CSIR - ECOLI - GREMLIN Contacts

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CSIR - HTH-type transcriptional repressor CsiR

UniProt:	P37338	Sequences: MTITSLDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLDIFDARANMEAMLVSLAIARGGDEWEADVLAKAHLLSKLEACDASEKMLDEWDLRHQAFHTAIVAGCGSHYLLQMRERLFDLAARYRFIWLRRTVLSVEMLEDKHDQHQTLTAAVLARDTARASELMRQHLLTPIPIIQQAMAGN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12386
Length:	220 (199)
Sequences:	23472 (17235)
Seq/√Len:	1221.8

ECOLI - CSIR YJJM YDFH MCBR PDHR DGOR GLCC NANR LLDR UXUR YIEP EXUR FADR FRLR YEGW YIDP
BACSU - YDHC GNTR LUTR YCBG YMFC YVOA YURK TRER YYDK YBGA
SULSO - Q97YR4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
105_L	191_L	3.685	1.00
90_S	199_S	3.281	1.00
194_D	197_R	2.888	1.00
112_S	184_Q	2.737	1.00
15_D	20_N	2.696	1.00
22_Q	25_E	2.646	1.00
15_D	35_R	2.367	1.00
83_N	87_M	2.306	1.00
29_M	40_V	2.246	1.00
103_D	137_A	2.230	1.00
76_D	145_H	2.166	1.00
82_A	207_L	2.085	1.00
9_Y	49_Q	2.008	1.00
57_T	67_A	2.004	1.00
8_G	38_L	1.955	1.00
79_D	91_L	1.952	1.00
13_K	53_E	1.939	1.00
94_A	195_T	1.936	1.00
58_V	64_Y	1.814	1.00
8_G	36_Y	1.810	1.00
140_A	148_L	1.796	1.00
101_E	191_L	1.778	1.00
189_A	197_R	1.772	1.00
100_W	143_G	1.752	1.00
137_A	140_A	1.720	1.00
11_W	15_D	1.691	1.00
97_G	100_W	1.690	1.00
123_M	126_E	1.676	1.00
86_A	203_R	1.669	1.00
108_A	187_T	1.659	1.00
90_S	195_T	1.623	1.00
80_A	150_M	1.609	1.00
182_Q	208_T	1.603	1.00
197_R	201_L	1.572	1.00
86_A	199_S	1.551	1.00
14_N	18_R	1.550	1.00
199_S	203_R	1.550	1.00
87_M	90_S	1.525	1.00
135_H	183_H	1.495	1.00
185_T	201_L	1.492	1.00
110_L	130_R	1.450	1.00
146_Y	157_L	1.419	1.00
149_Q	153_R	1.415	1.00
139_V	151_R	1.407	1.00
100_W	141_G	1.405	1.00
82_A	203_R	1.404	1.00
89_V	198_A	1.385	1.00
9_Y	53_E	1.384	1.00
136_T	152_E	1.383	1.00
188_A	192_A	1.367	1.00
105_L	187_T	1.361	1.00
112_S	180_H	1.356	1.00
59_V	62_K	1.349	1.00
107_K	130_R	1.338	1.00
30_S	34_S	1.335	1.00
82_A	210_I	1.334	1.00
192_A	197_R	1.326	1.00
76_D	146_Y	1.318	1.00
184_Q	188_A	1.295	1.00
195_T	199_S	1.279	1.00
96_G	101_E	1.277	1.00
105_L	109_H	1.265	1.00
106_A	110_L	1.239	1.00
110_L	133_A	1.230	1.00
31_L	35_R	1.226	1.00
108_A	184_Q	1.222	1.00
26_K	65_R	1.214	1.00
28_R	31_L	1.196	1.00
107_K	137_A	1.187	1.00
32_L	43_L	1.187	1.00
59_V	65_R	1.178	1.00
82_A	86_A	1.177	1.00
182_Q	205_H	1.175	1.00
200_E	204_Q	1.169	1.00
7_D	11_W	1.167	1.00
11_W	14_N	1.165	1.00
133_A	137_A	1.148	1.00
11_W	36_Y	1.144	1.00
203_R	207_L	1.141	1.00
51_V	58_V	1.138	1.00
136_T	140_A	1.137	1.00
81_R	85_E	1.134	1.00
197_R	200_E	1.122	1.00
15_D	36_Y	1.122	1.00
96_G	193_R	1.121	1.00
126_E	129_L	1.115	1.00
