TORR - ECOLI - GREMLIN Contacts

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TORR - TorCAD operon transcriptional regulatory protein TorR

UniProt:	P38684	Sequences: MPHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRIDLARQAQPHTQDNCYRFAGYCLNVSRHTLERDGEPIKLTRAEYEMLVAFVTNPGEILSRERLLRMLSARRVENPDLRTVDVLIRRLRHKLSADLLVTQHGEGYFLAADVC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12615
Length:	230 (200)
Sequences:	71226 (51077)
Seq/√Len:	3611.7

ECOLI - TORR BASR QSEB YEDW ARCA PHOB RSTA BAER PHOP KDPE CPXR CUSR OMPR CREB UVRY DPIA DCUR YHJB FIMZ EVGA NARP YJJQ NARL YGEK RCSB BARA RSSB TORS BGLJ UHPA RCSC CHEB YEHT RCSA CSGD ARCB EVGS YPDB NTRC GLRR ZRAR ATOC RCSD
BACSU - YYCF CSSR YVRH YVCP YRKP PHOP YCLJ YXDJ YCBL RESD BCER YKOG CITT YFIK YBDJ DCTR MALR CMPA YXJL DEGU LIAR YDFI YVFU DESR YHCZ YESN GLNL CHEB LYTT SP0A NATR CHEV CHEY
HALSA - CHEB Q9HR09 Q9HRE5 Q9HNM3 BAT O51970 Q9HP91 F2Z6H5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_Q	31_V	3.619	1.00
15_Q	33_A	3.103	1.00
19_Q	31_V	2.939	1.00
8_V	38_L	2.636	1.00
36_A	58_D	2.550	1.00
34_S	58_D	2.515	1.00
30_S	47_V	2.501	1.00
35_G	59_E	2.495	1.00
43_Q	71_R	2.388	1.00
39_R	67_A	2.380	1.00
59_E	67_A	2.326	1.00
4_H	30_S	2.088	1.00
4_H	28_T	2.075	1.00
19_Q	23_T	2.018	1.00
21_Y	106_L	1.965	1.00
88_R	108_E	1.958	1.00
197_R	200_D	1.943	1.00
32_T	41_I	1.923	1.00
161_A	164_E	1.903	1.00
52_L	64_L	1.869	1.00
25_E	110_V	1.829	1.00
33_A	37_G	1.826	1.00
55_N	82_R	1.801	1.00
65_T	76_I	1.786	1.00
179_R	200_D	1.778	1.00
85_R	105_E	1.761	1.00
34_S	37_G	1.753	1.00
78_L	91_G	1.735	1.00
6_V	32_T	1.670	1.00
78_L	96_A	1.662	1.00
60_N	63_M	1.656	1.00
69_R	97_D	1.621	1.00
30_S	41_I	1.596	1.00
67_A	71_R	1.566	1.00
167_V	171_T	1.546	1.00
59_E	63_M	1.540	1.00
202_L	205_R	1.523	1.00
67_A	70_E	1.502	1.00
168_A	185_M	1.496	1.00
41_I	45_Q	1.496	1.00
35_G	64_L	1.491	1.00
136_R	141_C	1.485	1.00
3_H	117_L	1.483	1.00
22_F	113_V	1.452	1.00
139_G	152_D	1.445	1.00
65_T	78_L	1.425	1.00
39_R	64_L	1.424	1.00
30_S	45_Q	1.416	1.00
82_R	87_D	1.402	1.00
54_I	78_L	1.396	1.00
98_D	112_R	1.392	1.00
41_I	44_N	1.391	1.00
162_E	209_K	1.383	1.00
52_L	65_T	1.379	1.00
63_M	66_R	1.369	1.00
49_L	113_V	1.366	1.00
42_M	68_L	1.365	1.00
77_I	116_L	1.359	1.00
50_I	74_V	1.354	1.00
148_T	155_P	1.346	1.00
177_L	185_M	1.340	1.00
9_E	15_Q	1.340	1.00
36_A	59_E	1.309	1.00
97_D	119_R	1.293	1.00
10_D	53_D	1.285	1.00
8_V	56_L	1.264	1.00
178_S	181_R	1.261	1.00
54_I	62_L	1.254	1.00
93_E	114_K	1.253	1.00
168_A	172_N	1.238	1.00
41_I	47_V	1.233	1.00
12_P	33_A	1.226	1.00
39_R	59_E	1.222	1.00
40_E	44_N	1.221	1.00
66_R	94_M	1.211	1.00
32_T	38_L	1.206	1.00
37_G	40_E	1.189	1.00
6_V	38_L	1.172	1.00
84_D	87_D	1.163	1.00
