YEDW - ECOLI - GREMLIN Contacts

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YEDW - Probable transcriptional regulatory protein YedW

UniProt:	P76340	Sequences: MKILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQILQTLRTAKQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQHHALNSTLEISGLRMDSVSHSVSRDNISITLTRKEFQLLWLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVDDPFPEKLIATIRGMGYSFVAVKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14045
Length:	223 (203)
Sequences:	79000 (56428)
Seq/√Len:	3960.5

ECOLI - YEDW PHOP CUSR BASR ARCA CREB KDPE QSEB BAER PHOB OMPR RSTA TORR CPXR UVRY FIMZ EVGA YHJB DPIA NARL YJJQ NARP DCUR RCSB YGEK BGLJ UHPA RCSA CSGD BARA RSSB YEHT TORS RCSC CHEB ARCB YPDB GLRR NTRC ZRAR ATOC EVGS RCSD
BACSU - YVRH YVCP YXDJ BCER PHOP YCBL YCLJ YYCF YKOG RESD YRKP CSSR CITT YFIK CMPA LIAR YXJL DCTR MALR YDFI YBDJ DEGU YHCZ YVFU DESR YESN GLNL LYTT CHEB NATR SP0A CHEV
HALSA - CHEB Q9HR09 Q9HRE5 Q9HNM3 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
13_Q	29_A	3.851	1.00
13_Q	31_S	3.420	1.00
17_T	29_A	3.395	1.00
6_I	36_G	2.875	1.00
37_L	65_T	2.840	1.00
34_R	56_G	2.611	1.00
28_D	45_Y	2.570	1.00
33_G	57_M	2.490	1.00
41_L	69_A	2.431	1.00
57_M	65_T	2.410	1.00
32_D	56_G	2.341	1.00
28_D	39_L	2.131	1.00
19_G	104_F	2.120	1.00
30_V	39_L	2.101	1.00
17_T	21_S	2.047	1.00
28_D	43_D	2.034	1.00
53_M	80_R	2.001	1.00
2_K	26_V	1.996	1.00
23_A	108_L	1.968	1.00
50_L	62_I	1.951	1.00
63_L	74_V	1.909	1.00
31_S	35_D	1.904	1.00
86_R	106_E	1.878	1.00
186_N	189_D	1.849	1.00
65_T	69_A	1.793	1.00
76_C	89_G	1.793	1.00
32_D	35_D	1.785	1.00
67_R	95_N	1.728	1.00
76_C	94_A	1.713	1.00
4_L	30_V	1.707	1.00
39_L	43_D	1.684	1.00
151_K	154_Q	1.669	1.00
64_Q	92_S	1.663	1.00
2_K	28_D	1.640	1.00
57_M	61_Q	1.637	1.00
83_V	103_S	1.620	1.00
58_D	61_Q	1.612	1.00
33_G	62_I	1.607	1.00
96_D	110_R	1.603	1.00
169_R	189_D	1.574	1.00
158_L	175_E	1.568	1.00
157_W	161_S	1.561	1.00
40_A	66_L	1.539	1.00
39_L	42_K	1.521	1.00
65_T	68_T	1.515	1.00
80_R	85_D	1.476	1.00
129_G	142_D	1.475	1.00
34_R	57_M	1.455	1.00
48_I	72_T	1.446	1.00
20_L	111_V	1.442	1.00
167_I	175_E	1.431	1.00
63_L	76_C	1.429	1.00
191_A	194_R	1.400	1.00
47_L	111_V	1.382	1.00
168_P	171_V	1.374	1.00
95_N	117_Q	1.370	1.00
37_L	62_I	1.361	1.00
61_Q	64_Q	1.335	1.00
52_I	60_W	1.324	1.00
10_Q	31_S	1.318	1.00
39_L	45_Y	1.303	1.00
75_I	114_Q	1.300	1.00
37_L	57_M	1.281	1.00
95_N	114_Q	1.278	1.00
7_E	13_Q	1.259	1.00
6_I	54_L	1.253	1.00
60_W	89_G	1.239	1.00
108_L	112_R	1.226	1.00
38_Y	42_K	1.223	1.00
52_I	76_C	1.203	1.00
50_L	63_L	1.199	1.00
192_I	196_R	1.198	1.00
8_D	51_D	1.195	1.00
25_Y	112_R	1.190	1.00
35_D	39_L	1.189	1.00
30_V	36_G	1.185	1.00
60_W	88_R	1.171	1.00
88_R	92_S	1.164	1.00
35_D	38_Y	1.157	1.00
4_L	45_Y	1.155	1.00
