YAFE - ECOLI - GREMLIN Contacts

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YAFE - Uncharacterized protein YafE

UniProt:	P30866	Sequences: MSGLPQGRPTFGAAQNVSAVVAYDLSAHMLDVVAQAAEARQLKNITTRQGYAESLPFADNAFDIVISRYSAHHWHDVGAALREVNRILKPGGRLIVMDVMSPGHPVRDIWLQTVEALRDTSHVRNYASGEWLTLINEANLIVDNLITDKLPLEFSSWVARMRTPEALVDAIRIYQQSASTEVRTYFALQNDGFFTSDIIMVDAHKAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11651
Length:	207 (173)
Sequences:	8370 (6729)
Seq/√Len:	511.6

ECOLI - YAFE BIOC SMTA YJHP TAM UBIE UBIG CMOA TEHB CMOB RLMA
BACSU - YCGJ YXBB MENG YODH YBAJ YRRT YRHH YDAC YQEM YXJB
HALSA - Q9HR63 Q9HR81 Q9HRX3 ARSM Q9HND6 Q9HMT2 Q9HSK6 Q9HQ85
SULSO - Q97WT7 Q97X57 Q97ZU8 Q97WH3 Q7LXN7 Q97YX4 Q97XD7 Q97WN4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_N	140_L	3.305	1.00
27_A	49_Q	2.844	1.00
23_Y	50_G	2.800	1.00
19_A	46_T	2.642	1.00
33_V	47_T	2.627	1.00
76_D	79_A	2.613	1.00
88_L	92_G	2.569	1.00
57_F	62_F	2.566	1.00
83_E	86_R	2.538	1.00
3_G	70_S	2.522	1.00
30_L	47_T	2.435	1.00
65_V	88_L	2.405	1.00
30_L	49_Q	2.306	1.00
4_L	10_T	2.225	1.00
21_V	62_F	2.210	1.00
27_A	31_D	2.103	1.00
78_G	137_E	2.061	1.00
65_V	84_V	2.024	1.00
63_D	89_K	1.994	1.00
84_V	94_L	1.991	1.00
4_L	22_A	1.975	1.00
32_V	35_Q	1.946	1.00
10_T	20_V	1.923	1.00
67_S	70_S	1.890	1.00
3_G	67_S	1.835	1.00
83_E	87_I	1.825	1.00
70_S	74_W	1.805	1.00
88_L	94_L	1.751	1.00
50_G	56_P	1.747	1.00
22_A	33_V	1.731	1.00
52_A	74_W	1.720	1.00
10_T	22_A	1.706	1.00
11_F	36_A	1.705	1.00
11_F	37_A	1.583	1.00
22_A	47_T	1.561	1.00
78_G	82_R	1.556	1.00
74_W	80_A	1.477	1.00
55_L	83_E	1.476	1.00
21_V	48_R	1.472	1.00
59_D	86_R	1.470	1.00
24_D	30_L	1.462	1.00
132_L	136_N	1.452	1.00
55_L	87_I	1.447	1.00
80_A	84_V	1.435	1.00
25_L	51_Y	1.431	1.00
48_R	57_F	1.418	1.00
53_E	74_W	1.380	1.00
31_D	35_Q	1.372	1.00
88_L	140_L	1.348	1.00
58_A	61_A	1.335	1.00
79_A	82_R	1.313	1.00
12_G	15_Q	1.303	1.00
24_D	29_M	1.302	1.00
52_A	70_S	1.300	1.00
28_H	31_D	1.295	1.00
156_S	159_A	1.294	1.00
77_V	134_L	1.283	1.00
31_D	34_A	1.262	1.00
133_T	137_E	1.242	1.00
107_R	110_W	1.222	1.00
78_G	134_L	1.198	1.00
68_R	97_M	1.192	1.00
21_V	46_T	1.182	1.00
6_Q	29_M	1.160	1.00
37_A	47_T	1.159	1.00
84_V	88_L	1.156	1.00
57_F	87_I	1.142	1.00
30_L	34_A	1.131	1.00
108_D	112_Q	1.125	1.00
4_L	33_V	1.121	1.00
37_A	45_I	1.110	1.00
51_Y	54_S	1.110	1.00
