YPDA - BACSU - GREMLIN Contacts

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YPDA - Uncharacterized protein YpdA

UniProt:	P50736	Sequences: MIQEKAIIIGGGPCGLSAAIHLKQIGIDALVIEKGNVVNSIYNYPTHQTFFSSSEKLEIGDVAFITENRKPVRIQALSYYREVVKRKNIRVNAFEMVRKVTKTQNNTFVIETSKETYTTPYCIIATGYYDHPNYMGVPGEDLPKVFHYFKEGHPYFDKDVVVIGGKNSSVDAALELVKSGARVTVLYRGNEYSPSIKPWILPEFEALVRNGTIRMEFGACVEKITENEVVFRSGEKELITIKNDFVFAMTGYHPDHQFLEKIGVEIDKETGRPFFNEETMETNVEGVFIAGVIAAGNNANEIFIENGRFHGGHIAAEIAKRENH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	324 (282)
Sequences:	61213 (43461)
Seq/√Len:	2588.1

ECOLI - GSHR RCLA STHA DLDH HCAD TRXB DHNA NORW AHPF GLTD PRET NIRB AEGA YGFT FADH YGFK
BACSU - YPDA DLDH2 CZCO DLDH3 DLDH1 FENR1 FENR2 DHNA TRXB YJLD YUMB YUTJ GLTB NASB NASD
HALSA - DLDH Q9HSN0 P82854 Q9HP48 Q9HR27 O54535
SULSO - Q97VD9 Q97WE3 Q97XZ3 FENR Q97W27 Q97V69 Q97Z19 Q97YT2 Q97VQ4 Q97WG1 Q97Y24 Q97Z14 Q97U72 Q97VJ3 Q97UP4 Q97ZB4 Q97UV0 Q980U1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
161_V	243_N	4.086	1.00
159_D	182_R	3.418	1.00
34_K	96_M	3.128	1.00
184_T	216_E	3.006	1.00
5_K	28_D	2.909	1.00
182_R	214_R	2.768	1.00
5_K	120_P	2.732	1.00
225_T	230_V	2.713	1.00
109_V	116_T	2.506	1.00
223_K	230_V	2.417	1.00
216_E	239_I	2.347	1.00
161_V	186_L	2.319	1.00
30_L	92_N	2.316	1.00
108_F	112_T	2.315	1.00
6_A	22_L	2.294	1.00
133_N	253_H	2.284	1.00
159_D	244_D	2.267	1.00
18_A	123_I	2.216	1.00
159_D	184_T	2.189	1.00
230_V	240_T	2.187	1.00
205_E	209_R	2.157	1.00
276_N	281_E	2.149	1.00
32_I	117_Y	2.140	1.00
265_E	274_F	2.137	1.00
222_E	232_R	2.127	1.00
7_I	32_I	2.123	1.00
111_E	116_T	2.041	1.00
4_E	30_L	2.034	1.00
123_I	314_I	2.008	1.00
138_P	223_K	2.003	1.00
108_F	286_G	1.995	1.00
7_I	110_I	1.944	1.00
220_C	232_R	1.925	1.00
109_V	118_T	1.831	1.00
99_K	111_E	1.785	1.00
7_I	117_Y	1.782	1.00
233_S	239_I	1.771	1.00
188_R	220_C	1.766	1.00
142_L	226_E	1.758	1.00
225_T	240_T	1.741	1.00
5_K	30_L	1.738	1.00
102_K	284_V	1.737	1.00
121_Y	286_G	1.736	1.00
7_I	119_T	1.721	1.00
186_L	241_I	1.713	1.00
184_T	214_R	1.709	1.00
159_D	242_K	1.703	1.00
39_N	42_Y	1.691	1.00
222_E	230_V	1.640	1.00
112_T	117_Y	1.632	1.00
131_H	255_D	1.621	1.00
28_D	90_R	1.619	1.00
119_T	122_C	1.613	1.00
265_E	283_N	1.599	1.00
