YEEZ - ECOLI - GREMLIN Contacts

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YEEZ - Protein YeeZ

UniProt:	P0AD12	Sequences: MKKVAIVGLGWLGMPLAMSLSARGWQVTGSKTTQDGVEAARMSGIDSYLLRMEPELVCDSDDLDALMDADALVITLPARRSGPGDEFYLQAVQELVDSALAHRIPRIIFTSSTSVYGDAQGTVKETTPRNPVTNSGRVLEELEDWLHNLPGTSVDILRLAGLVGPGRHPGRFFAGKTAPDGEHGVNLVHLEDVIGAITLLLQAPKGGHIYNICAPAHPARNVFYPQMARLLGLEPPQFRNSLDSGKGKIIDGSRICNELGFEYQYPDPLVMPLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13393
Length:	274 (253)
Sequences:	63057 (44287)
Seq/√Len:	2784.3

ECOLI - YEEZ RMLB2 GM4D RMLB1 GALE YBJS HLDD YFCH FCL RMLD QOR2 YRAR YBJT ARNA
BACSU - RMLB YFNG GALE YTCB YFHF SPSK YTBQ YWNB YHFK YHEG YESF
HALSA - Q9HSU9 Q9HSE7 Q9HSV1 Q9HRD1 Q9HS50 Q9HPF1 Q9HML4 Q9HSQ3 Q9HNV3 Q9HR86
SULSO - Q97VN5 Q7LXG5 Q980W1 Q97UM3 Q7LX44 Q7LXE8 Q97XJ9 Q97XG1 Q7LXE6 Q97XF9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_L	29_G	3.088	1.00
19_S	195_G	2.634	1.00
3_K	26_Q	2.599	1.00
196_A	212_I	2.595	1.00
86_E	90_Q	2.528	1.00
110_T	197_I	2.458	1.00
71_A	201_L	2.424	1.00
208_H	254_R	2.413	1.00
19_S	198_T	2.352	1.00
210_Y	258_E	2.250	1.00
30_S	50_L	2.182	1.00
19_S	23_R	2.092	1.00
106_R	153_S	2.090	1.00
74_I	109_F	2.079	1.00
3_K	28_T	2.046	1.00
124_K	127_T	1.981	1.00
221_N	225_P	1.981	1.00
73_V	201_L	1.980	1.00
159_L	197_I	1.965	1.00
28_T	69_A	1.901	1.00
28_T	46_D	1.892	1.00
23_R	198_T	1.883	1.00
50_L	57_V	1.855	1.00
219_A	222_V	1.844	1.00
5_A	69_A	1.843	1.00
157_L	200_L	1.842	1.00
93_Q	145_W	1.840	1.00
7_V	74_I	1.837	1.00
146_L	154_V	1.804	1.00
28_T	48_Y	1.799	1.00
253_S	257_N	1.778	1.00
140_E	144_D	1.723	1.00
23_R	202_Q	1.716	1.00
6_I	17_A	1.715	1.00
195_G	199_L	1.713	1.00
16_L	194_I	1.711	1.00
26_Q	46_D	1.692	1.00
198_T	202_Q	1.676	1.00
85_D	141_E	1.637	1.00
93_Q	97_D	1.637	1.00
226_Q	229_R	1.633	1.00
54_P	57_V	1.616	1.00
4_V	25_W	1.596	1.00
226_Q	230_L	1.561	1.00
199_L	203_A	1.559	1.00
90_Q	93_Q	1.548	1.00
92_V	142_L	1.540	1.00
16_L	73_V	1.532	1.00
55_E	97_D	1.494	1.00
170_G	173_F	1.493	1.00
106_R	155_D	1.492	1.00
255_I	259_L	1.490	1.00
16_L	75_T	1.487	1.00
61_D	65_A	1.473	1.00
53_E	86_E	1.471	1.00
19_S	194_I	1.462	1.00
19_S	22_A	1.456	1.00
63_L	101_A	1.456	1.00
159_L	193_V	1.451	1.00
111_S	115_V	1.450	1.00
75_T	110_T	1.435	1.00
70_D	105_P	1.430	1.00
55_E	94_E	1.405	1.00
184_G	217_H	1.398	1.00
160_A	250_I	1.383	1.00
125_E	254_R	1.378	1.00
135_S	139_L	1.377	1.00
12_L	162_L	1.375	1.00
33_T	36_G	1.373	1.00
96_V	149_L	1.359	1.00
72_L	99_A	1.358	1.00
110_T	159_L	1.354	1.00