71_A	74_W	1.108	1.00
127_A	130_E	1.098	1.00
164_P	167_L	1.097	1.00
14_A	44_N	1.093	1.00
65_V	87_I	1.088	1.00
128_S	132_L	1.084	1.00
13_A	66_I	1.076	1.00
71_A	96_V	1.073	1.00
56_P	83_E	1.060	1.00
4_L	30_L	1.058	1.00
69_Y	72_H	1.044	1.00
111_L	115_E	1.024	1.00
10_T	47_T	1.007	1.00
11_F	15_Q	1.007	1.00
71_A	81_L	1.001	1.00
109_I	113_T	0.996	1.00
59_D	83_E	0.996	1.00
157_W	161_M	0.983	1.00
21_V	57_F	0.975	1.00
9_P	68_R	0.973	1.00
64_I	93_R	0.973	1.00
9_P	66_I	0.971	1.00
54_S	79_A	0.960	1.00
133_T	136_N	0.946	1.00
26_S	29_M	0.945	1.00
71_A	80_A	0.943	1.00
3_G	74_W	0.942	1.00
99_V	103_G	0.937	1.00
69_Y	99_V	0.933	1.00
107_R	111_L	0.925	1.00
160_R	163_T	0.916	1.00
157_W	160_R	0.911	1.00
12_G	16_N	0.911	1.00
62_F	87_I	0.910	1.00
163_T	167_L	0.905	1.00
52_A	80_A	0.903	1.00
155_S	159_A	0.902	1.00
69_Y	73_H	0.898	1.00
85_N	138_A	0.883	1.00
11_F	47_T	0.880	1.00
108_D	111_L	0.879	1.00
53_E	75_H	0.875	1.00
162_R	165_E	0.866	1.00
94_L	135_I	0.862	1.00
4_L	24_D	0.855	1.00
36_A	39_A	0.848	1.00
54_S	83_E	0.848	1.00
23_Y	48_R	0.835	1.00
50_G	55_L	0.828	1.00
69_Y	97_M	0.820	1.00
130_E	133_T	0.819	1.00
35_Q	39_A	0.813	1.00
158_V	162_R	0.812	1.00
111_L	114_V	0.810	1.00
4_L	23_Y	0.810	1.00
72_H	98_D	0.808	1.00
81_L	135_I	0.791	1.00
17_V	20_V	0.790	1.00
158_V	163_T	0.788	1.00
124_R	130_E	0.787	1.00
60_N	90_P	0.785	1.00
78_G	138_A	0.780	1.00
160_R	164_P	0.773	1.00
35_Q	38_E	0.769	1.00
100_M	104_H	0.766	1.00
23_Y	55_L	0.765	1.00
25_L	49_Q	0.763	1.00
82_R	138_A	0.762	1.00
159_A	162_R	0.761	1.00
68_R	73_H	0.760	1.00
110_W	114_V	0.757	1.00
68_R	72_H	0.755	1.00
53_E	79_A	0.751	1.00
132_L	145_L	0.749	1.00
34_A	38_E	0.735	1.00
34_A	46_T	0.734	1.00
64_I	95_I	0.732	1.00
57_F	61_A	0.730	1.00
6_Q	32_V	0.729	1.00
29_M	73_H	0.727	1.00
129_G	132_L	0.727	1.00
9_P	12_G	0.725	1.00
158_V	161_M	0.720	1.00
161_M	165_E	0.719	1.00
53_E	80_A	0.717	1.00
17_V	44_N	0.717	1.00
67_S	96_V	0.714	1.00
109_I	112_Q	0.712	1.00
53_E	76_D	0.712	1.00
93_R	96_V	0.710	1.00
106_V	109_I	0.707	1.00
10_T	45_I	0.705	1.00
59_D	87_I	0.703	1.00
13_A	64_I	0.702	1.00
81_L	134_L	0.702	1.00
170_A	175_Q	0.700	1.00
101_S	104_H	0.686	1.00
73_H	98_D	0.686	1.00
60_N	89_K	0.683	1.00
135_I	142_V	0.679	1.00
119_D	122_H	0.677	1.00
169_D	173_I	0.675	1.00
112_Q	115_E	0.674	1.00
168_V	172_R	0.673	1.00
32_V	36_A	0.673	1.00
143_D	147_T	0.669	1.00