82_S	85_D	1.147	1.00
171_V	175_E	1.144	1.00
34_R	38_Y	1.138	1.00
152_E	198_K	1.130	1.00
4_L	36_G	1.094	1.00
4_L	39_L	1.091	1.00
83_V	87_V	1.083	1.00
24_G	112_R	1.077	1.00
133_D	136_S	1.074	1.00
37_L	41_L	1.073	1.00
109_A	113_A	1.073	1.00
36_G	62_I	1.067	1.00
87_V	91_D	1.061	1.00
153_F	157_W	1.051	1.00
47_L	115_L	1.050	1.00
154_Q	157_W	1.048	1.00
64_Q	88_R	1.047	1.00
2_K	43_D	1.044	1.00
14_E	29_A	1.041	1.00
158_L	167_I	1.040	1.00
190_V	193_R	1.031	1.00
187_T	191_A	1.031	1.00
5_L	16_V	1.029	1.00
91_D	112_R	1.027	1.00
106_E	109_A	1.025	1.00
3_I	25_Y	1.019	1.00
201_D	210_T	1.017	1.00
30_V	35_D	1.013	1.00
170_T	185_T	1.008	1.00
84_D	88_R	1.007	1.00
23_A	112_R	0.985	1.00
167_I	171_V	0.983	1.00
131_R	140_S	0.981	1.00
86_R	99_V	0.973	1.00
138_S	145_S	0.972	1.00
36_G	40_A	0.971	1.00
10_Q	14_E	0.960	1.00
48_I	66_L	0.954	1.00
186_N	190_V	0.949	1.00
4_L	28_D	0.944	1.00
48_I	74_V	0.940	1.00
52_I	58_D	0.940	1.00
11_R	15_W	0.939	1.00
83_V	86_R	0.935	1.00
73_P	95_N	0.931	1.00
150_R	154_Q	0.931	1.00
38_Y	41_L	0.918	1.00
63_L	92_S	0.917	1.00
132_M	160_A	0.914	1.00
60_W	92_S	0.913	1.00
134_S	157_W	0.910	1.00
63_L	94_A	0.910	1.00
6_I	30_V	0.909	1.00
50_L	74_V	0.906	1.00
14_E	17_T	0.895	1.00
16_V	77_L	0.885	1.00
4_L	40_A	0.879	1.00
50_L	76_C	0.874	1.00
88_R	91_D	0.870	1.00
61_Q	65_T	0.869	1.00
49_I	107_L	0.867	1.00
75_I	110_R	0.866	1.00
6_I	48_I	0.864	1.00
132_M	153_F	0.857	1.00
18_Q	22_E	0.854	1.00
81_D	99_V	0.853	1.00
106_E	110_R	0.846	1.00
185_T	189_D	0.841	1.00
104_F	108_L	0.841	1.00
73_P	121_L	0.840	1.00
52_I	85_D	0.831	1.00
62_I	66_L	0.827	1.00
140_S	145_S	0.826	1.00
155_L	159_L	0.826	1.00
25_Y	108_L	0.822	1.00
114_Q	117_Q	0.821	1.00
10_Q	13_Q	0.816	1.00
40_A	72_T	0.795	1.00
85_D	88_R	0.789	1.00
52_I	80_R	0.788	1.00
54_L	62_I	0.786	1.00
186_N	193_R	0.780	1.00
126_E	131_R	0.778	1.00
96_D	113_A	0.777	1.00
40_A	45_Y	0.774	1.00
64_Q	68_T	0.768	1.00
57_M	62_I	0.763	1.00
87_V	105_S	0.762	1.00
103_S	106_E	0.762	1.00
73_P	117_Q	0.760	1.00
66_L	74_V	0.758	1.00
113_A	116_R	0.751	1.00
158_L	172_I	0.749	1.00
171_V	174_S	0.747	1.00
17_T	27_I	0.746	1.00
33_G	37_L	0.746	1.00
149_T	152_E	0.744	1.00
194_R	197_A	0.741	1.00
102_F	107_L	0.739	1.00
77_L	102_F	0.737	1.00
14_E	18_Q	0.736	1.00
201_D	204_P	0.735	1.00
170_T	174_S	0.734	1.00
12_T	102_F	0.732	1.00
6_I	62_I	0.731	1.00
49_I	77_L	0.725	1.00
115_L	118_H	0.725	1.00
16_V	107_L	0.722	1.00
84_D	105_S	0.719	1.00
53_M	79_A	0.716	1.00
193_R	197_A	0.707	1.00
33_G	56_G	0.703	1.00
37_L	40_A	0.701	1.00
66_L	70_K	0.698	1.00
149_T	198_K	0.693	1.00
200_D	206_K	0.692	1.00
15_W	19_G	0.688	1.00
140_S	143_N	0.687	1.00
49_I	111_V	0.684	1.00
40_A	48_I	0.683	1.00
158_L	161_S	0.680	1.00
33_G	54_L	0.679	1.00
113_A	118_H	0.679	1.00
90_L	110_R	0.679	1.00