131_H	253_H	1.598	1.00
158_K	244_D	1.596	1.00
267_D	270_T	1.578	1.00
72_V	75_Q	1.571	1.00
219_A	233_S	1.557	1.00
14_C	290_A	1.545	1.00
161_V	229_V	1.538	1.00
145_V	148_Y	1.529	1.00
81_R	85_K	1.495	1.00
267_D	272_R	1.486	1.00
8_I	15_G	1.464	1.00
19_A	31_V	1.444	1.00
219_A	239_I	1.440	1.00
159_D	181_A	1.432	1.00
276_N	279_T	1.431	1.00
101_T	104_Q	1.424	1.00
92_N	95_E	1.423	1.00
95_E	113_S	1.391	1.00
126_T	293_I	1.387	1.00
131_H	257_Q	1.386	1.00
7_I	30_L	1.381	1.00
224_I	246_V	1.379	1.00
123_I	290_A	1.374	1.00
121_Y	314_I	1.369	1.00
95_E	112_T	1.362	1.00
190_N	218_G	1.359	1.00
267_D	295_A	1.353	1.00
184_T	243_N	1.348	1.00
311_G	315_A	1.347	1.00
216_E	219_A	1.346	1.00
121_Y	288_F	1.342	1.00
40_S	43_N	1.320	1.00
11_G	33_E	1.317	1.00
267_D	274_F	1.308	1.00
59_I	62_V	1.308	1.00
112_T	115_E	1.301	1.00
160_V	176_L	1.300	1.00
78_S	82_E	1.298	1.00
288_F	313_H	1.286	1.00
307_G	311_G	1.271	1.00
36_N	40_S	1.239	1.00
136_G	140_E	1.221	1.00
281_E	285_E	1.217	1.00
60_G	63_A	1.216	1.00
21_H	312_G	1.199	1.00
92_N	115_E	1.198	1.00
95_E	115_E	1.197	1.00
275_F	294_A	1.189	1.00
6_A	123_I	1.180	1.00
21_H	24_Q	1.174	1.00
8_I	19_A	1.172	1.00
165_G	187_Y	1.171	1.00
310_H	314_I	1.160	1.00
146_F	149_F	1.156	1.00
101_T	109_V	1.152	1.00
37_V	40_S	1.149	1.00
207_L	210_N	1.140	1.00
187_Y	217_F	1.137	1.00
231_F	241_I	1.131	1.00
101_T	111_E	1.127	1.00
198_P	202_P	1.122	1.00
156_F	181_A	1.119	1.00
82_E	86_R	1.110	1.00
30_L	117_Y	1.109	1.00
160_V	245_F	1.100	1.00
309_F	313_H	1.095	1.00
83_V	87_K	1.084	1.00
6_A	27_I	1.082	1.00
75_Q	78_S	1.080	1.00
284_V	287_V	1.078	1.00
170_V	185_V	1.076	1.00
82_E	85_K	1.076	1.00
38_V	42_Y	1.070	1.00
125_A	290_A	1.063	1.00
4_E	28_D	1.058	1.00
151_E	155_Y	1.048	1.00
202_P	205_E	1.046	1.00
157_D	181_A	1.046	1.00
191_E	201_L	1.043	1.00
177_V	213_I	1.042	1.00
219_A	231_F	1.036	1.00
100_V	122_C	1.032	1.00
177_V	182_R	1.025	1.00
14_C	303_F	1.017	1.00
77_L	81_R	1.010	1.00
173_A	185_V	1.005	1.00
162_V	173_A	1.003	1.00
160_V	181_A	1.001	1.00
32_I	97_V	1.001	1.00
273_P	289_I	0.999	1.00
4_E	7_I	0.998	1.00
99_K	102_K	0.993	1.00
95_E	98_R	0.993	1.00
163_I	246_V	0.993	1.00
32_I	112_T	0.993	1.00
6_A	121_Y	0.991	1.00
97_V	102_K	0.985	1.00
203_E	207_L	0.984	1.00
