_Y	1.486	1.00
28_L	73_I	1.472	1.00
68_A	71_R	1.470	1.00
59_F	68_A	1.458	1.00
43_Q	46_E	1.454	1.00
35_G	39_T	1.436	1.00
146_A	149_V	1.433	1.00
40_R	43_Q	1.428	1.00
165_M	169_S	1.425	1.00
27_A	65_L	1.391	1.00
147_G	151_S	1.369	1.00
149_V	156_P	1.369	1.00
28_L	69_V	1.365	1.00
26_A	30_T	1.355	1.00
18_A	22_A	1.352	1.00
35_G	38_G	1.351	1.00
67_I	71_R	1.347	1.00
72_Q	76_I	1.339	1.00
34_F	38_G	1.287	1.00
82_K	140_E	1.284	1.00
54_N	57_Y	1.283	1.00
71_R	129_E	1.272	1.00
50_V	54_N	1.252	1.00
148_W	153_K	1.247	1.00
41_L	55_L	1.239	1.00
148_W	154_L	1.203	1.00
64_A	68_A	1.202	1.00
92_A	96_E	1.202	1.00
25_S	72_Q	1.194	1.00
80_P	100_L	1.172	1.00
95_K	99_R	1.171	1.00
18_A	21_K	1.155	1.00
31_F	36_F	1.137	1.00
27_A	69_V	1.137	1.00
52_K	56_L	1.131	1.00
149_V	157_I	1.124	1.00
144_L	148_W	1.121	1.00
67_I	129_E	1.120	1.00
138_I	164_F	1.118	1.00
138_I	142_S	1.104	1.00
26_A	48_A	1.095	1.00
28_L	32_S	1.091	1.00
63_E	67_I	1.076	1.00
24_L	59_F	1.075	1.00
34_F	47_L	1.068	1.00
158_D	161_H	1.061	1.00
55_L	65_L	1.060	1.00
93_A	144_L	1.051	1.00
96_E	99_R	1.051	1.00
56_L	61_S	1.048	1.00
24_L	72_Q	1.048	1.00
51_S	57_Y	1.041	1.00
91_L	95_K	1.037	1.00
25_S	29_D	1.033	1.00
19_K	58_Y	1.023	1.00
140_E	143_A	1.019	1.00
24_L	69_V	1.016	1.00
53_T	57_Y	1.005	1.00
168_A	172_H	1.003	1.00
88_F	96_E	1.001	1.00
71_R	75_D	0.992	1.00
64_A	67_I	0.991	1.00
112_S	115_F	0.981	1.00
157_I	162_L	0.977	1.00
36_F	66_Y	0.976	1.00
54_N	58_Y	0.972	1.00
63_E	123_A	0.970	1.00
142_S	159_P	0.957	1.00
44_I	65_L	0.956	1.00
135_K	139_D	0.954	1.00
19_K	50_V	0.947	1.00
143_A	147_G	0.943	1.00
16_V	57_Y	0.934	1.00
29_D	110_Q	0.927	1.00
90_P	151_S	0.919	1.00
96_E	100_L	0.916	1.00
100_L	103_E	0.916	1.00
149_V	159_P	0.914	1.00
73_I	76_I	0.909	1.00
92_A	95_K	0.908	1.00
15_A	18_A	0.907	1.00
144_L	147_G	0.907	1.00
80_P	83_A	0.904	1.00
78_L	82_K	0.903	1.00
78_L	136_A	0.900	1.00
129_E	132_G	0.897	1.00
99_R	195_N	0.891	1.00
68_A	72_Q	0.889	1.00
13_S	17_S	0.887	1.00
17_S	21_K	0.881	1.00
22_A	25_S	0.880	1.00
160_Q	164_F	0.872	1.00
90_P	148_W	0.860	1.00
177_A	180_V	0.859	1.00
45_A	52_K	0.852	1.00
147_G	150_K	0.851	1.00
132_G	136_A	0.850	1.00
89_A	153_K	0.850	1.00
72_Q	75_D	0.849	1.00
139_D	143_A	0.849	1.00
78_L	140_E	0.847	1.00
46_E	52_K	0.844	1.00
52_K	57_Y	0.839	1.00
136_A	140_E	0.839	1.00
127_M	131_T	0.839	1.00
104_V	108_Y	0.835	1.00
111_A	114_L	0.832	1.00
23_I	55_L	0.830	1.00
128_D	132_G	0.808	1.00
63_E	125_L	0.806	1.00
22_A	48_A	0.804	1.00
142_S	163_I	0.802	1.00
23_I	48_A	0.801	1.00
138_I	160_Q	0.800	1.00
124_P	128_D	0.799	1.00
14_R	18_A	0.798	1.00
129_E	133_D	0.796	1.00
145_I	166_I	0.796	1.00
87_D	93_A	0.789	1.00
143_A	146_A	0.789	1.00
159_P	163_I	0.785	1.00
84_F	96_E	0.780	1.00
113_R	116_C	0.777	1.00
30_T	33_Q	0.775	1.00
76_I	79_A	0.774	1.00
149_V	154_L	0.773	1.00