86_A	90_S	1.110	1.00
89_V	202_M	1.110	1.00
108_A	111_L	1.109	1.00
96_G	141_G	1.106	1.00
138_I	190_V	1.102	1.00
89_V	93_I	1.098	1.00
76_D	144_S	1.092	1.00
107_K	133_A	1.092	1.00
90_S	196_A	1.086	1.00
131_H	135_H	1.076	1.00
101_E	187_T	1.068	1.00
137_A	141_G	1.064	1.00
21_F	66_V	1.061	1.00
187_T	191_L	1.053	1.00
96_G	100_W	1.051	1.00
188_A	191_L	1.044	1.00
88_L	139_V	1.040	1.00
108_A	112_S	1.040	1.00
103_D	140_A	1.035	1.00
79_D	144_S	1.033	1.00
75_L	210_I	1.028	1.00
105_L	184_Q	1.022	1.00
130_R	133_A	1.019	1.00
57_T	65_R	1.017	1.00
101_E	193_R	1.013	1.00
109_H	112_S	1.004	1.00
103_D	106_A	0.996	1.00
150_M	153_R	0.992	1.00
51_V	56_V	0.988	1.00
189_A	194_D	0.980	1.00
93_I	195_T	0.978	1.00
45_E	48_S	0.978	1.00
91_L	95_R	0.961	1.00
15_D	21_F	0.959	1.00
47_L	64_Y	0.955	1.00
70_S	73_E	0.954	1.00
134_F	187_T	0.950	1.00
16_I	66_V	0.949	1.00
87_M	199_S	0.947	1.00
129_L	133_A	0.941	1.00
59_V	63_G	0.941	1.00
185_T	204_Q	0.939	1.00
181_D	185_T	0.936	1.00
185_T	197_R	0.934	1.00
103_D	107_K	0.931	1.00
135_H	205_H	0.929	1.00
102_A	106_A	0.914	1.00
142_C	148_L	0.914	1.00
183_H	205_H	0.912	1.00
93_I	190_V	0.906	1.00
26_K	63_G	0.900	1.00
196_A	200_E	0.898	1.00
185_T	188_A	0.896	1.00
49_Q	52_A	0.896	1.00
95_R	143_G	0.895	1.00
85_E	135_H	0.894	1.00
148_L	152_E	0.894	1.00
186_L	202_M	0.881	1.00
101_E	105_L	0.881	1.00
9_Y	13_K	0.875	1.00
5_S	49_Q	0.872	1.00
29_M	44_R	0.871	1.00
80_A	146_Y	0.870	1.00
13_K	55_L	0.865	1.00
56_V	64_Y	0.864	1.00
62_K	65_R	0.852	1.00
39_G	42_P	0.852	1.00
107_K	110_L	0.851	1.00
87_M	91_L	0.848	1.00
96_G	190_V	0.845	1.00
196_A	199_S	0.843	1.00
131_H	183_H	0.842	1.00
180_H	184_Q	0.837	1.00
48_S	51_V	0.837	1.00
114_L	126_E	0.825	1.00
73_E	146_Y	0.825	1.00
33_T	43_L	0.823	1.00
81_R	206_L	0.823	1.00
105_L	188_A	0.822	1.00
72_Q	143_G	0.822	1.00
98_D	102_A	0.817	1.00
110_L	113_K	0.810	1.00
185_T	189_A	0.805	1.00
31_L	34_S	0.804	1.00
100_W	103_D	0.801	1.00
6_L	49_Q	0.800	1.00
13_K	17_I	0.799	1.00
93_I	198_A	0.791	1.00
186_L	201_L	0.787	1.00
93_I	193_R	0.787	1.00
146_Y	150_M	0.787	1.00
189_A	201_L	0.786	1.00
47_L	56_V	0.783	1.00
38_L	43_L	0.782	1.00
109_H	184_Q	0.780	1.00
92_A	141_G	0.780	1.00
48_S	58_V	0.774	1.00
98_D	193_R	0.774	1.00
109_H	113_K	0.771	1.00
79_D	210_I	0.770	1.00
90_S	94_A	0.768	1.00
32_L	47_L	0.767	1.00
104_V	137_A	0.765	1.00
104_V	187_T	0.756	1.00
201_L	204_Q	0.749	1.00
177_E	181_D	0.747	1.00
146_Y	149_Q	0.746	1.00
91_L	94_A	0.742	1.00
136_T	155_F	0.739	1.00
80_A	147_L	0.737	1.00
91_L	144_S	0.730	1.00
72_Q	76_D	0.727	1.00
92_A	96_G	0.723	1.00
5_S	9_Y	0.722	1.00
111_L	127_W	0.720	1.00
207_L	211_P	0.718	1.00
126_E	130_R	0.716	1.00