273_P	293_I	0.983	1.00
144_K	226_E	0.983	1.00
39_N	43_N	0.982	1.00
99_K	261_K	0.982	1.00
102_K	287_V	0.980	1.00
38_V	41_I	0.977	1.00
145_V	149_F	0.973	1.00
36_N	81_R	0.970	1.00
78_S	81_R	0.962	1.00
207_L	211_G	0.962	1.00
79_Y	82_E	0.961	1.00
20_I	24_Q	0.960	1.00
178_K	211_G	0.954	1.00
184_T	241_I	0.952	1.00
9_I	124_I	0.937	1.00
23_K	89_I	0.935	1.00
227_N	242_K	0.935	1.00
202_P	206_A	0.931	1.00
290_A	310_H	0.930	1.00
278_E	281_E	0.928	1.00
32_I	92_N	0.925	1.00
30_L	119_T	0.922	1.00
98_R	111_E	0.918	1.00
58_E	61_D	0.916	1.00
4_E	121_Y	0.910	1.00
9_I	126_T	0.908	1.00
206_A	209_R	0.905	1.00
30_L	90_R	0.904	1.00
22_L	311_G	0.896	1.00
206_A	210_N	0.895	1.00
294_A	306_N	0.891	1.00
92_N	117_Y	0.889	1.00
302_I	306_N	0.886	1.00
186_L	231_F	0.886	1.00
38_V	43_N	0.886	1.00
205_E	217_F	0.883	1.00
169_S	187_Y	0.881	1.00
161_V	241_I	0.874	1.00
280_M	309_F	0.874	1.00
257_Q	260_E	0.873	1.00
275_F	289_I	0.872	1.00
180_G	183_V	0.870	1.00
22_L	27_I	0.868	1.00
5_K	118_T	0.867	1.00
95_E	99_K	0.864	1.00
163_I	250_T	0.864	1.00
80_Y	83_V	0.863	1.00
103_T	109_V	0.861	1.00
21_H	308_R	0.859	1.00
289_I	293_I	0.852	1.00
18_A	290_A	0.846	1.00
8_I	18_A	0.844	1.00
280_M	294_A	0.843	1.00
23_K	29_A	0.833	1.00
36_N	41_I	0.832	1.00
214_R	239_I	0.827	1.00
15_G	125_A	0.825	1.00
216_E	241_I	0.823	1.00
288_F	314_I	0.823	1.00
303_F	307_G	0.820	1.00
231_F	239_I	0.819	1.00
19_A	29_A	0.819	1.00
36_N	39_N	0.819	1.00
139_G	142_L	0.818	1.00
18_A	307_G	0.816	1.00
97_V	110_I	0.809	1.00
27_I	315_A	0.805	1.00
5_K	27_I	0.805	1.00
11_G	31_V	0.801	1.00
306_N	310_H	0.800	1.00
73_R	80_Y	0.795	1.00
108_F	284_V	0.793	1.00
161_V	246_V	0.793	1.00
59_I	63_A	0.790	1.00
292_V	303_F	0.788	1.00
122_C	287_V	0.786	1.00
225_T	228_E	0.782	1.00
192_Y	217_F	0.782	1.00
80_Y	84_V	0.779	1.00
201_L	205_E	0.779	1.00
163_I	248_A	0.779	1.00
137_V	140_E	0.775	1.00
74_I	78_S	0.770	1.00
289_I	294_A	0.769	1.00
79_Y	83_V	0.769	1.00
191_E	198_P	0.767	1.00
219_A	232_R	0.765	1.00
32_I	95_E	0.759	1.00
6_A	314_I	0.755	1.00
37_V	42_Y	0.755	1.00
73_R	77_L	0.751	1.00
280_M	310_H	0.750	1.00
134_Y	140_E	0.749	1.00
18_A	310_H	0.748	1.00
139_G	223_K	0.747	1.00
128_Y	252_Y	0.745	1.00
140_E	248_A	0.740	1.00
203_E	206_A	0.738	1.00
123_I	310_H	0.738	1.00