42_L	45_I	0.664	1.00
81_L	138_A	0.662	1.00
56_P	87_I	0.661	1.00
94_L	140_L	0.661	1.00
106_V	112_Q	0.660	1.00
29_M	72_H	0.659	1.00
165_E	169_D	0.659	1.00
15_Q	42_L	0.658	1.00
67_S	84_V	0.656	1.00
162_R	166_A	0.654	1.00
127_A	131_W	0.645	1.00
77_V	80_A	0.644	1.00
164_P	168_V	0.644	1.00
108_D	115_E	0.643	1.00
14_A	45_I	0.640	1.00
163_T	166_A	0.635	1.00
170_A	174_Y	0.634	1.00
11_F	42_L	0.632	1.00
150_L	154_F	0.630	1.00
150_L	153_E	0.630	1.00
22_A	45_I	0.627	1.00
126_Y	130_E	0.624	1.00
107_R	114_V	0.624	1.00
108_D	114_V	0.615	1.00
17_V	64_I	0.609	1.00
56_P	86_R	0.609	1.00
100_M	103_G	0.609	1.00
61_A	87_I	0.595	0.99
115_E	118_R	0.595	0.99
72_H	99_V	0.593	0.99
38_E	43_K	0.593	0.99
10_T	13_A	0.590	0.99
168_V	171_I	0.589	0.99
145_L	148_D	0.587	0.99
67_S	72_H	0.586	0.99
3_G	73_H	0.584	0.99
70_S	73_H	0.582	0.99
118_R	121_S	0.582	0.99
8_R	12_G	0.575	0.99
107_R	115_E	0.570	0.99
96_V	135_I	0.568	0.99
126_Y	134_L	0.566	0.99
118_R	122_H	0.563	0.99
55_L	86_R	0.561	0.99
8_R	29_M	0.559	0.99
73_H	99_V	0.558	0.99
98_D	131_W	0.556	0.99
166_A	169_D	0.556	0.99
157_W	163_T	0.551	0.99
25_L	30_L	0.549	0.99
25_L	53_E	0.546	0.99
81_L	85_N	0.546	0.99
82_R	137_E	0.543	0.99
108_D	113_T	0.542	0.99
8_R	11_F	0.541	0.99
7_G	33_V	0.534	0.99
106_V	115_E	0.530	0.99
167_L	172_R	0.530	0.99
109_I	114_V	0.530	0.99
3_G	25_L	0.529	0.99
157_W	164_P	0.529	0.99
174_Y	177_S	0.528	0.99
28_H	32_V	0.528	0.99
102_P	105_P	0.528	0.99
37_A	42_L	0.527	0.99
14_A	20_V	0.527	0.99
107_R	113_T	0.527	0.99
61_A	86_R	0.526	0.99
64_I	92_G	0.526	0.99
159_A	163_T	0.524	0.99
173_I	177_S	0.523	0.99
9_P	97_M	0.517	0.98
68_R	98_D	0.514	0.98
81_L	131_W	0.513	0.98
106_V	110_W	0.513	0.98
112_Q	116_A	0.510	0.98
128_S	145_L	0.509	0.98
34_A	47_T	0.509	0.98
8_R	69_Y	0.507	0.98
130_E	134_L	0.506	0.98
110_W	115_E	0.502	0.98
24_D	69_Y	0.500	0.98

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
1vl5A	1	1	100	0.353	Contact Map
1xxlA	1	1	100	0.357	Contact Map
4ineA	2	0.9807	100	0.396	Contact Map
4kriA	1	0.9807	100	0.399	Contact Map
3ccfA	1	0.971	100	0.404	Contact Map
2o57A	2	0.9807	100	0.406	Contact Map
2yqzA	1	0.9855	100	0.411	Contact Map
3ujcA	1	0.971	99.9	0.413	Contact Map
4pneA	2	0.9614	99.9	0.416	Contact Map
2p35A	2	0.9517	99.9	0.426	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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