YDEA - BACSU - GREMLIN Contacts

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YDEA - Uncharacterized protease YdeA

UniProt:	P96658	Sequences: MKKALFLILDQYADWEGVYLASALNQREDWSVHTVSLDPIVSSIGGFKTSVDYIIGLEPANFNLLVMIGGDSWSNDNKKLLHFVKTAFQKNIPIAAICGAVDFLAKNGLLNNHSHTGNFVYLWKDYKQYKPISSFVEKQAVRDKNLVTANGTAPIEFTNLILEMIDFDTPENIEKMMYMNRYGFYHFCDKYGNPFVD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	197 (168)
Sequences:	15395 (10464)
Seq/√Len:	807.3

ECOLI - YAJL YHBO
BACSU - YDEA YOAZ YRAA GS18
HALSA - Q9HMG4 Q9HRT2
SULSO - Q97Z65

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_R	164_M	2.915	1.00
5_L	62_F	2.710	1.00
40_I	50_S	2.704	1.00
3_K	31_S	2.632	1.00
160_L	163_E	2.512	1.00
5_L	35_V	2.468	1.00
33_H	62_F	2.411	1.00
113_H	144_K	2.378	1.00
113_H	143_D	2.221	1.00
33_H	53_Y	2.134	1.00
3_K	33_H	2.117	1.00
110_L	115_H	2.104	1.00
111_N	131_P	2.087	1.00
168_D	172_N	2.014	1.00
142_R	160_L	1.992	1.00
12_Y	43_S	1.853	1.00
21_A	25_N	1.843	1.00
88_F	145_N	1.786	1.00
23_A	162_L	1.779	1.00
113_H	146_L	1.773	1.00
87_A	92_I	1.691	1.00
88_F	94_I	1.627	1.00
42_S	48_K	1.602	1.00
163_E	168_D	1.589	1.00
40_I	48_K	1.582	1.00
37_L	77_N	1.577	1.00
114_S	143_D	1.560	1.00
54_I	57_L	1.557	1.00
93_P	164_M	1.548	1.00
142_R	147_V	1.544	1.00
114_S	135_F	1.493	1.00
96_A	148_T	1.466	1.00
30_W	165_I	1.440	1.00
83_F	87_A	1.402	1.00
14_D	18_V	1.396	1.00
95_A	161_I	1.380	1.00
113_H	145_N	1.373	1.00
6_F	66_V	1.369	1.00
56_G	79_K	1.366	1.00
81_L	85_K	1.362	1.00
27_R	162_L	1.342	1.00
166_D	170_P	1.333	1.00
139_Q	156_E	1.331	1.00
82_H	86_T	1.330	1.00
96_A	104_L	1.317	1.00
4_A	64_L	1.304	1.00
114_S	134_S	1.303	1.00
64_L	93_P	1.297	1.00
86_T	90_K	1.295	1.00
6_F	21_A	1.287	1.00
115_H	132_I	1.283	1.00
147_V	164_M	1.278	1.00
88_F	146_L	1.273	1.00
78_K	82_H	1.272	1.00
160_L	164_M	1.268	1.00
82_H	85_K	1.268	1.00
48_K	52_D	1.258	1.00
142_R	145_N	1.237	1.00
95_A	157_F	1.225	1.00
10_D	42_S	1.224	1.00
125_D	134_S	1.210	1.00
79_K	82_H	1.208	1.00
8_I	34_T	1.198	1.00
167_F	170_P	1.198	1.00
76_D	106_K	1.194	1.00
22_S	26_Q	1.193	1.00
53_Y	57_L	1.189	1.00
105_A	132_I	1.175	1.00
88_F	109_L	1.174	1.00
91_N	94_I	1.157	1.00
114_S	136_V	1.155	1.00
91_N	145_N	1.154	1.00
114_S	133_S	1.140	1.00
17_G	34_T	1.140	1.00