36_N	43_N	0.736	1.00
134_Y	248_A	0.734	1.00
310_H	313_H	0.734	1.00
22_L	314_I	0.732	1.00
159_D	243_N	0.728	1.00
25_I	315_A	0.725	1.00
308_R	312_G	0.724	1.00
279_T	313_H	0.723	1.00
279_T	282_T	0.722	1.00
204_F	208_V	0.720	1.00
281_E	286_G	0.720	1.00
163_I	221_V	0.718	1.00
305_E	308_R	0.713	1.00
99_K	104_Q	0.713	1.00
19_A	89_I	0.708	1.00
124_I	293_I	0.703	1.00
32_I	119_T	0.703	1.00
151_E	154_P	0.699	1.00
15_G	19_A	0.697	1.00
62_V	86_R	0.695	1.00
243_N	246_V	0.694	1.00
17_S	21_H	0.692	1.00
135_M	248_A	0.692	1.00
71_P	75_Q	0.692	1.00
37_V	93_A	0.690	1.00
8_I	125_A	0.689	1.00
274_F	283_N	0.687	1.00
150_K	154_P	0.685	1.00
143_P	226_E	0.685	1.00
266_I	274_F	0.684	1.00
191_E	194_P	0.684	1.00
174_L	178_K	0.683	1.00
276_N	280_M	0.683	1.00
281_E	284_V	0.678	1.00
5_K	117_Y	0.678	1.00
22_L	29_A	0.676	1.00
172_A	175_E	0.675	1.00
177_V	212_T	0.671	1.00
83_V	86_R	0.670	1.00
102_K	108_F	0.669	1.00
221_V	229_V	0.668	1.00
9_I	97_V	0.667	1.00
153_H	156_F	0.665	1.00
200_I	203_E	0.665	1.00
186_L	216_E	0.660	1.00
177_V	211_G	0.658	1.00
305_E	309_F	0.658	1.00
299_A	302_I	0.658	1.00
77_L	80_Y	0.656	1.00
228_E	240_T	0.656	1.00
187_Y	194_P	0.655	1.00
256_H	266_I	0.651	1.00
25_I	312_G	0.651	1.00
124_I	258_F	0.650	1.00
198_P	201_L	0.646	1.00
280_M	313_H	0.644	1.00
155_Y	245_F	0.643	1.00
259_L	262_I	0.641	1.00
290_A	307_G	0.630	1.00
158_K	245_F	0.625	1.00
172_A	249_M	0.624	1.00
99_K	103_T	0.623	1.00
301_E	304_I	0.622	1.00
290_A	314_I	0.620	1.00
17_S	20_I	0.620	1.00
172_A	247_F	0.620	1.00
5_K	119_T	0.619	1.00
27_I	120_P	0.619	1.00
208_V	215_M	0.619	1.00
272_R	275_F	0.618	1.00
205_E	215_M	0.617	1.00
199_W	203_E	0.616	1.00
154_P	157_D	0.615	1.00
98_R	102_K	0.615	1.00
187_Y	190_N	0.614	1.00
216_E	231_F	0.614	1.00
8_I	31_V	0.613	1.00
295_A	306_N	0.609	1.00
84_V	87_K	0.607	1.00
275_F	280_M	0.607	1.00
134_Y	141_D	0.607	1.00
186_L	219_A	0.606	1.00
260_E	266_I	0.606	1.00
150_K	153_H	0.604	1.00
281_E	313_H	0.603	1.00
150_K	155_Y	0.603	1.00
282_T	289_I	0.601	1.00
312_G	316_A	0.600	1.00
108_F	287_V	0.598	1.00
262_I	266_I	0.596	1.00
161_V	184_T	0.594	1.00
257_Q	261_K	0.594	1.00
37_V	41_I	0.592	1.00
133_N	136_G	0.592	1.00
288_F	310_H	0.591	1.00
166_K	251_G	0.590	1.00
158_K	181_A	0.587	1.00