205_E	208_I	0.675	1.00
71_Q	121_L	0.674	1.00
67_R	73_P	0.673	1.00
129_G	141_R	0.671	1.00
148_L	152_E	0.669	1.00
7_E	54_L	0.667	1.00
190_V	194_R	0.663	1.00
37_L	69_A	0.659	1.00
203_F	206_K	0.657	1.00
124_T	131_R	0.657	1.00
105_S	109_A	0.657	1.00
5_L	29_A	0.654	1.00
19_G	108_L	0.654	1.00
41_L	65_T	0.651	1.00
2_K	46_A	0.649	1.00
9_N	12_T	0.646	1.00
89_G	94_A	0.645	1.00
110_R	114_Q	0.644	1.00
206_K	209_A	0.640	1.00
5_L	17_T	0.636	1.00
187_T	192_I	0.635	1.00
204_P	207_L	0.635	1.00
49_I	75_I	0.633	1.00
13_Q	17_T	0.633	1.00
184_D	187_T	0.630	1.00
137_H	154_Q	0.628	1.00
75_I	96_D	0.628	1.00
102_F	106_E	0.627	1.00
63_L	67_R	0.625	1.00
129_G	133_D	0.621	1.00
91_D	109_A	0.618	1.00
73_P	115_L	0.618	1.00
109_A	112_R	0.618	1.00
112_R	116_R	0.617	1.00
154_Q	158_L	0.616	1.00
84_D	87_V	0.615	1.00
86_R	103_S	0.614	1.00
132_M	139_V	0.613	1.00
169_R	185_T	0.608	1.00
52_I	89_G	0.607	1.00
152_E	155_L	0.604	1.00
127_I	130_L	0.602	1.00
12_T	15_W	0.602	1.00
188_V	192_I	0.600	1.00
9_N	79_A	0.600	1.00
60_W	85_D	0.596	1.00
132_M	157_W	0.595	1.00
118_H	122_N	0.594	1.00
73_P	118_H	0.592	1.00
141_R	144_I	0.591	1.00
67_R	72_T	0.589	1.00
50_L	54_L	0.588	1.00
117_Q	121_L	0.587	1.00
83_V	105_S	0.587	1.00
161_S	175_E	0.586	1.00
161_S	167_I	0.578	1.00
152_E	159_L	0.575	1.00
183_S	188_V	0.575	1.00
51_D	100_K	0.574	1.00
201_D	206_K	0.574	1.00
137_H	153_F	0.571	1.00
156_L	159_L	0.569	1.00
189_D	192_I	0.562	1.00
202_P	205_E	0.557	1.00
19_G	23_A	0.555	1.00
5_L	27_I	0.553	1.00
201_D	205_E	0.553	1.00
66_L	72_T	0.547	1.00
8_D	78_T	0.547	1.00
40_A	69_A	0.545	1.00
5_L	13_Q	0.544	1.00
20_L	25_Y	0.544	1.00
183_S	187_T	0.543	1.00
3_I	47_L	0.542	1.00
130_L	141_R	0.540	1.00
196_R	201_D	0.540	1.00
159_L	192_I	0.539	1.00
110_R	113_A	0.537	1.00
78_T	86_R	0.536	1.00
25_Y	115_L	0.535	1.00
40_A	62_I	0.534	1.00
71_Q	120_A	0.531	1.00
78_T	100_K	0.530	1.00
202_P	206_K	0.527	1.00
35_D	56_G	0.524	1.00
50_L	66_L	0.516	1.00
192_I	204_P	0.511	1.00
21_S	26_V	0.511	1.00
197_A	200_D	0.510	1.00
79_A	101_P	0.510	1.00
40_A	70_K	0.508	1.00
134_S	137_H	0.506	1.00
116_R	120_A	0.503	1.00
133_D	138_S	0.503	1.00
127_I	131_R	0.502	1.00
188_V	191_A	0.502	1.00
151_K	191_A	0.501	1.00
32_D	54_L	0.501	1.00
209_A	212_R	0.501	1.00
44_D	70_K	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
1ys7A	2	0.9865	100	0.203	Contact Map
3r0jA	2	0.9641	100	0.205	Contact Map
2gwrA	1	0.9821	100	0.209	Contact Map
1kgsA	1	0.9686	100	0.217	Contact Map
4b09A	2	0.9417	100	0.218	Contact Map
2oqrA	2	0.9821	100	0.221	Contact Map
4kfcA	2	0.9821	100	0.224	Contact Map
2hqrA	2	0.9731	100	0.235	Contact Map
3q9sA	1	0.9372	100	0.245	Contact Map
1p2fA	1	0.9552	100	0.253	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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