27_Y	114_K	1.157	1.00
36_A	40_E	1.154	1.00
141_C	150_E	1.142	1.00
4_H	45_Q	1.138	1.00
143_N	146_R	1.126	1.00
37_G	41_I	1.122	1.00
66_R	90_V	1.115	1.00
6_V	47_V	1.111	1.00
97_D	116_L	1.109	1.00
142_L	170_V	1.107	1.00
168_A	177_L	1.102	1.00
62_L	90_V	1.093	1.00
201_V	204_R	1.090	1.00
26_G	114_K	1.078	1.00
25_E	114_K	1.076	1.00
85_R	89_I	1.075	1.00
161_A	187_S	1.046	1.00
49_L	117_L	1.032	1.00
5_I	27_Y	1.031	1.00
181_R	185_M	1.030	1.00
198_T	202_L	1.025	1.00
3_H	27_Y	1.022	1.00
110_V	114_K	1.021	1.00
62_L	91_G	1.021	1.00
38_L	42_M	1.018	1.00
62_L	94_M	1.006	1.00
38_L	64_L	1.001	1.00
8_V	50_I	0.996	1.00
197_R	201_V	0.993	1.00
108_E	111_V	0.992	1.00
52_L	76_I	0.990	1.00
6_V	41_I	0.986	1.00
144_V	167_V	0.980	1.00
164_E	167_V	0.979	1.00
86_I	90_V	0.978	1.00
163_Y	167_V	0.974	1.00
90_V	94_M	0.973	1.00
180_E	196_L	0.968	1.00
18_L	79_V	0.964	1.00
6_V	42_M	0.963	1.00
111_V	115_N	0.942	1.00
50_I	68_L	0.941	1.00
147_H	164_E	0.937	1.00
168_A	182_L	0.934	1.00
13_V	17_R	0.927	1.00
203_I	207_R	0.925	1.00
7_I	29_V	0.924	1.00
54_I	60_N	0.924	1.00
39_R	43_Q	0.921	1.00
7_I	18_L	0.921	1.00
56_L	64_L	0.918	1.00
116_L	119_R	0.909	1.00
16_A	31_V	0.905	1.00
89_I	93_E	0.903	1.00
63_M	67_A	0.901	1.00
8_V	32_T	0.899	1.00
19_Q	29_V	0.899	1.00
52_L	78_L	0.892	1.00
12_P	15_Q	0.891	1.00
12_P	16_A	0.891	1.00
32_T	37_G	0.884	1.00
88_R	101_T	0.883	1.00
142_L	163_Y	0.883	1.00
150_E	155_P	0.879	1.00
85_R	88_R	0.876	1.00
27_Y	110_V	0.875	1.00
40_E	43_Q	0.875	1.00
65_T	94_M	0.871	1.00
51_L	109_L	0.869	1.00
65_T	96_A	0.865	1.00
205_R	208_H	0.864	1.00
196_L	200_D	0.861	1.00
18_L	109_L	0.859	1.00
90_V	93_E	0.850	1.00
197_R	204_R	0.850	1.00
92_L	112_R	0.849	1.00
77_I	112_R	0.842	1.00
177_L	181_R	0.836	1.00
50_I	76_I	0.836	1.00
4_H	47_V	0.833	1.00
20_S	24_Q	0.832	1.00
83_S	101_T	0.831	1.00
51_L	79_V	0.829	1.00
89_I	107_R	0.823	1.00
204_R	208_H	0.820	1.00
159_T	209_K	0.812	1.00
68_L	72_S	0.806	1.00
160_R	164_E	0.801	1.00
54_I	87_D	0.795	1.00
64_L	68_L	0.794	1.00
55_N	81_G	0.792	1.00
180_E	184_R	0.784	1.00
108_E	112_R	0.783	1.00
3_H	121_D	0.779	1.00
59_E	64_L	0.778	1.00
54_I	82_R	0.776	1.00
42_M	74_V	0.776	1.00
214_L	217_T	0.775	1.00
16_A	19_Q	0.775	1.00
66_R	70_E	0.773	1.00
86_I	107_R	0.770	1.00
106_L	110_V	0.763	1.00
75_G	97_D	0.755	1.00
115_N	118_W	0.752	1.00
77_I	98_D	0.748	1.00
207_R	212_A	0.747	1.00
42_M	47_V	0.738	1.00
171_T	185_M	0.737	1.00
39_R	42_M	0.735	1.00
35_G	58_D	0.734	1.00
35_G	39_R	0.732	1.00
7_I	19_Q	0.729	1.00
200_D	203_I	0.723	1.00
136_R	139_G	0.718	1.00
142_L	149_L	0.715	1.00
9_E	56_L	0.714	1.00
85_R	107_R	0.710	1.00
150_E	153_G	0.706	1.00
104_L	109_L	0.705	1.00
87_D	90_V	0.704	1.00
179_R	196_L	0.703	1.00
7_I	31_V	0.699	1.00
16_A	20_S	0.697	1.00
