DCUR - ECOLI - GREMLIN Contacts

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DCUR - Transcriptional regulatory protein DcuR

UniProt:	P0AD01	Sequences: MINVLIIDDDAMVAELNRRYVAQIPGFQCCGTASTLEKAKEIIFNSDTPIDLILLDIYMQKENGLDLLPVLHNARCKSDVIVISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGWRQKKMALEKHQYYDQAELDQLIHGSSSNEQDPRRLPKGLTPQTLRTLCQWIDAHQDYEFSTDELANEVNISRVSCRKYLIWLVNCHILFTSIHYGVTGRPVYRYRIQAEHYSLLKQYCQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12464
Length:	239 (198)
Sequences:	78322 (55995)
Seq/√Len:	3979.4

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_A	32_T	3.720	1.00
14_A	34_S	3.291	1.00
18_R	32_T	3.202	1.00
7_I	39_A	2.741	1.00
40_K	70_V	2.655	1.00
37_E	61_K	2.581	1.00
36_L	62_E	2.459	1.00
44_F	74_A	2.412	1.00
35_T	61_K	2.324	1.00
62_E	70_V	2.320	1.00
3_N	28_Q	2.095	1.00
20_Y	110_A	2.039	1.00
33_A	42_I	2.001	1.00
24_I	114_E	1.956	1.00
18_R	22_A	1.945	1.00
92_I	112_R	1.921	1.00
34_S	38_K	1.873	1.00
193_V	196_R	1.863	1.00
58_Y	86_A	1.828	1.00
68_L	80_V	1.811	1.00
55_L	67_L	1.802	1.00
31_G	42_I	1.796	1.00
181_T	196_R	1.755	1.00
89_A	109_Q	1.731	1.00
35_T	38_K	1.725	1.00
82_V	95_S	1.707	1.00
70_V	74_A	1.700	1.00
5_L	33_A	1.663	1.00
169_Q	173_A	1.659	1.00
31_G	50_I	1.638	1.00
82_V	100_V	1.638	1.00
72_H	101_V	1.608	1.00
42_I	48_T	1.597	1.00
31_G	48_T	1.584	1.00
63_N	66_D	1.580	1.00
62_E	66_D	1.579	1.00
36_L	67_L	1.569	1.00
198_Y	201_W	1.526	1.00
69_P	98_Y	1.521	1.00
102_D	116_A	1.484	1.00
42_I	45_N	1.482	1.00
43_I	71_L	1.481	1.00
180_S	183_E	1.474	1.00
21_V	117_L	1.469	1.00
140_Q	153_R	1.459	1.00
70_V	73_N	1.453	1.00
170_W	187_E	1.438	1.00
137_E	142_I	1.411	1.00
68_L	82_V	1.411	1.00
179_F	187_E	1.390	1.00
86_A	91_T	1.388	1.00
3_N	31_G	1.386	1.00
101_V	123_K	1.378	1.00
53_I	78_S	1.375	1.00
66_D	69_P	1.356	1.00
40_K	67_L	1.353	1.00
37_E	62_E	1.344	1.00
81_I	120_W	1.331	1.00
52_L	117_L	1.312	1.00
75_R	78_S	1.281	1.00
8_D	14_A	1.275	1.00
11_A	34_S	1.273	1.00
42_I	50_I	1.269	1.00
149_E	156_P	1.253	1.00
55_L	68_L	1.250	1.00
7_I	59_M	1.244	1.00
27_F	118_T	1.243	1.00
57_I	65_L	1.242	1.00
101_V	120_W	1.238	1.00
9_D	56_D	1.230	1.00
41_E	45_N	1.219	1.00
162_Q	165_R	1.215	1.00
40_K	62_E	1.208	1.00
163_T	205_C	1.199	1.00
3_N	48_T	1.199	1.00
45_N	48_T	1.195	1.00
210_T	213_H	1.192	1.00
57_I	82_V	1.187	1.00
142_I	151_D	1.179	1.00
33_A	39_A	1.171	1.00
38_K	41_E	1.162	1.00
24_I	118_T	1.151	1.00
37_E	41_E	1.148	1.00
38_K	42_I	1.147	1.00
5_L	50_I	1.133	1.00
183_E	187_E	1.131	1.00
114_E	118_T	1.126	1.00
88_D	91_T	1.115	1.00
65_L	95_S	1.115	1.00
65_L	94_D	1.107	1.00
