YBHA - ECOLI - GREMLIN Contacts

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YBHA - Pyridoxal phosphate phosphatase YbhA

UniProt:	P21829	Sequences: MTTRVIALDLDGTLLTPKKTLLPSSIEALARAREAGYQLIIVTGRHHVAIHPFYQALALDTPAICCNGTYLYDYHAKTVLEADPMPVIKALQLIEMLNEHHIHGLMYVDDAMVYEHPTGHVIRTSNWAQTLPPEQRPTFTQVASLAETAQQVNAVWKFALTHDDLPQLQHFGKHVEHELGLECEWSWHDQVDIARGGNSKGKRLTKWVEAQGWSMENVVAFGDNFNDISMLEAAGTGVAMGNADDAVKARANIVIGDNTTDSIAQFIYSHLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11239
Length:	272 (254)
Sequences:	10809 (8874)
Seq/√Len:	556.8

ECOLI - YBHA YIDA SUPH YBJI YIGL COF MPGP
BACSU - YHAX YWPJ YXEH YWTE YKRA YITU YCSE NTDB
HALSA - PGP
SULSO - PGP1 PGP2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
256_G	265_Q	4.215	1.00
17_P	259_T	3.586	1.00
220_A	234_A	3.123	1.00
257_D	260_T	2.851	1.00
231_L	237_G	2.829	1.00
4_R	217_N	2.813	1.00
22_L	261_D	2.756	1.00
24_S	261_D	2.560	1.00
208_V	218_V	2.539	1.00
245_D	249_A	2.458	1.00
24_S	268_Y	2.421	1.00
232_E	250_R	2.413	1.00
16_T	20_T	2.397	1.00
205_T	233_A	2.391	1.00
8_L	39_L	2.376	1.00
43_T	50_I	2.274	1.00
215_M	233_A	2.084	1.00
199_S	229_S	2.031	1.00
81_E	206_K	1.923	1.00
31_R	34_E	1.899	1.00
225_F	246_A	1.898	1.00
228_I	247_V	1.893	1.00
237_G	252_N	1.882	1.00
23_P	27_E	1.861	1.00
225_F	244_D	1.836	1.00
239_A	251_A	1.829	1.00
29_L	39_L	1.813	1.00
228_I	250_R	1.804	1.00
32_A	37_Y	1.763	1.00
86_P	89_K	1.758	1.00
256_G	260_T	1.750	1.00
31_R	268_Y	1.742	1.00
5_V	40_I	1.737	1.00
26_I	56_A	1.713	1.00
245_D	248_K	1.712	1.00
214_S	217_N	1.699	1.00
3_T	219_V	1.693	1.00
236_T	253_I	1.667	1.00
7_A	204_L	1.654	1.00
206_K	210_A	1.650	1.00
205_T	209_E	1.645	1.00
253_I	270_H	1.645	1.00
31_R	35_A	1.622	1.00
206_K	209_E	1.607	1.00
238_V	266_F	1.588	1.00
202_K	205_T	1.585	1.00
236_T	252_N	1.572	1.00
83_D	206_K	1.549	1.00
201_G	233_A	1.542	1.00
204_L	230_M	1.534	1.00
22_L	25_S	1.528	1.00
73_D	76_A	1.524	1.00
247_V	250_R	1.522	1.00
38_Q	211_Q	1.519	1.00
10_L	15_L	1.501	1.00
253_I	266_F	1.495	1.00
3_T	37_Y	1.487	1.00
8_L	221_F	1.483	1.00
216_E	235_G	1.462	1.00
97_L	160_L	1.456	1.00
98_N	115_E	1.451	1.00
27_E	31_R	1.450	1.00
220_A	230_M	1.447	1.00
24_S	265_Q	1.441	1.00
221_F	263_I	1.435	1.00
25_S	261_D	1.434	1.00
26_I	30_A	1.407	1.00
144_S	147_E	1.384	1.00
33_R	60_D	1.380	1.00
172_G	176_E	1.372	1.00
3_T	236_T	1.340	1.00
3_T	217_N	1.329	1.00
221_F	266_F	1.314	1.00
28_A	264_A	1.312	1.00
239_A	243_A	1.299	1.00
7_A	42_V	1.293	1.00
228_I	232_E	1.286	1.00