139_D	142_S	0.766	1.00
34_F	39_T	0.765	1.00
149_V	152_G	0.765	1.00
95_K	195_N	0.754	1.00
131_T	135_K	0.751	1.00
108_Y	111_A	0.749	1.00
88_F	92_A	0.748	1.00
122_G	125_L	0.747	1.00
98_I	166_I	0.746	1.00
124_P	127_M	0.742	1.00
24_L	28_L	0.741	1.00
161_H	196_Q	0.740	1.00
115_F	118_E	0.735	1.00
84_F	100_L	0.735	1.00
75_D	79_A	0.729	1.00
83_A	100_L	0.723	1.00
79_A	83_A	0.719	1.00
33_Q	43_Q	0.717	1.00
161_H	165_M	0.712	1.00
16_V	19_K	0.701	1.00
14_R	17_S	0.694	1.00
136_A	139_D	0.694	1.00
32_S	110_Q	0.687	1.00
25_S	28_L	0.686	1.00
99_R	103_E	0.685	1.00
71_R	132_G	0.685	1.00
168_A	171_Q	0.682	1.00
79_A	82_K	0.681	1.00
104_V	107_D	0.680	1.00
145_I	159_P	0.675	1.00
95_K	98_I	0.674	1.00
36_F	62_K	0.673	1.00
176_F	179_Q	0.671	1.00
176_F	180_V	0.671	1.00
41_L	62_K	0.669	1.00
15_A	19_K	0.667	1.00
52_K	55_L	0.667	1.00
110_Q	113_R	0.663	1.00
42_E	56_L	0.655	1.00
103_E	107_D	0.652	1.00
19_K	54_N	0.652	1.00
48_A	51_S	0.645	1.00
113_R	117_M	0.636	1.00
118_E	121_A	0.633	1.00
41_L	45_A	0.633	1.00
80_P	104_V	0.632	1.00
36_F	39_T	0.624	1.00
133_D	136_A	0.619	1.00
145_I	149_V	0.619	1.00
117_M	121_A	0.609	1.00
89_A	93_A	0.603	1.00
71_R	133_D	0.602	1.00
131_T	134_L	0.595	1.00
100_L	104_V	0.591	1.00
169_S	172_H	0.589	1.00
162_L	165_M	0.589	1.00
158_D	162_L	0.586	1.00
165_M	168_A	0.585	1.00
161_H	164_F	0.583	1.00
168_A	176_F	0.580	1.00
171_Q	175_D	0.578	1.00
98_I	101_K	0.576	1.00
36_F	63_E	0.574	1.00
45_A	50_V	0.566	1.00
177_A	181_E	0.565	1.00
23_I	58_Y	0.565	1.00
101_K	105_S	0.563	1.00
37_H	121_A	0.559	1.00
74_L	136_A	0.557	1.00
31_F	66_Y	0.556	1.00
16_V	20_K	0.555	1.00
42_E	51_S	0.553	1.00
82_K	85_R	0.553	1.00
20_K	59_F	0.551	1.00
171_Q	174_A	0.541	1.00
75_D	133_D	0.541	1.00
156_P	162_L	0.539	1.00
101_K	171_Q	0.537	1.00
17_S	20_K	0.536	1.00
102_L	106_R	0.533	1.00
90_P	93_A	0.532	1.00
16_V	58_Y	0.529	1.00
111_A	115_F	0.529	1.00
134_L	138_I	0.529	1.00
125_L	128_D	0.527	1.00
82_K	143_A	0.522	1.00
19_K	51_S	0.522	1.00
169_S	173_Y	0.518	1.00
19_K	57_Y	0.518	1.00
51_S	55_L	0.517	1.00
128_D	131_T	0.515	1.00
90_P	153_K	0.511	1.00
122_G	126_L	0.510	1.00
14_R	22_A	0.510	1.00
48_A	52_K	0.510	1.00
28_L	76_I	0.509	1.00
133_D	137_L	0.509	1.00
93_A	148_W	0.507	1.00
32_S	108_Y	0.505	1.00
14_R	19_K	0.505	1.00
140_E	144_L	0.505	1.00
19_K	23_I	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
4jykA	2	0.9481	100	0.171	Contact Map
3npiA	2	0.9292	100	0.223	Contact Map
2qtqA	2	0.9481	100	0.24	Contact Map
3cwrA	2	0.9009	100	0.247	Contact Map
3g1oA	2	0.8915	100	0.251	Contact Map
3gziA	2	0.9434	100	0.252	Contact Map
3f0cA	2	0.9057	100	0.255	Contact Map
3dewA	2	0.9009	100	0.259	Contact Map
3dcfA	2	0.8585	100	0.262	Contact Map
3qqaA	2	0.9151	100	0.263	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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