5_L	39_A	1.099	1.00
182_D	192_R	1.088	1.00
69_P	94_D	1.077	1.00
4_V	27_F	1.075	1.00
94_D	98_Y	1.075	1.00
52_L	121_R	1.072	1.00
97_H	118_T	1.070	1.00
5_L	42_I	1.050	1.00
209_F	213_H	1.035	1.00
193_V	197_K	1.035	1.00
197_K	200_I	1.031	1.00
115_E	119_G	1.027	1.00
144_G	147_S	1.019	1.00
138_L	141_L	1.019	1.00
112_R	115_E	1.017	1.00
170_W	179_F	1.016	1.00
165_R	169_Q	1.015	1.00
143_H	172_D	1.012	1.00
40_K	44_F	1.002	1.00
194_S	198_Y	1.001	1.00
39_A	67_L	0.985	1.00
39_A	43_I	0.959	1.00
53_I	71_L	0.957	1.00
89_A	93_K	0.956	1.00
15_E	32_T	0.954	1.00
65_L	98_Y	0.952	1.00
11_A	15_E	0.951	1.00
179_F	183_E	0.947	1.00
26_G	118_T	0.946	1.00
7_I	53_I	0.944	1.00
33_A	38_K	0.939	1.00
90_A	94_D	0.938	1.00
6_I	17_N	0.925	1.00
92_I	105_I	0.922	1.00
5_L	31_G	0.919	1.00
57_I	63_N	0.915	1.00
17_N	83_I	0.913	1.00
5_L	43_I	0.900	1.00
93_K	97_H	0.896	1.00
41_E	44_F	0.896	1.00
53_I	80_V	0.895	1.00
3_N	50_I	0.880	1.00
55_L	82_V	0.879	1.00
89_A	92_I	0.873	1.00
94_D	97_H	0.873	1.00
66_D	70_V	0.872	1.00
55_L	80_V	0.872	1.00
54_L	113_F	0.870	1.00
7_I	33_A	0.869	1.00
12_M	16_L	0.869	1.00
68_L	98_Y	0.867	1.00
148_N	165_R	0.863	1.00
151_D	156_P	0.861	1.00
18_R	29_C	0.860	1.00
68_L	100_V	0.855	1.00
182_D	186_N	0.846	1.00
170_W	184_L	0.845	1.00
27_F	114_E	0.844	1.00
183_E	186_N	0.836	1.00
81_I	116_A	0.835	1.00
79_D	101_V	0.830	1.00
15_E	18_R	0.829	1.00
192_R	196_R	0.826	1.00
120_W	123_K	0.825	1.00
11_A	14_A	0.823	1.00
57_I	91_T	0.822	1.00
87_A	105_I	0.821	1.00
69_P	73_N	0.819	1.00
19_R	23_Q	0.819	1.00
197_K	201_W	0.814	1.00
67_L	71_L	0.810	1.00
59_M	67_L	0.807	1.00
110_A	114_E	0.807	1.00
6_I	29_C	0.804	1.00
119_G	122_Q	0.784	1.00
199_L	203_V	0.776	1.00
43_I	75_R	0.775	1.00
93_K	111_S	0.772	1.00
79_D	127_L	0.771	1.00
17_N	113_F	0.770	1.00
209_F	212_I	0.767	1.00
13_V	108_F	0.759	1.00
201_W	204_N	0.759	1.00
137_E	140_Q	0.753	1.00
207_I	213_H	0.750	1.00
54_L	117_L	0.744	1.00
43_I	78_S	0.742	1.00
36_L	40_K	0.740	1.00
112_R	116_A	0.738	1.00
15_E	19_R	0.738	1.00
108_F	113_F	0.737	1.00
205_C	213_H	0.735	1.00
148_N	164_L	0.731	1.00
43_I	50_I	0.731	1.00
54_L	83_I	0.731	1.00
58_Y	85_S	0.731	1.00
3_N	51_D	0.730	1.00
7_I	67_L	0.728	1.00
121_R	124_K	0.727	1.00
207_I	210_T	0.725	1.00
109_Q	112_R	0.724	1.00
91_T	94_D	0.723	1.00
77_K	127_L	0.721	1.00
62_E	67_L	0.720	1.00
6_I	18_R	0.710	1.00
102_D	119_G	0.708	1.00
29_C	32_T	0.706	1.00
124_K	128_E	0.705	1.00
119_G	124_K	0.704	1.00
207_I	211_S	0.703	1.00
169_Q	172_D	0.703	1.00
151_D	154_R	0.703	1.00
57_I	86_A	0.703	1.00
71_L	76_C	0.698	1.00
36_L	61_K	0.697	1.00
90_A	111_S	0.694	1.00