167_Q	170_H	1.274	1.00
89_K	92_Q	1.274	1.00
241_G	257_D	1.274	1.00
82_A	154_A	1.257	1.00
231_L	247_V	1.255	1.00
215_M	218_V	1.252	1.00
83_D	195_R	1.249	1.00
79_V	82_A	1.242	1.00
248_K	254_V	1.241	1.00
96_M	100_H	1.240	1.00
100_H	174_H	1.238	1.00
182_E	229_S	1.238	1.00
253_I	269_S	1.235	1.00
82_A	156_W	1.225	1.00
28_A	268_Y	1.225	1.00
208_V	215_M	1.221	1.00
87_V	91_L	1.195	1.00
30_A	34_E	1.194	1.00
246_A	249_A	1.190	1.00
266_F	270_H	1.170	1.00
92_Q	178_E	1.165	1.00
6_I	267_I	1.163	1.00
40_I	207_W	1.158	1.00
5_V	213_W	1.147	1.00
64_I	203_R	1.147	1.00
24_S	28_A	1.146	1.00
6_I	32_A	1.135	1.00
218_V	234_A	1.129	1.00
73_D	77_K	1.128	1.00
220_A	231_L	1.121	1.00
263_I	267_I	1.115	1.00
16_T	259_T	1.114	1.00
264_A	268_Y	1.102	1.00
219_V	270_H	1.088	1.00
5_V	208_V	1.085	1.00
70_Y	79_V	1.083	1.00
71_L	206_K	1.082	1.00
242_N	258_N	1.077	1.00
6_I	37_Y	1.068	1.00
244_D	247_V	1.067	1.00
62_P	211_Q	1.049	1.00
89_K	181_L	1.047	1.00
169_Q	173_K	1.047	1.00
182_E	197_G	1.045	1.00
30_A	33_R	1.042	1.00
255_I	266_F	1.038	1.00
17_P	258_N	1.035	1.00
157_K	192_D	1.033	1.00
23_P	26_I	1.033	1.00
215_M	235_G	1.028	1.00
199_S	202_K	1.025	1.00
224_N	244_D	1.021	1.00
142_V	145_L	1.020	1.00
96_M	99_E	1.014	1.00
240_M	262_S	1.010	1.00
7_A	218_V	1.010	1.00
71_L	81_E	1.007	1.00
208_V	233_A	1.007	1.00
10_L	53_F	1.007	1.00
238_V	253_I	1.006	1.00
204_L	234_A	1.000	1.00
238_V	255_I	0.998	1.00
30_A	58_A	0.996	1.00
184_E	194_A	0.990	1.00
14_L	25_S	0.990	1.00
255_I	262_S	0.990	1.00
266_F	269_S	0.987	1.00
234_A	237_G	0.984	1.00
219_V	236_T	0.976	1.00
91_L	95_E	0.963	1.00
84_P	154_A	0.962	1.00
169_Q	185_W	0.961	1.00
95_E	99_E	0.957	1.00
219_V	266_F	0.955	1.00
82_A	109_D	0.952	1.00
265_Q	269_S	0.948	1.00
69_T	198_N	0.948	1.00
241_G	248_K	0.947	1.00
5_V	218_V	0.944	1.00
201_G	229_S	0.942	1.00
219_V	238_V	0.940	1.00
47_H	65_C	0.940	1.00
170_H	173_K	0.940	1.00
208_V	213_W	0.939	1.00
207_W	211_Q	0.938	1.00
162_H	167_Q	0.930	1.00
83_D	197_G	0.928	1.00
225_F	228_I	0.927	1.00
195_R	198_N	0.926	1.00
14_L	29_L	0.924	1.00
8_L	263_I	0.921	1.00
256_G	262_S	0.918	1.00
243_A	248_K	0.910	1.00
239_A	247_V	0.908	1.00
205_T	215_M	0.905	1.00
246_A	250_R	0.900	1.00
265_Q	268_Y	0.893	1.00
173_K	176_E	0.893	1.00
162_H	168_L	0.891	1.00
143_A	146_A	0.888	1.00
241_G	256_G	0.888	1.00
27_E	30_A	0.875	1.00
71_L	203_R	0.875	1.00
25_S	264_A	0.874	1.00
174_H	178_E	0.871	1.00
170_H	174_H	0.867	1.00
194_A	199_S	0.866	1.00
240_M	255_I	0.862	1.00
140_T	143_A	0.860	1.00