157_L	197_I	1.352	1.00
33_T	47_S	1.324	1.00
150_P	154_V	1.323	1.00
25_W	202_Q	1.321	1.00
188_V	193_V	1.315	1.00
144_D	147_H	1.311	1.00
73_V	197_I	1.305	1.00
18_M	166_G	1.302	1.00
17_A	29_G	1.299	1.00
137_R	141_E	1.289	1.00
147_H	156_I	1.282	1.00
129_R	140_E	1.271	1.00
222_V	225_P	1.267	1.00
9_L	17_A	1.255	1.00
190_L	194_I	1.233	1.00
208_H	258_E	1.218	1.00
20_L	198_T	1.213	1.00
116_Y	211_N	1.213	1.00
15_P	191_E	1.201	1.00
123_V	127_T	1.199	1.00
109_F	142_L	1.194	1.00
254_R	258_E	1.193	1.00
15_P	190_L	1.181	1.00
252_G	263_Y	1.172	1.00
52_M	91_A	1.169	1.00
106_R	204_P	1.166	1.00
97_D	100_L	1.161	1.00
158_R	209_I	1.153	1.00
5_A	30_S	1.153	1.00
4_V	20_L	1.146	1.00
145_W	148_N	1.145	1.00
19_S	191_E	1.142	1.00
163_V	189_H	1.131	1.00
79_R	82_G	1.129	1.00
74_I	92_V	1.128	1.00
186_N	215_P	1.126	1.00
147_H	154_V	1.124	1.00
109_F	156_I	1.124	1.00
29_G	45_I	1.111	1.00
143_E	158_R	1.110	1.00
182_E	219_A	1.108	1.00
124_K	251_D	1.104	1.00
182_E	221_N	1.103	1.00
147_H	209_I	1.100	1.00
108_I	157_L	1.100	1.00
195_G	261_F	1.093	1.00
21_S	45_I	1.092	1.00
21_S	44_G	1.083	1.00
57_V	61_D	1.083	1.00
88_Y	138_V	1.080	1.00
126_T	254_R	1.071	1.00
192_D	214_A	1.070	1.00
52_M	76_L	1.067	1.00
99_A	107_I	1.062	1.00
78_A	87_F	1.062	1.00
199_L	259_L	1.055	1.00
85_D	89_L	1.055	1.00
98_S	102_H	1.054	1.00
196_A	255_I	1.051	1.00
11_W	164_G	1.047	1.00
97_D	101_A	1.043	1.00
225_P	228_A	1.042	1.00
218_P	222_V	1.040	1.00
153_S	206_G	1.039	1.00
228_A	235_P	1.039	1.00
96_V	107_I	1.038	1.00
61_D	64_D	1.036	1.00
217_H	247_G	1.036	1.00
109_F	146_L	1.034	1.00
95_L	107_I	1.031	1.00
94_E	97_D	1.028	1.00
90_Q	94_E	1.026	1.00
4_V	71_A	1.023	1.00
228_A	234_E	1.022	1.00
97_D	149_L	1.022	1.00
11_W	190_L	1.022	1.00
213_C	250_I	1.022	1.00
18_M	22_A	1.022	1.00
158_R	211_N	1.014	1.00
217_H	249_I	1.013	1.00
221_N	239_R	1.009	1.00
7_V	95_L	1.005	1.00
189_H	192_D	0.999	1.00
87_F	91_A	0.991	1.00
155_D	200_L	0.986	1.00
184_G	219_A	0.978	1.00
3_K	69_A	0.978	1.00
63_L	69_A	0.977	1.00
162_L	193_V	0.970	1.00
199_L	202_Q	0.967	1.00
63_L	102_H	0.963	1.00
241_S	244_S	0.962	1.00
75_T	197_I	0.959	1.00
14_M	166_G	0.959	1.00
89_L	141_E	0.954	1.00
34_Q	49_L	0.941	1.00
84_G	138_V	0.937	1.00
107_I	146_L	0.931	1.00
215_P	252_G	0.927	1.00
78_A	83_P	0.926	1.00
85_D	90_Q	0.925	1.00
99_A	104_I	0.923	1.00
71_A	106_R	0.918	1.00
195_G	198_T	0.918	1.00
15_P	18_M	0.916	1.00
100_L	149_L	0.909	1.00
96_V	146_L	0.906	1.00
210_Y	254_R	0.906	1.00
7_V	76_L	0.900	1.00
46_D	67_M	0.897	1.00