115_N	120_I	0.694	1.00
136_R	140_Y	0.691	1.00
147_H	163_Y	0.688	1.00
8_V	64_L	0.688	1.00
91_G	96_A	0.685	1.00
151_R	213_D	0.684	1.00
4_H	48_D	0.680	1.00
14_T	104_L	0.678	1.00
43_Q	67_A	0.678	1.00
93_E	111_V	0.677	1.00
168_A	171_T	0.677	1.00
79_V	104_L	0.675	1.00
139_G	151_R	0.675	1.00
17_R	21_Y	0.674	1.00
181_R	184_R	0.674	1.00
144_V	171_T	0.672	1.00
42_M	50_I	0.670	1.00
11_E	14_T	0.668	1.00
105_E	108_E	0.666	1.00
137_F	140_Y	0.664	1.00
194_P	199_V	0.662	1.00
169_F	203_I	0.661	1.00
151_R	211_S	0.659	1.00
201_V	205_R	0.642	1.00
80_T	88_R	0.642	1.00
120_I	124_R	0.635	1.00
22_F	27_Y	0.632	1.00
88_R	105_E	0.627	1.00
142_L	167_V	0.626	1.00
107_R	111_V	0.622	1.00
117_L	120_I	0.619	1.00
69_R	74_V	0.618	1.00
73_T	122_L	0.617	1.00
183_L	187_S	0.616	1.00
11_E	81_G	0.614	1.00
75_G	117_L	0.613	1.00
140_Y	151_R	0.612	1.00
21_Y	110_V	0.610	1.00
73_T	123_A	0.608	1.00
3_H	48_D	0.606	1.00
68_L	76_I	0.603	1.00
211_S	214_L	0.599	1.00
15_Q	19_Q	0.599	1.00
51_L	77_I	0.597	1.00
62_L	87_D	0.596	1.00
5_I	22_F	0.595	1.00
51_L	113_V	0.595	1.00
135_Y	144_V	0.594	1.00
143_N	148_T	0.589	1.00
54_I	91_G	0.589	1.00
23_T	28_T	0.585	1.00
5_I	49_L	0.584	1.00
23_T	29_V	0.578	1.00
171_T	177_L	0.573	1.00
39_R	71_R	0.571	1.00
112_R	116_L	0.569	1.00
42_M	64_L	0.568	1.00
52_L	56_L	0.568	1.00
65_T	69_R	0.566	1.00
69_R	75_G	0.564	1.00
165_M	169_F	0.564	1.00
135_Y	170_V	0.555	1.00
10_D	80_T	0.555	1.00
81_G	103_P	0.555	1.00
184_R	187_S	0.555	1.00
5_I	113_V	0.555	1.00
98_D	115_N	0.553	1.00
162_E	205_R	0.550	1.00
104_L	108_E	0.550	1.00
149_L	156_I	0.548	1.00
151_R	154_E	0.542	1.00
91_G	99_Y	0.541	1.00
89_I	92_L	0.541	1.00
42_M	72_S	0.540	1.00
7_I	15_Q	0.535	1.00
179_R	183_L	0.535	1.00
46_S	72_S	0.534	1.00
141_C	153_G	0.533	1.00
8_V	35_G	0.531	1.00
151_R	212_A	0.530	1.00
86_I	89_I	0.523	1.00
161_A	202_L	0.521	1.00
195_D	198_T	0.520	1.00
53_D	102_K	0.517	1.00
42_M	71_R	0.517	1.00
35_G	56_L	0.513	1.00
11_E	103_P	0.513	1.00
83_S	103_P	0.511	1.00
14_T	17_R	0.510	1.00
17_R	20_S	0.509	1.00
34_S	56_L	0.509	1.00
27_Y	117_L	0.506	1.00
8_V	52_L	0.504	1.00
111_V	114_K	0.504	1.00
113_V	117_L	0.501	1.00
75_G	120_I	0.501	1.00
172_N	185_M	0.501	1.00
135_Y	138_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
2gwrA	1	0.9478	100	0.203	Contact Map
4b09A	2	0.9043	100	0.218	Contact Map
2oqrA	2	0.9609	100	0.219	Contact Map
3r0jA	2	0.9435	100	0.226	Contact Map
1ys7A	2	0.9652	100	0.228	Contact Map
4kfcA	2	0.9522	100	0.228	Contact Map
1kgsA	1	0.9304	100	0.229	Contact Map
1p2fA	1	0.9174	100	0.267	Contact Map
3q9sA	1	0.8913	100	0.277	Contact Map
2hqrA	2	0.9261	100	0.279	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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