95_E	146_A	0.858	1.00
85_M	195_R	0.857	1.00
172_G	185_W	0.853	1.00
65_C	70_Y	0.851	1.00
119_G	123_R	0.846	1.00
235_G	252_N	0.844	1.00
143_A	147_E	0.843	1.00
64_I	207_W	0.842	1.00
169_Q	172_G	0.840	1.00
119_G	122_I	0.837	1.00
51_H	55_Q	0.834	1.00
72_Y	79_V	0.834	1.00
92_Q	95_E	0.833	1.00
43_T	65_C	0.833	1.00
32_A	39_L	0.832	1.00
65_C	72_Y	0.824	1.00
42_V	64_I	0.823	1.00
47_H	72_Y	0.822	1.00
218_V	235_G	0.820	1.00
208_V	235_G	0.818	1.00
80_L	210_A	0.817	1.00
92_Q	96_M	0.817	1.00
88_I	92_Q	0.814	1.00
84_P	156_W	0.814	1.00
25_S	28_A	0.805	1.00
218_V	233_A	0.804	1.00
7_A	40_I	0.804	1.00
256_G	269_S	0.800	1.00
231_L	250_R	0.798	1.00
183_C	193_I	0.798	1.00
96_M	174_H	0.796	1.00
165_L	169_Q	0.794	1.00
28_A	31_R	0.787	1.00
241_G	260_T	0.785	1.00
32_A	267_I	0.785	1.00
16_T	22_L	0.777	1.00
6_I	219_V	0.776	1.00
8_L	14_L	0.775	1.00
46_H	66_C	0.772	1.00
99_E	174_H	0.762	1.00
37_Y	219_V	0.756	1.00
10_L	41_I	0.754	1.00
94_I	98_N	0.750	1.00
220_A	237_G	0.749	1.00
24_S	264_A	0.748	1.00
14_L	21_L	0.747	1.00
231_L	251_A	0.745	1.00
174_H	177_H	0.738	1.00
202_K	206_K	0.734	1.00
100_H	170_H	0.725	1.00
96_M	178_E	0.724	1.00
240_M	243_A	0.723	1.00
204_L	220_A	0.711	1.00
205_T	208_V	0.706	1.00
217_N	235_G	0.704	1.00
33_R	61_T	0.698	1.00
50_I	65_C	0.698	1.00
18_K	259_T	0.697	1.00
111_A	140_T	0.697	1.00
62_P	207_W	0.693	1.00
16_T	258_N	0.692	1.00
159_A	192_D	0.690	1.00
67_N	192_D	0.683	1.00
42_V	230_M	0.682	1.00
182_E	196_G	0.680	1.00
223_D	243_A	0.677	1.00
198_N	202_K	0.675	1.00
98_N	104_G	0.674	1.00
91_L	146_A	0.674	1.00
87_V	154_A	0.672	1.00
221_F	238_V	0.664	1.00
96_M	179_L	0.664	1.00
229_S	232_E	0.663	1.00
146_A	149_A	0.662	1.00
243_A	247_V	0.660	1.00
253_I	265_Q	0.660	1.00
70_Y	156_W	0.658	1.00
237_G	247_V	0.657	1.00
253_I	256_G	0.657	1.00
236_T	266_F	0.656	1.00
14_L	258_N	0.653	1.00
168_L	172_G	0.646	1.00
24_S	27_E	0.646	1.00
54_Y	63_A	0.646	1.00
109_D	154_A	0.645	1.00
41_I	50_I	0.644	1.00
69_T	195_R	0.643	1.00
182_E	199_S	0.642	1.00
12_G	240_M	0.640	1.00
120_H	124_T	0.640	1.00
221_F	255_I	0.639	1.00
165_L	188_H	0.636	1.00
150_Q	153_N	0.634	1.00
40_I	62_P	0.633	1.00
47_H	51_H	0.631	1.00
101_H	167_Q	0.630	1.00
40_I	61_T	0.629	1.00
60_D	75_H	0.629	1.00
50_I	63_A	0.628	1.00
223_D	240_M	0.627	1.00
88_I	91_L	0.625	1.00
173_K	177_H	0.625	1.00
141_Q	144_S	0.623	1.00
10_L	50_I	0.620	1.00
237_G	251_A	0.619	1.00
261_D	264_A	0.616	1.00
139_F	143_A	0.615	1.00
176_E	180_G	0.614	1.00
228_I	231_L	0.614	1.00