48_Y	65_A	0.895	1.00
3_K	70_D	0.892	1.00
31_K	47_S	0.891	1.00
98_S	101_A	0.891	1.00
141_E	144_D	0.890	1.00
121_G	127_T	0.889	1.00
240_N	243_D	0.879	1.00
121_G	124_K	0.878	1.00
113_T	160_A	0.877	1.00
63_L	98_S	0.877	1.00
100_L	152_T	0.874	1.00
94_E	98_S	0.873	1.00
157_L	212_I	0.871	1.00
213_C	252_G	0.868	1.00
16_L	20_L	0.861	1.00
80_R	83_P	0.858	1.00
72_L	95_L	0.852	1.00
4_V	73_V	0.851	1.00
156_I	209_I	0.846	1.00
3_K	25_W	0.842	1.00
21_S	27_V	0.840	1.00
160_A	213_C	0.835	1.00
78_A	84_G	0.833	1.00
15_P	19_S	0.827	1.00
155_D	204_P	0.826	1.00
222_V	226_Q	0.825	1.00
184_G	247_G	0.820	1.00
30_S	57_V	0.820	1.00
228_A	233_L	0.817	1.00
133_T	136_G	0.814	1.00
113_T	250_I	0.810	1.00
149_L	152_T	0.809	1.00
17_A	27_V	0.807	1.00
92_V	146_L	0.805	1.00
92_V	96_V	0.803	1.00
32_T	51_R	0.803	1.00
33_T	49_L	0.800	1.00
144_D	148_N	0.798	1.00
165_P	189_H	0.791	1.00
111_S	143_E	0.785	1.00
4_V	201_L	0.784	1.00
181_G	221_N	0.781	1.00
83_P	87_F	0.779	1.00
105_P	153_S	0.775	1.00
199_L	260_G	0.770	1.00
134_N	137_R	0.770	1.00
96_V	145_W	0.768	1.00
15_P	194_I	0.766	1.00
162_L	188_V	0.764	1.00
239_R	243_D	0.763	1.00
58_C	98_S	0.762	1.00
196_A	261_F	0.754	1.00
200_L	255_I	0.753	1.00
122_T	127_T	0.751	1.00
74_I	95_L	0.751	1.00
12_L	193_V	0.748	1.00
16_L	197_I	0.744	1.00
218_P	223_F	0.741	1.00
235_P	238_F	0.738	1.00
83_P	86_E	0.734	1.00
141_E	145_W	0.733	1.00
28_T	68_D	0.728	1.00
100_L	151_G	0.723	1.00
24_G	27_V	0.721	1.00
72_L	107_I	0.719	1.00
154_V	207_G	0.716	1.00
115_V	143_E	0.714	1.00
212_I	255_I	0.712	1.00
53_E	87_F	0.712	1.00
200_L	259_L	0.710	1.00
55_E	101_A	0.709	1.00
170_G	174_A	0.709	1.00
194_I	198_T	0.707	1.00
145_W	149_L	0.706	1.00
161_G	185_V	0.697	1.00
184_G	249_I	0.695	1.00
51_R	54_P	0.692	1.00
199_L	261_F	0.688	1.00
33_T	37_V	0.685	1.00
23_R	199_L	0.684	1.00
137_R	144_D	0.681	1.00
28_T	67_M	0.681	1.00
119_A	123_V	0.681	1.00
25_W	70_D	0.681	1.00
85_D	138_V	0.678	1.00
56_L	61_D	0.678	1.00
30_S	58_C	0.675	1.00
150_P	207_G	0.672	1.00
14_M	18_M	0.671	1.00
237_Q	241_S	0.671	1.00
5_A	50_L	0.671	1.00
159_L	162_L	0.669	1.00
240_N	244_S	0.668	1.00
137_R	148_N	0.667	1.00
74_I	107_I	0.663	1.00
186_N	214_A	0.662	1.00
67_M	102_H	0.661	1.00
91_A	94_E	0.656	1.00
254_R	257_N	0.655	1.00
57_V	62_D	0.655	1.00
255_I	258_E	0.654	1.00
245_G	248_K	0.650	1.00
93_Q	149_L	0.650	1.00
205_K	258_E	0.648	1.00
131_P	136_G	0.647	1.00
64_D	67_M	0.646	1.00
225_P	229_R	0.644	1.00
218_P	226_Q	0.643	1.00
82_G	86_E	0.642	1.00
147_H	150_P	0.639	1.00
89_L	93_Q	0.639	1.00
