YDJP - BACSU - GREMLIN Contacts

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YDJP - AB hydrolase superfamily protein YdjP

UniProt:	O34592	Sequences: MPYIILEDQTRLYYETHGSGTPILFIHGVLMSGQFFHKQFSVLSANYQCIRLDLRGHGESDKVLHGHTISQYARDIREFLNAMELDHVVLAGWSMGAFVVWDYLNQFGNDNIQAAVIIDQSASDYQWEGWEHGPFDFDGLKTAMHAIQTDPLPFYESFIQNMFAEPPAETETEWMLAEILKQPAAISSTILFNQTAADYRGTLQNINVPALLCFGEDKKFFSTAAGEHLRSNIPNATLVTFPKSSHCPFLEEPDAFNSTLLSFLDGVIGKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	271 (251)
Sequences:	63008 (50913)
Seq/√Len:	3213.6

ECOLI - MHPC RUTD YBFF PLDB BIOH MENH YCJY YFHR
BACSU - YDJP YISY RSBQ YVAM YUGF NAP YRAK YFHM MENH YCGS YBFK YBDG YCLE YBAC YQJL PLBAC EST YQKD CAH
HALSA - Q9HPT9 Q9HHP4 Q9HRJ0 Q9HPY2
SULSO - PIP Q7LXY9 Q97WG0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_T	48_Q	4.833	1.00
89_V	114_A	4.459	1.00
55_R	75_D	4.191	1.00
39_Q	257_N	3.241	1.00
77_R	103_Y	2.863	1.00
216_E	242_P	2.790	1.00
119_D	218_K	2.771	1.00
211_L	263_F	2.622	1.00
252_E	255_A	2.615	1.00
239_V	259_T	2.534	1.00
87_H	113_Q	2.529	1.00
89_V	113_Q	2.527	1.00
118_I	256_F	2.440	1.00
97_A	120_Q	2.274	1.00
241_F	259_T	2.250	1.00
80_L	88_V	2.157	1.00
230_R	236_A	2.145	1.00
11_R	61_D	2.140	1.00
103_Y	107_F	2.126	1.00
81_N	111_N	2.120	1.00
77_R	107_F	2.060	1.00
90_L	100_V	2.049	1.00
15_E	33_G	2.047	1.00
77_R	111_N	1.969	1.00
46_N	261_L	1.940	1.00
216_E	240_T	1.939	1.00
74_R	106_Q	1.936	1.00
77_R	81_N	1.922	1.00
13_Y	59_E	1.900	1.00
89_V	116_V	1.891	1.00
14_Y	79_F	1.879	1.00
104_L	115_A	1.781	1.00
27_H	57_H	1.774	1.00
102_D	106_Q	1.768	1.00
244_S	252_E	1.737	1.00
100_V	115_A	1.736	1.00
89_V	264_L	1.707	1.00
22_P	50_I	1.681	1.00
16_T	50_I	1.681	1.00
42_V	257_N	1.660	1.00
21_T	89_V	1.658	1.00
223_T	240_T	1.648	1.00
17_H	51_R	1.644	1.00
47_Y	89_V	1.635	1.00
52_L	76_I	1.612	1.00
27_H	54_L	1.609	1.00
70_S	106_Q	1.597	1.00
211_L	239_V	1.581	1.00
22_P	85_L	1.557	1.00
107_F	111_N	1.553	1.00
210_A	233_I	1.544	1.00
13_Y	33_G	1.541	1.00
76_I	103_Y	1.538	1.00
116_V	260_L	1.515	1.00
54_L	99_V	1.497	1.00
258_S	262_S	1.494	1.00
22_P	48_Q	1.492	1.00
259_T	262_S	1.491	1.00
21_T	113_Q	1.469	1.00
228_H	232_N	1.467	1.00
26_I	100_V	1.448	1.00
45_A	261_L	1.440	1.00
68_T	71_Q	1.425	1.00
31_M	35_F	1.424	1.00
26_I	54_L	1.417	1.00
103_Y	112_I	1.404	1.00
168_A	171_E	1.400	1.00
202_T	205_N	1.367	1.00
107_F	110_D	1.359	1.00
117_I	120_Q	1.340	1.00
25_F	91_A	1.332	1.00
50_I	79_F	1.332	1.00
73_A	102_D	1.331	1.00