143_H	164_L	0.694	1.00
44_F	70_V	0.694	1.00
81_I	102_D	0.694	1.00
161_P	165_R	0.693	1.00
83_I	108_F	0.692	1.00
177_Y	183_E	0.689	1.00
160_T	163_T	0.683	1.00
200_I	204_N	0.683	1.00
71_L	80_V	0.678	1.00
193_V	200_I	0.676	1.00
72_H	79_D	0.675	1.00
143_H	150_Q	0.672	1.00
181_T	192_R	0.670	1.00
111_S	115_E	0.670	1.00
196_R	199_L	0.668	1.00
96_L	116_A	0.668	1.00
97_H	115_E	0.665	1.00
40_K	43_I	0.665	1.00
177_Y	187_E	0.665	1.00
23_Q	26_G	0.659	1.00
89_A	111_S	0.658	1.00
79_D	123_K	0.658	1.00
14_A	18_R	0.651	1.00
199_L	211_S	0.650	1.00
8_D	59_M	0.648	1.00
168_C	172_D	0.647	1.00
6_I	32_T	0.644	1.00
84_S	92_I	0.639	1.00
54_L	81_I	0.637	1.00
160_T	205_C	0.636	1.00
140_Q	152_P	0.635	1.00
20_Y	114_E	0.633	1.00
49_P	75_R	0.631	1.00
139_D	143_H	0.627	1.00
43_I	53_I	0.621	1.00
116_A	120_W	0.620	1.00
203_V	208_L	0.618	1.00
44_F	75_R	0.612	1.00
90_A	93_K	0.609	1.00
92_I	109_Q	0.609	1.00
140_Q	143_H	0.606	1.00
24_I	27_F	0.604	1.00
28_Q	31_G	0.604	1.00
21_V	27_F	0.603	1.00
55_L	59_M	0.601	1.00
173_A	187_E	0.601	1.00
118_T	122_Q	0.600	1.00
79_D	121_R	0.599	1.00
36_L	59_M	0.598	1.00
190_I	195_C	0.592	1.00
16_L	20_Y	0.592	1.00
22_A	29_C	0.586	1.00
40_K	74_A	0.586	1.00
10_D	85_S	0.583	1.00
95_S	100_V	0.577	1.00
167_L	170_W	0.574	1.00
152_P	155_L	0.564	1.00
171_I	199_L	0.563	1.00
181_T	185_A	0.560	1.00
208_L	213_H	0.558	1.00
136_A	139_D	0.557	1.00
68_L	72_H	0.554	1.00
85_S	107_P	0.552	1.00
162_Q	198_Y	0.552	1.00
194_S	197_K	0.551	1.00
77_K	126_A	0.550	1.00
143_H	169_Q	0.550	1.00
108_F	112_R	0.549	1.00
72_H	78_S	0.546	1.00
27_F	121_R	0.533	1.00
65_L	91_T	0.533	1.00
71_L	78_S	0.531	1.00
43_I	67_L	0.528	1.00
10_D	13_V	0.522	1.00
167_L	171_I	0.522	1.00
115_E	118_T	0.522	1.00
136_A	143_H	0.521	1.00
152_P	207_I	0.521	1.00
22_A	28_Q	0.520	1.00
79_D	124_K	0.515	1.00
93_K	96_L	0.511	1.00
164_L	169_Q	0.511	1.00
9_D	84_S	0.508	1.00
13_V	16_L	0.508	1.00
159_L	163_T	0.507	1.00
150_Q	157_K	0.507	1.00
119_G	123_K	0.507	1.00
184_L	187_E	0.505	1.00
4_V	52_L	0.505	1.00
49_P	76_C	0.503	1.00
144_G	149_E	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
4gvpA	1	0.8703	100	0.279	Contact Map
3c3wA	2	0.8828	100	0.286	Contact Map
4b09A	2	0.8787	100	0.299	Contact Map
1a04A	1	0.8536	100	0.3	Contact Map
4ldzA	2	0.8117	100	0.304	Contact Map
3r0jA	2	0.8954	100	0.306	Contact Map
1yioA	1	0.8243	100	0.31	Contact Map
2oqrA	2	0.9247	100	0.315	Contact Map
1ys7A	2	0.9247	100	0.316	Contact Map
4kfcA	2	0.9163	100	0.318	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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