12_Y	17_G	1.134	1.00
124_K	128_Q	1.132	1.00
15_W	19_Y	1.118	1.00
19_Y	22_S	1.118	1.00
129_Y	132_I	1.109	1.00
85_K	89_Q	1.101	1.00
19_Y	155_I	1.100	1.00
114_S	141_V	1.099	1.00
30_W	166_D	1.092	1.00
140_A	160_L	1.088	1.00
108_G	111_N	1.082	1.00
24_L	158_T	1.081	1.00
93_P	165_I	1.079	1.00
102_D	124_K	1.072	1.00
81_L	107_N	1.068	1.00
86_T	89_Q	1.062	1.00
21_A	34_T	1.059	1.00
126_Y	136_V	1.056	1.00
63_N	92_I	1.054	1.00
66_V	157_F	1.045	1.00
72_S	75_N	1.037	1.00
7_L	80_L	1.015	1.00
88_F	91_N	1.012	1.00
12_Y	49_T	1.002	1.00
35_V	53_Y	1.002	1.00
118_N	151_G	1.001	1.00
93_P	145_N	0.993	1.00
106_K	128_Q	0.982	1.00
8_I	17_G	0.981	1.00
147_V	157_F	0.971	1.00
114_S	138_K	0.971	1.00
14_D	47_F	0.967	1.00
99_G	121_Y	0.959	1.00
149_A	157_F	0.954	1.00
30_W	162_L	0.952	1.00
67_M	84_V	0.952	1.00
37_L	79_K	0.948	1.00
37_L	55_I	0.939	1.00
36_S	51_V	0.938	1.00
40_I	51_V	0.935	1.00
22_S	25_N	0.928	1.00
35_V	58_E	0.926	1.00
122_L	129_Y	0.925	1.00
6_F	32_V	0.924	1.00
19_Y	158_T	0.919	1.00
101_V	117_G	0.911	1.00
87_A	90_K	0.902	1.00
135_F	138_K	0.890	1.00
53_Y	58_E	0.886	1.00
147_V	161_I	0.871	1.00
67_M	100_A	0.870	1.00
23_A	158_T	0.868	1.00
81_L	106_K	0.868	1.00
116_T	141_V	0.866	1.00
8_I	12_Y	0.862	1.00
64_L	165_I	0.859	1.00
20_L	154_P	0.857	1.00
20_L	66_V	0.854	1.00
65_L	87_A	0.845	1.00
62_F	87_A	0.845	1.00
136_V	139_Q	0.844	1.00
4_A	30_W	0.844	1.00
19_Y	154_P	0.841	1.00
66_V	95_A	0.838	1.00
93_P	147_V	0.828	1.00
96_A	101_V	0.826	1.00
83_F	86_T	0.814	1.00
23_A	26_Q	0.812	1.00
67_M	80_L	0.812	1.00
67_M	103_F	0.811	1.00
122_L	136_V	0.793	1.00
155_I	159_N	0.780	1.00
14_D	43_S	0.777	1.00
21_A	32_V	0.772	1.00
17_G	21_A	0.771	1.00
29_D	166_D	0.767	1.00
85_K	107_N	0.762	1.00
6_F	17_G	0.761	1.00
30_W	64_L	0.756	1.00
33_H	52_D	0.746	1.00
14_D	45_G	0.745	1.00
10_D	38_D	0.742	1.00
88_F	113_H	0.742	1.00
106_K	129_Y	0.742	1.00
163_E	171_E	0.739	1.00
39_P	51_V	0.737	1.00
154_P	158_T	0.735	1.00
147_V	160_L	0.728	1.00
97_I	154_P	0.727	1.00
136_V	141_V	0.725	1.00
12_Y	68_I	0.725	1.00
124_K	127_K	0.724	1.00
53_Y	59_P	0.723	1.00
81_L	84_V	0.720	1.00
134_S	137_E	0.720	1.00
121_Y	124_K	0.716	1.00
64_L	161_I	0.716	1.00
122_L	126_Y	0.713	1.00
23_A	159_N	0.712	1.00
5_L	58_E	0.709	1.00