18_G	48_Q	1.295	1.00
25_F	49_C	1.292	1.00
26_I	76_I	1.284	1.00
30_L	57_H	1.260	1.00
53_D	58_G	1.252	1.00
40_F	51_R	1.246	1.00
13_Y	53_D	1.237	1.00
81_N	107_F	1.233	1.00
214_F	226_G	1.230	1.00
42_V	261_L	1.229	1.00
103_Y	111_N	1.221	1.00
255_A	259_T	1.213	1.00
93_W	249_F	1.210	1.00
33_G	53_D	1.207	1.00
227_E	231_S	1.204	1.00
223_T	227_E	1.196	1.00
85_L	88_V	1.187	1.00
52_L	79_F	1.186	1.00
10_T	55_R	1.177	1.00
33_G	59_E	1.175	1.00
102_D	105_N	1.172	1.00
20_G	48_Q	1.172	1.00
216_E	243_K	1.172	1.00
79_F	83_M	1.170	1.00
24_L	80_L	1.163	1.00
30_L	94_S	1.156	1.00
12_L	60_S	1.147	1.00
101_W	117_I	1.144	1.00
42_V	45_A	1.140	1.00
116_V	211_L	1.131	1.00
256_F	260_L	1.127	1.00
91_A	118_I	1.125	1.00
17_H	40_F	1.123	1.00
80_L	85_L	1.116	1.00
233_I	236_A	1.110	1.00
12_L	75_D	1.109	1.00
94_S	246_H	1.108	1.00
80_L	103_Y	1.100	1.00
241_F	244_S	1.099	1.00
88_V	112_I	1.084	1.00
244_S	248_P	1.058	1.00
255_A	258_S	1.054	1.00
213_C	241_F	1.051	1.00
204_Q	232_N	1.049	1.00
35_F	249_F	1.047	1.00
21_T	47_Y	1.037	1.00
105_N	202_T	1.036	1.00
228_H	231_S	1.033	1.00
42_V	254_D	1.027	1.00
33_G	51_R	1.008	1.00
23_I	47_Y	1.006	1.00
77_R	80_L	1.001	1.00
47_Y	264_L	0.998	1.00
169_E	173_E	0.996	1.00
254_D	258_S	0.996	1.00
14_Y	83_M	0.994	1.00
227_E	240_T	0.992	1.00
115_A	210_A	0.992	1.00
70_S	102_D	0.977	1.00
46_N	265_D	0.968	1.00
141_K	145_H	0.964	1.00
93_W	247_C	0.964	1.00
244_S	251_E	0.963	1.00
73_A	99_V	0.961	1.00
26_I	90_L	0.959	1.00
24_L	76_I	0.950	1.00
214_F	223_T	0.950	1.00
237_T	259_T	0.947	1.00
28_G	94_S	0.947	1.00
50_I	83_M	0.940	1.00
88_V	111_N	0.938	1.00
214_F	238_L	0.936	1.00
230_R	238_L	0.935	1.00
173_E	177_A	0.934	1.00
213_C	259_T	0.927	1.00
227_E	238_L	0.918	1.00
91_A	260_L	0.913	1.00
47_Y	265_D	0.903	1.00
241_F	255_A	0.902	1.00
77_R	106_Q	0.901	1.00
24_L	88_V	0.901	1.00
26_I	52_L	0.899	1.00
108_G	111_N	0.894	1.00
118_I	249_F	0.894	1.00
214_F	240_T	0.894	1.00
21_T	87_H	0.888	1.00
245_S	251_E	0.888	1.00
211_L	237_T	0.888	1.00
173_E	176_L	0.888	1.00
151_P	154_F	0.882	1.00
38_K	41_S	0.881	1.00
176_L	180_L	0.881	1.00
22_P	47_Y	0.880	1.00
23_I	49_C	0.879	1.00
114_A	209_P	0.878	1.00
37_H	51_R	0.867	1.00
92_G	97_A	0.861	1.00
192_F	195_T	0.858	1.00
261_L	265_D	0.858	1.00
102_D	202_T	0.854	1.00
92_G	100_V	0.853	1.00
104_L	112_I	0.852	1.00
78_E	82_A	0.852	1.00
239_V	262_S	0.846	1.00
78_E	81_N	0.842	1.00
54_L	95_M	0.842	1.00
241_F	252_E	0.832	1.00
187_S	190_I	0.828	1.00
212_L	236_A	0.823	1.00