22_L	264_A	0.612	1.00
142_V	148_T	0.612	1.00
176_E	183_C	0.612	1.00
94_I	106_M	0.610	1.00
5_V	207_W	0.608	1.00
90_A	155_V	0.607	1.00
108_V	153_N	0.607	1.00
225_F	247_V	0.604	1.00
21_L	26_I	0.601	1.00
183_C	191_V	0.598	1.00
163_D	166_P	0.595	1.00
261_D	265_Q	0.595	1.00
121_V	125_S	0.595	1.00
201_G	205_T	0.592	1.00
242_N	257_D	0.591	1.00
28_A	32_A	0.591	1.00
240_M	258_N	0.590	1.00
242_N	248_K	0.589	1.00
255_I	265_Q	0.589	1.00
10_L	14_L	0.589	1.00
41_I	54_Y	0.584	1.00
182_E	194_A	0.579	1.00
146_A	150_Q	0.576	0.99
197_G	202_K	0.575	0.99
6_I	221_F	0.572	0.99
143_A	148_T	0.572	0.99
91_L	150_Q	0.571	0.99
108_V	155_V	0.569	0.99
157_K	186_S	0.567	0.99
247_V	251_A	0.565	0.99
122_I	125_S	0.564	0.99
17_P	257_D	0.563	0.99
25_S	29_L	0.562	0.99
71_L	207_W	0.561	0.99
52_P	55_Q	0.561	0.99
187_W	224_N	0.555	0.99
147_E	150_Q	0.555	0.99
213_W	218_V	0.554	0.99
74_Y	77_K	0.553	0.99
38_Q	62_P	0.552	0.99
37_Y	217_N	0.551	0.99
29_L	267_I	0.549	0.99
264_A	267_I	0.548	0.99
165_L	185_W	0.548	0.99
15_L	258_N	0.547	0.99
120_H	123_R	0.546	0.99
90_A	94_I	0.546	0.99
92_Q	179_L	0.545	0.99
66_C	156_W	0.545	0.99
70_Y	109_D	0.543	0.99
122_I	126_N	0.539	0.99
138_T	141_Q	0.538	0.99
71_L	210_A	0.536	0.99
32_A	264_A	0.535	0.99
143_A	149_A	0.535	0.99
51_H	54_Y	0.533	0.99
221_F	267_I	0.531	0.99
159_A	190_Q	0.531	0.99
239_A	250_R	0.530	0.99
145_L	148_T	0.529	0.99
63_A	74_Y	0.528	0.99
5_V	38_Q	0.527	0.99
106_M	155_V	0.527	0.99
160_L	193_I	0.527	0.99
256_G	266_F	0.527	0.99
105_L	159_A	0.526	0.99
33_R	58_A	0.525	0.99
102_I	160_L	0.521	0.99
50_I	53_F	0.521	0.99
117_P	122_I	0.520	0.99
166_P	170_H	0.519	0.99
14_L	41_I	0.518	0.99
52_P	56_A	0.515	0.99
66_C	69_T	0.515	0.99
109_D	156_W	0.513	0.99
96_M	175_V	0.512	0.99
213_W	235_G	0.512	0.99
102_I	171_F	0.508	0.99
3_T	38_Q	0.508	0.99
4_R	37_Y	0.505	0.99
244_D	248_K	0.504	0.99
29_L	33_R	0.503	0.99
16_T	261_D	0.502	0.99
168_L	185_W	0.501	0.99
213_W	217_N	0.501	0.99
98_N	146_A	0.500	0.99

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
3pgvA	3	0.9375	100	0.206	Contact Map
1nrwA	1	0.9853	100	0.209	Contact Map
2b30A	2	0.9632	100	0.232	Contact Map
1rkqA	1	0.9669	100	0.238	Contact Map
3l7yA	1	0.9522	100	0.242	Contact Map
4qjbA	1	0.9559	100	0.243	Contact Map
1nf2A	4	0.9559	100	0.247	Contact Map
4dw8A	1	0.9596	100	0.252	Contact Map
2pq0A	1	0.9412	100	0.256	Contact Map
3daoA	1	0.9559	100	0.259	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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