64_L	95_A	0.709	1.00
77_N	80_L	0.709	1.00
125_D	129_Y	0.693	1.00
11_Q	42_S	0.688	1.00
96_A	100_A	0.683	1.00
93_P	161_I	0.678	1.00
4_A	24_L	0.678	1.00
104_L	107_N	0.675	1.00
61_N	90_K	0.670	1.00
21_A	47_F	0.657	1.00
94_I	145_N	0.656	1.00
84_V	103_F	0.654	1.00
24_L	161_I	0.653	1.00
6_F	20_L	0.649	1.00
25_N	32_V	0.645	1.00
39_P	50_S	0.643	1.00
133_S	136_V	0.642	1.00
169_T	172_N	0.640	1.00
78_K	81_L	0.637	1.00
59_P	86_T	0.636	1.00
62_F	65_L	0.632	1.00
29_D	170_P	0.629	1.00
81_L	103_F	0.628	1.00
105_A	110_L	0.627	1.00
30_W	63_N	0.627	1.00
97_I	157_F	0.627	1.00
7_L	65_L	0.626	1.00
94_I	109_L	0.619	1.00
117_G	135_F	0.615	1.00
119_F	151_G	0.613	1.00
20_L	24_L	0.609	1.00
84_V	107_N	0.604	1.00
16_E	69_G	0.603	1.00
35_V	62_F	0.602	1.00
156_E	159_N	0.600	1.00
123_W	127_K	0.593	1.00
118_N	152_T	0.589	1.00
13_A	44_I	0.586	1.00
24_L	30_W	0.586	1.00
94_I	146_L	0.585	1.00
38_D	54_I	0.584	1.00
125_D	128_Q	0.582	1.00
3_K	63_N	0.574	1.00
19_Y	23_A	0.574	1.00
58_E	62_F	0.571	1.00
111_N	132_I	0.571	1.00
122_L	135_F	0.569	1.00
140_A	147_V	0.563	1.00
7_L	35_V	0.559	1.00
11_Q	71_D	0.557	1.00
78_K	85_K	0.551	1.00
102_D	121_Y	0.549	1.00
94_I	104_L	0.549	1.00
85_K	109_L	0.549	1.00
156_E	160_L	0.548	1.00
5_L	33_H	0.546	1.00
14_D	49_T	0.542	1.00
42_S	52_D	0.542	1.00
95_A	147_V	0.542	1.00
71_D	74_S	0.541	1.00
8_I	41_V	0.541	1.00
5_L	83_F	0.535	1.00
65_L	83_F	0.531	1.00
36_S	41_V	0.531	1.00
58_E	83_F	0.530	1.00
134_S	139_Q	0.523	1.00
13_A	22_S	0.522	1.00
35_V	83_F	0.521	1.00
138_K	156_E	0.518	1.00
15_W	22_S	0.517	1.00
8_I	51_V	0.516	1.00
51_V	54_I	0.512	1.00
123_W	136_V	0.511	1.00
17_G	68_I	0.511	1.00
67_M	104_L	0.510	1.00
145_N	164_M	0.509	1.00
14_D	44_I	0.508	1.00
16_E	152_T	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
3mgkA	2	0.9848	100	0.181	Contact Map
3er6A	2	0.9289	100	0.192	Contact Map
3efeA	2	0.9797	100	0.199	Contact Map
3graA	2	0.8934	100	0.208	Contact Map
3ewnA	2	0.9848	100	0.215	Contact Map
3noqA	2	0.9797	100	0.224	Contact Map
3bhnA	2	0.9645	100	0.227	Contact Map
2rk3A	2	0.9036	100	0.238	Contact Map
4e08A	2	0.9036	100	0.242	Contact Map
3f5dA	2	0.9695	100	0.243	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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