90_L	103_Y	0.819	1.00
227_E	230_R	0.817	1.00
183_P	187_S	0.816	1.00
73_A	106_Q	0.816	1.00
143_A	147_I	0.815	1.00
23_I	91_A	0.814	1.00
217_D	243_K	0.813	1.00
239_V	255_A	0.808	1.00
174_W	178_E	0.802	1.00
22_P	88_V	0.793	1.00
140_L	147_I	0.793	1.00
21_T	114_A	0.791	1.00
84_E	87_H	0.790	1.00
116_V	264_L	0.789	1.00
53_D	59_E	0.789	1.00
27_H	52_L	0.787	1.00
184_A	188_S	0.780	1.00
140_L	143_A	0.777	1.00
33_G	52_L	0.771	1.00
226_G	238_L	0.770	1.00
185_A	189_T	0.769	1.00
10_T	61_D	0.767	1.00
141_K	144_M	0.766	1.00
114_A	263_F	0.765	1.00
178_E	181_K	0.763	1.00
224_A	227_E	0.762	1.00
243_K	252_E	0.759	1.00
74_R	77_R	0.757	1.00
71_Q	74_R	0.752	1.00
140_L	144_M	0.739	1.00
174_W	177_A	0.737	1.00
215_G	248_P	0.735	1.00
213_C	256_F	0.735	1.00
29_V	95_M	0.733	1.00
137_F	141_K	0.731	1.00
207_N	234_P	0.728	1.00
66_G	71_Q	0.727	1.00
118_I	248_P	0.727	1.00
30_L	95_M	0.726	1.00
50_I	85_L	0.726	1.00
175_M	179_I	0.721	1.00
34_Q	37_H	0.721	1.00
12_L	55_R	0.717	1.00
25_F	36_F	0.717	1.00
114_A	264_L	0.704	1.00
90_L	112_I	0.703	1.00
73_A	103_Y	0.703	1.00
74_R	78_E	0.702	1.00
184_A	187_S	0.699	1.00
119_D	214_F	0.696	1.00
119_D	248_P	0.695	1.00
40_F	49_C	0.693	1.00
48_Q	85_L	0.690	1.00
183_P	186_I	0.690	1.00
72_Y	95_M	0.689	1.00
185_A	188_S	0.685	1.00
172_T	175_M	0.685	1.00
86_D	111_N	0.683	1.00
54_L	57_H	0.681	1.00
54_L	72_Y	0.676	1.00
188_S	192_F	0.676	1.00
112_I	208_V	0.674	1.00
199_Y	202_T	0.672	1.00
47_Y	261_L	0.668	1.00
19_S	48_Q	0.668	1.00
41_S	44_S	0.665	1.00
24_L	90_L	0.664	1.00
257_N	261_L	0.661	1.00
91_A	116_V	0.661	1.00
150_D	154_F	0.656	1.00
116_V	263_F	0.653	1.00
171_E	174_W	0.652	1.00
39_Q	42_V	0.650	1.00
93_W	119_D	0.648	1.00
156_E	159_I	0.648	1.00
54_L	76_I	0.644	1.00
55_R	72_Y	0.644	1.00
153_P	157_S	0.644	1.00
159_I	163_F	0.641	1.00
36_F	39_Q	0.641	1.00
92_G	96_G	0.640	1.00
93_W	118_I	0.640	1.00
172_T	176_L	0.638	1.00
119_D	215_G	0.636	1.00
23_I	43_L	0.635	1.00
74_R	107_F	0.631	1.00
23_I	264_L	0.630	1.00
186_I	189_T	0.629	1.00
104_L	208_V	0.628	1.00
88_V	113_Q	0.628	1.00
23_I	89_V	0.627	1.00
39_Q	256_F	0.626	1.00
216_E	223_T	0.625	1.00
137_F	144_M	0.622	1.00
150_D	153_P	0.622	1.00
237_T	262_S	0.620	1.00
15_E	37_H	0.619	1.00
154_F	158_F	0.616	1.00
101_W	120_Q	0.616	1.00
152_L	155_Y	0.615	1.00
138_D	141_K	0.610	1.00
189_T	193_N	0.610	1.00
212_L	238_L	0.609	1.00
36_F	40_F	0.609	1.00
25_F	51_R	0.608	1.00
97_A	117_I	0.607	1.00
117_I	212_L	0.604	1.00
157_S	160_Q	0.604	1.00
212_L	233_I	0.603	1.00