191_E	205_E	0.587	1.00
301_E	305_E	0.586	1.00
165_G	192_Y	0.586	1.00
104_Q	109_V	0.586	1.00
23_K	90_R	0.585	1.00
232_R	236_K	0.580	1.00
224_I	229_V	0.580	1.00
4_E	120_P	0.579	1.00
21_H	25_I	0.579	1.00
96_M	99_K	0.578	1.00
74_I	77_L	0.572	1.00
173_A	183_V	0.567	1.00
200_I	204_F	0.567	1.00
8_I	29_A	0.566	1.00
140_E	143_P	0.564	1.00
17_S	304_I	0.563	1.00
175_E	178_K	0.563	1.00
68_N	75_Q	0.562	1.00
266_I	273_P	0.562	1.00
136_G	141_D	0.560	1.00
304_I	308_R	0.559	1.00
23_K	88_N	0.558	1.00
104_Q	116_T	0.556	1.00
159_D	241_I	0.556	1.00
97_V	104_Q	0.555	1.00
299_A	303_F	0.553	1.00
173_A	213_I	0.552	1.00
209_R	214_R	0.549	1.00
187_Y	215_M	0.546	1.00
192_Y	201_L	0.546	1.00
162_V	169_S	0.545	1.00
28_D	120_P	0.544	1.00
281_E	288_F	0.544	1.00
14_C	125_A	0.542	1.00
214_R	241_I	0.541	1.00
18_A	311_G	0.541	1.00
84_V	89_I	0.540	1.00
300_N	303_F	0.536	1.00
256_H	293_I	0.536	1.00
29_A	90_R	0.536	1.00
199_W	202_P	0.535	1.00
186_L	243_N	0.534	1.00
164_G	251_G	0.533	1.00
20_I	87_K	0.531	1.00
175_E	179_S	0.529	1.00
135_M	140_E	0.529	1.00
135_M	250_T	0.528	1.00
153_H	245_F	0.526	1.00
268_K	274_F	0.525	1.00
109_V	112_T	0.525	1.00
155_Y	158_K	0.525	1.00
158_K	182_R	0.524	1.00
138_P	142_L	0.523	1.00
142_L	223_K	0.518	1.00
111_E	114_K	0.514	1.00
227_N	240_T	0.514	1.00
6_A	311_G	0.514	1.00
295_A	298_N	0.513	1.00
176_L	183_V	0.513	1.00
151_E	157_D	0.512	1.00
230_V	233_S	0.511	1.00
201_L	204_F	0.509	1.00
75_Q	79_Y	0.506	1.00
100_V	110_I	0.506	1.00
169_S	249_M	0.505	1.00
303_F	306_N	0.504	1.00
146_F	172_A	0.504	1.00
168_S	249_M	0.504	1.00
70_K	73_R	0.503	1.00
36_N	42_Y	0.502	1.00
300_N	304_I	0.501	1.00
156_F	179_S	0.501	1.00
62_V	87_K	0.501	1.00
110_I	119_T	0.500	1.00
18_A	22_L	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
4c5oA	5	0.9475	100	0.261	Contact Map
4usrA	1	0.963	100	0.268	Contact Map
4usqA	3	0.9506	100	0.279	Contact Map
1lvlA	2	0.966	100	0.293	Contact Map
3d1cA	2	0.9506	100	0.296	Contact Map
2zbwA	2	0.9444	100	0.296	Contact Map
3ab1A	2	0.9444	100	0.301	Contact Map
3ctyA	2	0.9043	100	0.301	Contact Map
1vdcA	2	0.9105	100	0.302	Contact Map
3lzwA	2	0.9352	100	0.302	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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