79_D	95_R	0.715	1.00
132_Q	159_A	0.713	1.00
78_F	209_P	0.713	1.00
103_D	133_A	0.707	1.00
102_A	105_L	0.703	1.00
186_L	198_A	0.698	1.00
102_A	191_L	0.695	1.00
132_Q	155_F	0.695	1.00
200_E	203_R	0.694	1.00
114_L	130_R	0.689	1.00
136_T	148_L	0.688	1.00
110_L	114_L	0.684	1.00
110_L	126_E	0.684	1.00
80_A	88_L	0.684	1.00
207_L	210_I	0.677	1.00
204_Q	208_T	0.676	1.00
101_E	190_V	0.671	1.00
20_N	35_R	0.666	1.00
108_A	180_H	0.664	1.00
49_Q	53_E	0.664	1.00
100_W	137_A	0.656	1.00
42_P	46_A	0.648	1.00
182_Q	185_T	0.648	1.00
106_A	109_H	0.647	1.00
21_F	25_E	0.646	1.00
133_A	136_T	0.643	1.00
100_W	140_A	0.639	1.00
79_D	87_M	0.639	1.00
83_N	147_L	0.637	1.00
92_A	142_C	0.634	1.00
89_V	195_T	0.630	1.00
186_L	205_H	0.629	1.00
85_E	183_H	0.624	1.00
208_T	212_I	0.624	1.00
80_A	84_M	0.613	1.00
88_L	142_C	0.612	1.00
15_D	19_G	0.611	1.00
82_A	206_L	0.604	1.00
88_L	147_L	0.603	1.00
114_L	123_M	0.602	1.00
114_L	122_K	0.602	1.00
99_E	103_D	0.585	1.00
86_A	202_M	0.582	1.00
24_D	68_S	0.582	1.00
72_Q	145_H	0.581	1.00
127_W	179_K	0.581	1.00
61_Q	64_Y	0.581	1.00
104_V	141_G	0.576	1.00
36_Y	43_L	0.571	1.00
149_Q	157_L	0.570	1.00
115_E	122_K	0.567	1.00
12_L	32_L	0.566	1.00
23_P	68_S	0.564	1.00
86_A	195_T	0.564	1.00
92_A	138_I	0.560	1.00
90_S	203_R	0.558	1.00
98_D	191_L	0.557	1.00
84_M	151_R	0.552	1.00
30_S	33_T	0.551	1.00
83_N	86_A	0.549	1.00
27_L	56_V	0.547	1.00
5_S	45_E	0.543	1.00
73_E	145_H	0.539	1.00
125_D	163_F	0.539	1.00
111_L	180_H	0.537	1.00
174_E	177_E	0.534	1.00
145_H	148_L	0.534	1.00
89_V	138_I	0.534	1.00
79_D	82_A	0.532	1.00
186_L	189_A	0.532	1.00
160_R	164_I	0.532	1.00
80_A	83_N	0.531	1.00
48_S	52_A	0.530	1.00
132_Q	136_T	0.529	1.00
34_S	37_A	0.527	1.00
65_R	68_S	0.524	1.00
104_V	108_A	0.523	1.00
182_Q	204_Q	0.522	1.00
139_V	155_F	0.519	1.00
178_D	181_D	0.519	1.00
181_D	184_Q	0.519	1.00
149_Q	152_E	0.518	1.00
204_Q	207_L	0.518	1.00
91_L	142_C	0.516	1.00
17_I	55_L	0.516	1.00
15_D	18_R	0.515	1.00
87_M	147_L	0.513	1.00
67_A	160_R	0.512	1.00
202_M	206_L	0.510	1.00
85_E	206_L	0.509	1.00
175_M	212_I	0.508	1.00
75_L	79_D	0.504	1.00
30_S	40_V	0.503	1.00
73_E	157_L	0.502	1.00
21_F	27_L	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
3c7jA	4	0.95	100	0.125	Contact Map
2hs5A	1	0.9409	100	0.127	Contact Map
3sxyA	2	0.9091	100	0.132	Contact Map
3ihuA	1	0.9273	100	0.135	Contact Map
4p9fA	1	0.9591	100	0.138	Contact Map
4p96A	2	0.9818	100	0.159	Contact Map
2di3A	2	0.9591	100	0.168	Contact Map
1hw1A	2	0.9364	100	0.202	Contact Map
3ic7A	2	0.5	99.8	0.541	Contact Map
3by6A	2	0.5227	99.8	0.545	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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