258_S	261_L	0.600	1.00
138_D	142_T	0.599	1.00
144_M	147_I	0.598	1.00
170_T	174_W	0.597	1.00
192_F	196_A	0.597	1.00
69_I	102_D	0.594	1.00
253_P	257_N	0.592	1.00
212_L	230_R	0.589	1.00
154_F	157_S	0.588	1.00
88_V	103_Y	0.588	1.00
157_S	161_N	0.586	1.00
206_I	233_I	0.585	1.00
164_A	167_P	0.584	1.00
70_S	74_R	0.584	1.00
139_G	143_A	0.583	1.00
198_D	202_T	0.580	1.00
98_F	121_S	0.580	1.00
155_Y	158_F	0.579	1.00
17_H	41_S	0.579	1.00
32_S	57_H	0.577	1.00
213_C	239_V	0.576	1.00
94_S	247_C	0.575	1.00
177_A	180_L	0.574	1.00
37_H	41_S	0.570	1.00
242_P	255_A	0.570	1.00
76_I	99_V	0.568	1.00
225_A	228_H	0.568	1.00
46_N	49_C	0.567	1.00
101_W	122_A	0.567	1.00
142_T	146_A	0.566	1.00
201_G	204_Q	0.565	1.00
159_I	162_M	0.562	1.00
137_F	140_L	0.561	1.00
144_M	148_Q	0.560	1.00
15_E	34_Q	0.559	1.00
145_H	149_T	0.559	1.00
260_L	264_L	0.558	1.00
87_H	111_N	0.556	1.00
169_E	172_T	0.555	1.00
79_F	82_A	0.554	1.00
191_L	194_Q	0.550	1.00
104_L	206_I	0.549	1.00
183_P	189_T	0.548	1.00
80_L	111_N	0.548	1.00
177_A	181_K	0.548	1.00
142_T	145_H	0.548	1.00
158_F	162_M	0.546	1.00
72_Y	99_V	0.545	1.00
186_I	190_I	0.544	1.00
152_L	156_E	0.543	1.00
156_E	160_Q	0.543	1.00
212_L	226_G	0.541	1.00
116_V	213_C	0.540	1.00
26_I	99_V	0.539	1.00
158_F	163_F	0.539	1.00
155_Y	162_M	0.535	1.00
35_F	93_W	0.534	1.00
120_Q	229_L	0.534	1.00
95_M	99_V	0.532	1.00
53_D	60_S	0.532	1.00
153_P	156_E	0.531	1.00
16_T	83_M	0.530	1.00
249_F	256_F	0.527	1.00
73_A	77_R	0.525	1.00
105_N	205_N	0.525	1.00
31_M	247_C	0.521	1.00
106_Q	202_T	0.521	1.00
25_F	43_L	0.520	1.00
175_M	178_E	0.520	1.00
154_F	159_I	0.518	1.00
200_R	232_N	0.516	1.00
63_V	67_H	0.515	1.00
193_N	196_A	0.514	1.00
107_F	112_I	0.512	1.00
13_Y	60_S	0.512	1.00
31_M	93_W	0.512	1.00
217_D	244_S	0.511	1.00
248_P	256_F	0.508	1.00
44_S	49_C	0.508	1.00
71_Q	75_D	0.506	1.00
123_S	228_H	0.503	1.00
214_F	221_F	0.503	1.00
145_H	148_Q	0.502	1.00
17_H	44_S	0.501	1.00
39_Q	249_F	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
1ehyA	1	0.9336	100	0.154	Contact Map
3om8A	4	0.9446	100	0.158	Contact Map
4inzA	1	0.9779	100	0.16	Contact Map
2xuaA	2	0.9446	100	0.164	Contact Map
1zoiA	3	0.9779	100	0.169	Contact Map
2pujA	4	0.9631	100	0.177	Contact Map
1iupA	2	0.9594	100	0.178	Contact Map
3oosA	1	0.9668	100	0.181	Contact Map
3fobA	3	0.9779	100	0.183	Contact Map
1a8qA	3	0.9742	100	0.184	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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