85_D	137_R	0.637	1.00
125_E	255_I	0.637	1.00
23_R	195_G	0.636	1.00
29_G	47_S	0.636	1.00
114_S	136_G	0.635	1.00
186_N	217_H	0.633	1.00
5_A	72_L	0.630	1.00
117_G	130_N	0.628	1.00
192_D	195_G	0.628	1.00
120_Q	127_T	0.627	1.00
142_L	146_L	0.626	1.00
65_A	69_A	0.626	1.00
71_A	108_I	0.624	1.00
25_W	71_A	0.622	1.00
224_Y	228_A	0.622	1.00
174_A	177_T	0.620	1.00
183_H	220_R	0.617	1.00
124_K	253_S	0.617	1.00
108_I	200_L	0.615	1.00
138_V	142_L	0.613	1.00
20_L	201_L	0.613	1.00
99_A	103_R	0.611	1.00
71_A	105_P	0.611	1.00
157_L	196_A	0.608	1.00
26_Q	44_G	0.606	1.00
15_P	166_G	0.605	1.00
3_K	68_D	0.600	1.00
108_I	197_I	0.599	1.00
48_Y	62_D	0.598	1.00
228_A	231_L	0.596	1.00
108_I	201_L	0.595	1.00
134_N	138_V	0.592	1.00
48_Y	67_M	0.591	1.00
153_S	205_K	0.590	1.00
62_D	65_A	0.586	1.00
122_T	247_G	0.584	1.00
72_L	104_I	0.579	1.00
237_Q	240_N	0.579	1.00
54_P	58_C	0.576	1.00
115_V	129_R	0.572	1.00
228_A	237_Q	0.570	1.00
16_L	198_T	0.569	1.00
252_G	261_F	0.566	1.00
18_M	191_E	0.565	1.00
3_K	67_M	0.562	1.00
99_A	102_H	0.558	1.00
64_D	102_H	0.554	1.00
185_V	220_R	0.553	1.00
38_E	43_S	0.547	1.00
17_A	21_S	0.546	1.00
112_S	139_L	0.545	1.00
193_V	212_I	0.544	1.00
58_C	62_D	0.543	1.00
135_S	138_V	0.543	1.00
6_I	20_L	0.541	1.00
17_A	45_I	0.541	1.00
92_V	109_F	0.540	1.00
54_P	61_D	0.539	1.00
160_A	186_N	0.538	1.00
235_P	239_R	0.538	1.00
78_A	88_Y	0.537	1.00
153_S	204_P	0.536	1.00
46_D	65_A	0.536	1.00
115_V	158_R	0.535	1.00
119_A	122_T	0.532	1.00
63_L	72_L	0.532	1.00
146_L	156_I	0.529	1.00
65_A	68_D	0.529	1.00
234_E	237_Q	0.528	1.00
232_G	236_P	0.526	1.00
63_L	67_M	0.526	1.00
24_G	44_G	0.524	1.00
161_G	187_L	0.523	1.00
156_I	207_G	0.521	1.00
11_W	15_P	0.517	1.00
15_P	165_P	0.516	1.00
163_V	214_A	0.513	1.00
25_W	198_T	0.512	1.00
75_T	159_L	0.511	1.00
163_V	187_L	0.509	1.00
142_L	145_W	0.507	1.00
20_L	25_W	0.506	1.00
155_D	210_Y	0.505	1.00
232_G	235_P	0.504	1.00
255_I	263_Y	0.504	1.00
236_P	239_R	0.501	1.00
233_L	236_P	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
1rkxA	3	0.9854	100	0.238	Contact Map
3m2pA	2	0.9562	100	0.243	Contact Map
1sb8A	2	0.9854	100	0.244	Contact Map
1orrA	3	0.9891	100	0.246	Contact Map
2c20A	2	0.9854	100	0.248	Contact Map
2pzmA	2	0.9891	100	0.249	Contact Map
1n7hA	4	0.9891	100	0.251	Contact Map
2c5aA	2	0.9818	100	0.251	Contact Map
3rufA	2	0.9745	100	0.251	Contact Map
2yy7A	2	0.9781	100	0.251	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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